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LibM078F_pair.vd.normalized.vepanno.annovar.hg19_multianno.txt

LibM078F_pair.vd.normalized.vepanno.annovar.hg19_multianno.txt 2.8 MB
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
  1. Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	PopFreqMax	gnomAD_genome_ALL	gnomAD_genome_AFR	gnomAD_genome_AMR	gnomAD_genome_ASJ	gnomAD_genome_EAS	gnomAD_genome_FIN	gnomAD_genome_NFE	gnomAD_genome_OTH	avsnp150	snp138NonFlagged	SIFT_score	SIFT_converted_rankscore	SIFT_pred	Polyphen2_HDIV_score	Polyphen2_HDIV_rankscore	Polyphen2_HDIV_pred	Polyphen2_HVAR_score	Polyphen2_HVAR_rankscore	Polyphen2_HVAR_pred	LRT_score	LRT_converted_rankscore	LRT_pred	MutationTaster_score	MutationTaster_converted_rankscore	MutationTaster_pred	MutationAssessor_score	MutationAssessor_score_rankscore	MutationAssessor_pred	FATHMM_score	FATHMM_converted_rankscore	FATHMM_pred	PROVEAN_score	PROVEAN_converted_rankscore	PROVEAN_pred	VEST3_score	VEST3_rankscore	MetaSVM_score	MetaSVM_rankscore	MetaSVM_pred	MetaLR_score	MetaLR_rankscore	MetaLR_pred	M-CAP_score	M-CAP_rankscore	M-CAP_pred	CADD_raw	CADD_raw_rankscore	CADD_phred	DANN_score	DANN_rankscore	fathmm-MKL_coding_score	fathmm-MKL_coding_rankscore	fathmm-MKL_coding_pred	Eigen_coding_or_noncoding	Eigen-raw	Eigen-PC-raw	GenoCanyon_score	GenoCanyon_score_rankscore	integrated_fitCons_score	integrated_fitCons_score_rankscore	integrated_confidence_value	GERP++_RS	GERP++_RS_rankscore	phyloP100way_vertebrate	phyloP100way_vertebrate_rankscore	phyloP20way_mammalian	phyloP20way_mammalian_rankscore	phastCons100way_vertebrate	phastCons100way_vertebrate_rankscore	phastCons20way_mammalian	phastCons20way_mammalian_rankscore	SiPhy_29way_logOdds	SiPhy_29way_logOdds_rankscore	Interpro_domain	GTEx_V6_gene	GTEx_V6_tissue	cosmic94	CLNALLELEID	CLNDN	CLNDISDB	CLNREVSTAT	CLNSIG	InterVar(automated)	PVS1	PS1	PS2	PS3	PS4	PM1	PM2	PM3	PM4	PM5	PM6	PP1	PP2	PP3	PP4	PP5	BA1	BS1	BS2	BS3	BS4	BP1	BP2	BP3	BP4	BP5	BP6	BP7	ICGC_Id	ICGC_Occurrence	Otherinfo1	Otherinfo2	Otherinfo3	Otherinfo4	Otherinfo5	Otherinfo6	Otherinfo7	Otherinfo8	Otherinfo9	Otherinfo10	Otherinfo11	Otherinfo12	Otherinfo13	Otherinfo14
    2. 

  2. 1	2490898	2490898	C	A	intronic	TNFRSF14	.	.	.	0.82	0.5671	0.7517	0.5358	0.4603	0.5143	0.5020	0.4867	0.5307	rs2257763	rs2257763	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63187619;OCCURENCE=1(lung)	137143	not_specified	MedGen:CN169374	no_assertion_provided	not_provided	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15519966	LUSC-KR|1|170|0.00588235	0.25	37	3	1	2490898	.	C	A	37	d5;v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=2;AF=0.5;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.28571;SOR=inf;LSEQ=ACAGATGGGAAACCCGTTTG;RSEQ=GGGGTGGGTGTCTGGGTGGG;CSQ=A|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_001297605.2|protein_coding||3/6|NM_001297605.2:c.305-364C>A|||||||rs2257763&COSV63187619||1||EntrezGene||||||1:g.2490898C>A|0.5411|0.7712|0.5397|0.456|0.5388|0.4865|0.4868|0.5183|0.6537|0.8162|AFR|not_provided|0&1|1&1,A|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_003820.4|protein_coding||3/7|NM_003820.4:c.305-364C>A|||||||rs2257763&COSV63187619||1||EntrezGene||YES||||1:g.2490898C>A|0.5411|0.7712|0.5397|0.456|0.5388|0.4865|0.4868|0.5183|0.6537|0.8162|AFR|not_provided|0&1|1&1,A|upstream_gene_variant|MODIFIER|LOC115110|115110|Transcript|NR_037844.2|lncRNA||||||||||rs2257763&COSV63187619|2448|-1||EntrezGene||YES||||1:g.2490898C>A|0.5411|0.7712|0.5397|0.456|0.5388|0.4865|0.4868|0.5183|0.6537|0.8162|AFR|not_provided|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:2,0:2,0:2,2:0.5:0,0:11:1:37:0:1:0:60:4:0.5:0:1	0/0:3:0:0,0:2,1:3,0:0:2,0:36.3:1:33:1:1:0:60:6:1:0:0.3
    3. 

  3. 1	2491205	2491205	C	T	intronic	TNFRSF14	.	.	.	0.83	0.5704	0.7639	0.5358	0.4603	0.5130	0.5006	0.4865	0.5320	rs2234161	rs2234161	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63185654;OCCURENCE=1(large_intestine),12(central_nervous_system),1(lung),17(upper_aerodigestive_tract)	137153	not_specified	MedGen:CN169374	no_assertion_provided	not_provided	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15520040	ESAD-UK|1|409|0.00244499,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.25	234	103	1	2491205	.	C	T	234	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=528;VD=88;AF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CTGTGGATGCTGTCCTGGCC;RSEQ=GTGGATGGTGTCCCGGCCTC;CSQ=T|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_001297605.2|protein_coding||3/6|NM_001297605.2:c.305-57C>T|||||||rs2234161&COSV63185654||1||EntrezGene||||||1:g.2491205C>T|0.5528|0.7968|0.5477|0.4602|0.5535|0.5095|0.503|0.5235|0.6558|0.8313|AFR|not_provided|0&1|1&1,T|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_003820.4|protein_coding||3/7|NM_003820.4:c.305-57C>T|||||||rs2234161&COSV63185654||1||EntrezGene||YES||||1:g.2491205C>T|0.5528|0.7968|0.5477|0.4602|0.5535|0.5095|0.503|0.5235|0.6558|0.8313|AFR|not_provided|0&1|1&1,T|upstream_gene_variant|MODIFIER|LOC115110|115110|Transcript|NR_037844.2|lncRNA||||||||||rs2234161&COSV63185654|2755|-1||EntrezGene||YES||||1:g.2491205C>T|0.5528|0.7968|0.5477|0.4602|0.5535|0.5095|0.503|0.5235|0.6558|0.8313|AFR|not_provided|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:528:88:58,30:295,145:440,88:0.1667:2,2:36.7:1:36.3:1:0.90134:1.05222:60:87:0.1667:0:1.6	0/0:103:0:0,0:70,33:103,0:0:2,0:33.9:1:36.7:1:1:0:60:206:1:0:0.1
    4. 

  4. 1	2491306	2491306	G	A	exonic	TNFRSF14	.	nonsynonymous SNV	TNFRSF14:NM_001297605:exon4:c.G349A:p.A117T,TNFRSF14:NM_003820:exon4:c.G349A:p.A117T	0.051	0.0152	0.0334	0.0084	0.0033	0.0525	0.0031	0.0046	0.0051	rs2234163	rs2234163	1.0	0.010	T	0.804	0.432	P	0.186	0.344	B	.	.	.	1	0.090	N	-2.005	0.002	N	-1.74	0.834	D	3.45	0.001	N	0.019	0.258	-0.892	0.487	T	0.036	0.156	T	.	.	.	-0.867	0.037	0.030	0.679	0.083	0.003	0.015	N	c	-1.382	-1.419	1.000	0.429	0.707	0.730	0	0.448	0.158	-1.249	0.030	-0.165	0.106	0.000	0.063	0.000	0.016	4.699	0.121	TNFR/NGFR cysteine-rich region	.	.	ID=COSV104672684;OCCURENCE=3(prostate),1(lung)	139092	not_specified	MedGen:CN169374	no_assertion_provided	not_provided	Likely benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	MU113544615	LAML-KR|1|205|0.00487805	0.25	280	251	1	2491306	.	G	A	280	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1393;VD=244;AF=0.1752;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=ACTGCTCCAGGACAGAGAAC;RSEQ=CCGTGTGTGGCTGCAGCCCA;CSQ=A|missense_variant|MODERATE|TNFRSF14|8764|Transcript|NM_001297605.2|protein_coding|4/7||NM_001297605.2:c.349G>A|NP_001284534.1:p.Ala117Thr|643|349|117|A/T|Gcc/Acc|rs2234163&CM130617&COSV104672684||1||EntrezGene||||||1:g.2491306G>A|0.01074|0.03682|0.003553|0.001754|0.03829|0.002319|0.006318|0.008901|0.01411|0.03829|gnomAD_EAS|not_provided|0&0&1|1&1&1,A|missense_variant|MODERATE|TNFRSF14|8764|Transcript|NM_003820.4|protein_coding|4/8||NM_003820.4:c.349G>A|NP_003811.2:p.Ala117Thr|643|349|117|A/T|Gcc/Acc|rs2234163&CM130617&COSV104672684||1||EntrezGene||YES||||1:g.2491306G>A|0.01074|0.03682|0.003553|0.001754|0.03829|0.002319|0.006318|0.008901|0.01411|0.03829|gnomAD_EAS|not_provided|0&0&1|1&1&1,A|upstream_gene_variant|MODIFIER|LOC115110|115110|Transcript|NR_037844.2|lncRNA||||||||||rs2234163&CM130617&COSV104672684|2856|-1||EntrezGene||YES||||1:g.2491306G>A|0.01074|0.03682|0.003553|0.001754|0.03829|0.002319|0.006318|0.008901|0.01411|0.03829|gnomAD_EAS|not_provided|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1393:244:126,118:604,543:1147,244:0.1752:2,2:37.8:1:35.4:1:0.77813:1.0417:60:23.4:0.1696:0:1.3	0/0:251:0:0,0:144,107:251,0:0:2,0:37:1:36.5:1:1:0:60:124.5:1:0:0.1
    5. 

  5. 1	2492981	2492981	G	A	intronic	TNFRSF14	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	111	1	2492981	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=727;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01741;SOR=0;LSEQ=TGAGGTCTCATCCTGGAGCT;RSEQ=CCACCAGCCCAGCCTCCCTG;CSQ=A|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_001297605.2|protein_coding||5/6|NM_001297605.2:c.551+828G>A|||||||||1||EntrezGene||||||1:g.2492981G>A||||||||||||||,A|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_003820.4|protein_coding||5/7|NM_003820.4:c.552-131G>A|||||||||1||EntrezGene||YES||||1:g.2492981G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|LOC115110|115110|Transcript|NR_037844.2|lncRNA|||||||||||4531|-1||EntrezGene||YES||||1:g.2492981G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|LOC100996583|100996583|Transcript|NR_121638.1|lncRNA|||||||||||4993|1||EntrezGene||YES||||1:g.2492981G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:727:0:0,0:456,271:727,0:0:2,0:38.2:1:36.7:1:1:0:60:241.333:1:0:0.1	0/1:111:2:1,1:77,32:109,2:0.018:2,2:51:0:37:0:0.50811:2.38487:60:4:0.0182:0:1
    6. 

  6. 1	2493089	2493089	C	T	intronic	TNFRSF14	.	.	.	0.0003	.	.	.	.	.	.	.	.	rs754657907	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	129	1	2493089	.	C	T	37	v3;f0.01;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1154;VD=2;AF=0.0017;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05257;SOR=0.11063;LSEQ=CGCTGCACCTGCCTCTCCCA;RSEQ=GTCCTCGGCCCCACTCCCGC;CSQ=T|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_001297605.2|protein_coding||5/6|NM_001297605.2:c.551+936C>T|||||||rs754657907||1||EntrezGene||||||1:g.2493089C>T|1.611e-05|0|0|0|0.0001091|0|8.964e-06|0.000165|0|0.000165|gnomAD_OTH|||,T|intron_variant|MODIFIER|TNFRSF14|8764|Transcript|NM_003820.4|protein_coding||5/7|NM_003820.4:c.552-23C>T|||||||rs754657907||1||EntrezGene||YES||||1:g.2493089C>T|1.611e-05|0|0|0|0.0001091|0|8.964e-06|0.000165|0|0.000165|gnomAD_OTH|||,T|upstream_gene_variant|MODIFIER|LOC115110|115110|Transcript|NR_037844.2|lncRNA||||||||||rs754657907|4639|-1||EntrezGene||YES||||1:g.2493089C>T|1.611e-05|0|0|0|0.0001091|0|8.964e-06|0.000165|0|0.000165|gnomAD_OTH|||,T|upstream_gene_variant|MODIFIER|LOC100996583|100996583|Transcript|NR_121638.1|lncRNA||||||||||rs754657907|4885|1||EntrezGene||YES||||1:g.2493089C>T|1.611e-05|0|0|0|0.0001091|0|8.964e-06|0.000165|0|0.000165|gnomAD_OTH|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1154:2:1,1:635,517:1152,2:0.0017:2,2:42.5:1:24:1:1:1.22801:60:1:0.0009:0:1	0/1:129:2:1,1:64,63:127,2:0.0155:2,2:58.5:1:37:0:1:1.01575:60:4:0.0156:0:1
    7. 

  7. 1	9780320	9780320	C	T	intronic	PIK3CD	.	.	.	0.	.	.	.	.	.	.	.	.	rs747768075	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	0	1	9780320	.	C	T	37	v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=2;AF=0.4;SHIFT3=0;MSI=2;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTCAGTGGGGGCCCCGCCG;RSEQ=GTGAGGCTGAGGGGCTGGCG;CSQ=T|intron_variant|MODIFIER|PIK3CD|5293|Transcript|NM_001350234.2|protein_coding||11/23|NM_001350234.2:c.1470+20C>T|||||||rs747768075||1||EntrezGene||||||1:g.9780320C>T|8.462e-06|0|5.88e-05|0|0|0|0|0|0|5.88e-05|gnomAD_AMR|||,T|intron_variant|MODIFIER|PIK3CD|5293|Transcript|NM_001350235.1|protein_coding||10/22|NM_001350235.1:c.1383+20C>T|||||||rs747768075||1||EntrezGene||||||1:g.9780320C>T|8.462e-06|0|5.88e-05|0|0|0|0|0|0|5.88e-05|gnomAD_AMR|||,T|intron_variant|MODIFIER|PIK3CD|5293|Transcript|NM_005026.5|protein_coding||11/23|NM_005026.5:c.1470+20C>T|||||||rs747768075||1||EntrezGene||YES||||1:g.9780320C>T|8.462e-06|0|5.88e-05|0|0|0|0|0|0|5.88e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:5:2:1,1:2,1:3,2:0.4:2,2:42.5:1:37:0:1:1.7321:60:4:0.4:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    8. 

  8. 1	9782371	9782371	A	G	exonic	PIK3CD	.	synonymous SNV	PIK3CD:NM_001350235:exon17:c.A2217G:p.A739A,PIK3CD:NM_001350234:exon18:c.A2301G:p.A767A,PIK3CD:NM_005026:exon18:c.A2304G:p.A768A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	1	1	9782371	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=2;AF=0.2857;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.75;SOR=inf;LSEQ=ATGTACAGCAACGAGGAGGC;RSEQ=GGCAGCGGCGGCAGCGTGGG;CSQ=G|synonymous_variant|LOW|PIK3CD|5293|Transcript|NM_001350234.2|protein_coding|18/24||NM_001350234.2:c.2301A>G|NP_001337163.1:p.Ala767%3D|2616|2301|767|A|gcA/gcG|||1||EntrezGene||||||1:g.9782371A>G||||||||||||||,G|synonymous_variant|LOW|PIK3CD|5293|Transcript|NM_001350235.1|protein_coding|17/23||NM_001350235.1:c.2217A>G|NP_001337164.1:p.Ala739%3D|2354|2217|739|A|gcA/gcG|||1||EntrezGene||||||1:g.9782371A>G||||||||||||||,G|synonymous_variant|LOW|PIK3CD|5293|Transcript|NM_005026.5|protein_coding|18/24||NM_005026.5:c.2304A>G|NP_005017.3:p.Ala768%3D|2513|2304|768|A|gcA/gcG|||1||EntrezGene||YES||||1:g.9782371A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:7:2:1,1:2,3:5,2:0.2857:2,2:65.5:1:37:0:1:1.41:60:4:0.2857:0:1	0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:37:0:1:0:60:2:1:0:0
    9. 

  9. 1	11167532	11167532	G	A	UTR3	MTOR	NM_004958:c.*10C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	142	1	11167532	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.12882;SOR=inf;LSEQ=AAAACGTGATGGGCACATCT;RSEQ=GGCCTCCAGTTACCAGAAAG;CSQ=A|3_prime_UTR_variant|MODIFIER|MTOR|2475|Transcript|NM_001386500.1|protein_coding|58/58||NM_001386500.1:c.*10C>T||7808|||||||-1||EntrezGene||YES||||1:g.11167532G>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|MTOR|2475|Transcript|NM_001386501.1|protein_coding|57/57||NM_001386501.1:c.*10C>T||7672|||||||-1||EntrezGene||||||1:g.11167532G>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|MTOR|2475|Transcript|NM_004958.4|protein_coding|58/58||NM_004958.4:c.*10C>T||7781|||||||-1||EntrezGene||||||1:g.11167532G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:47,31:78,2:0.025:2,2:50:1:37:0:1:1.508:60:4:0.026:0:1	0/0:142:0:0,0:71,71:142,0:0:2,0:42.9:1:36.2:1:1:0:60:141:1:0:0.1
    10. 

  10. 1	11167549	11167549	A	-	exonic	MTOR	.	frameshift deletion	MTOR:NM_004958:exon58:c.7643delT:p.F2548Sfs*20	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	140	1	11167548	.	GA	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=80;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.4039;SOR=0;LSEQ=ATCTGGGCCTCCAGTTACCA;RSEQ=AAGGGCACCTAAGAAGGCAG;CSQ=-|frameshift_variant|HIGH|MTOR|2475|Transcript|NM_001386500.1|protein_coding|58/58||NM_001386500.1:c.7643del|NP_001373429.1:p.Phe2548SerfsTer20|7791|7643|2548|F/X|tTc/tc|||-1||EntrezGene||YES||||1:g.11167551del||||||||||||||,-|frameshift_variant|HIGH|MTOR|2475|Transcript|NM_001386501.1|protein_coding|57/57||NM_001386501.1:c.6395del|NP_001373430.1:p.Phe2132SerfsTer20|7655|6395|2132|F/X|tTc/tc|||-1||EntrezGene||||||1:g.11167551del||||||||||||||,-|frameshift_variant|HIGH|MTOR|2475|Transcript|NM_004958.4|protein_coding|58/58||NM_004958.4:c.7643del|NP_004949.1:p.Phe2548SerfsTer20|7764|7643|2548|F/X|tTc/tc|||-1||EntrezGene||||||1:g.11167551del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:80:0:0,0:45,35:80,0:0:2,0:35.2:1:36.4:1:1:0:60:79:1:0:0.1	0/1:140:2:1,1:61,77:138,2:0.0143:2,2:42.5:1:37:0:1:1.26:60:4:0.0146:0:0.5
    11. 

  11. 1	11174439	11174439	G	A	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon53:c.C7236T:p.D2412D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	68	255	1	11174439	.	G	A	68	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1564;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00038;SOR=0;LSEQ=TCCAGCACGGCCATGACACT;RSEQ=TCCTTGTGCTCTCGCAGCAC;CSQ=A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|53/58||NM_001386500.1:c.7236C>T|NP_001373429.1:p.Asp2412%3D|7384|7236|2412|D|gaC/gaT|||-1||EntrezGene||YES||||1:g.11174439G>A||||||||||||||,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|52/57||NM_001386501.1:c.5988C>T|NP_001373430.1:p.Asp1996%3D|7248|5988|1996|D|gaC/gaT|||-1||EntrezGene||||||1:g.11174439G>A||||||||||||||,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|53/58||NM_004958.4:c.7236C>T|NP_004949.1:p.Asp2412%3D|7357|7236|2412|D|gaC/gaT|||-1||EntrezGene||||||1:g.11174439G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1564:0:0,0:783,781:1564,0:0:2,0:37.8:1:36.6:1:1:0:60:194.5:1:0:0.1	0/1:255:4:2,2:121,130:251,4:0.0157:2,2:6:1:34:1:1:1.07:60:8:0.016:0:1
    12. 

  12. 1	11181327	11181327	C	T	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon49:c.G6909A:p.L2303L	0.44	0.2797	0.4310	0.1337	0.3633	0.0593	0.2270	0.2368	0.2459	rs11121691	rs11121691	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63870864;OCCURENCE=23(meninges),1(large_intestine),1(stomach),2(haematopoietic_and_lymphoid_tissue)	497964	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	.	.	0.25	224	172	1	11181327	.	C	T	224	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=767;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=GAGCTGGGGCTTTTCAGCCA;RSEQ=AGCAGCTTGGCCAGGTCGTC;CSQ=T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|49/58||NM_001386500.1:c.6909G>A|NP_001373429.1:p.Leu2303%3D|7057|6909|2303|L|ctG/ctA|rs11121691&COSV63870864||-1||EntrezGene||YES||||1:g.11181327C>T|0.2131|0.4411|0.1176|0.3242|0.06101|0.225|0.2347|0.2262|0.1635|0.4411|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|48/57||NM_001386501.1:c.5661G>A|NP_001373430.1:p.Leu1887%3D|6921|5661|1887|L|ctG/ctA|rs11121691&COSV63870864||-1||EntrezGene||||||1:g.11181327C>T|0.2131|0.4411|0.1176|0.3242|0.06101|0.225|0.2347|0.2262|0.1635|0.4411|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|49/58||NM_004958.4:c.6909G>A|NP_004949.1:p.Leu2303%3D|7030|6909|2303|L|ctG/ctA|rs11121691&COSV63870864||-1||EntrezGene||||||1:g.11181327C>T|0.2131|0.4411|0.1176|0.3242|0.06101|0.225|0.2347|0.2262|0.1635|0.4411|gnomAD_AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:767:0:0,0:431,336:767,0:0:2,0:36.5:1:36.7:1:1:0:60:190.75:1:0:0.1	0/1:172:78:51,27:50,44:94,78:0.4535:2,2:38.5:1:35.7:1:0.1212:1.66:60:38:0.4471:0:1
    13. 

  13. 1	11182220	11182220	-	G	intronic	MTOR	.	.	.	0.0007	9.711e-05	0	0	0	0.0018	0	0	0	rs760249508	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	345	187	1	11182220	.	A	AG	345	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=980;VD=781;AF=0.7969;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=AGCAGGGTTAGTGTACCGTA;RSEQ=AGAGAGTATACCCTTGAGCA;CSQ=G|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386500.1|protein_coding||47/57|NM_001386500.1:c.6663-38_6663-37insC|||||||rs760249508||-1||EntrezGene||YES||||1:g.11182220_11182221insG|4.4e-05|0|0|0.0002002|0.0004353|0|8.878e-06|0|0|0.0004353|gnomAD_EAS|||,G|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386501.1|protein_coding||46/56|NM_001386501.1:c.5415-38_5415-37insC|||||||rs760249508||-1||EntrezGene||||||1:g.11182220_11182221insG|4.4e-05|0|0|0.0002002|0.0004353|0|8.878e-06|0|0|0.0004353|gnomAD_EAS|||,G|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_004958.4|protein_coding||47/57|NM_004958.4:c.6663-38_6663-37insC|||||||rs760249508||-1||EntrezGene||||||1:g.11182220_11182221insG|4.4e-05|0|0|0.0002002|0.0004353|0|8.878e-06|0|0|0.0004353|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:980:781:260,521:74,121:195,781:0.7969:2,2:36.1:1:36:1:0.23767:1.22521:60:51.067:0.8055:0.1092:0.2	0/0:187:0:0,0:51,136:187,0:0:2,0:34.1:1:36.2:1:1:0:60:61.333:1:0:0.1
    14. 

  14. 1	11184503	11184503	G	T	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	216	1	11184503	.	G	T	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=293;VD=3;AF=0.0102;SHIFT3=1;MSI=6;MSILEN=1;SSF=0.18991;SOR=inf;LSEQ=ACTACACGAGACAAATGTAG;RSEQ=AAAAAACCAGAAGACTTCTC;CSQ=T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386500.1|protein_coding||47/57|NM_001386500.1:c.6662+52C>A|||||||||-1||EntrezGene||YES||||1:g.11184503G>T||||||||||||||,T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386501.1|protein_coding||46/56|NM_001386501.1:c.5414+52C>A|||||||||-1||EntrezGene||||||1:g.11184503G>T||||||||||||||,T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_004958.4|protein_coding||47/57|NM_004958.4:c.6662+52C>A|||||||||-1||EntrezGene||||||1:g.11184503G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:293:3:2,1:210,80:290,3:0.0102:2,2:15:1:28.3:1:1:1.31122:60:2:0.007:0:2	0/0:216:0:0,0:154,62:216,0:0:2,2:40:1:11:0:1:0:60:0:0:0:3.5
    15. 

  15. 1	11188975	11188975	C	A	exonic	MTOR	.	nonsynonymous SNV	MTOR:NM_004958:exon41:c.G5748T:p.W1916C	0.0003	.	.	.	.	.	.	.	.	rs758900805	.	0.176	0.223	T	0.014	0.156	B	0.008	0.127	B	0.000	0.843	D	1	0.810	D	1.01	0.254	L	-1.47	0.811	T	-5.65	0.881	D	0.855	0.842	-0.560	0.664	T	0.396	0.749	T	0.049	0.640	D	5.974	0.821	27.7	0.943	0.241	0.992	0.920	D	c	0.165	0.385	1.000	0.747	0.707	0.730	0	6.06	0.983	7.539	0.808	0.935	0.490	1.000	0.715	0.998	0.697	20.621	0.995	PIK-related kinase	.	.	.	626592	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Likely_benign	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	129	1	11188975	.	C	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=627;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02893;SOR=0;LSEQ=AAGGCCTCATTGACATCTGG;RSEQ=CAGTGACCATAATCAAACCA;CSQ=A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386500.1|protein_coding|41/58||NM_001386500.1:c.5748G>T|NP_001373429.1:p.Trp1916Cys|5896|5748|1916|W/C|tgG/tgT|rs758900805||-1||EntrezGene||YES||||1:g.11188975C>A|2.791e-05|0|0.0001739|0|0|0|0|0.0001633|0|0.0001739|gnomAD_AMR|uncertain_significance||1,A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386501.1|protein_coding|40/57||NM_001386501.1:c.4500G>T|NP_001373430.1:p.Trp1500Cys|5760|4500|1500|W/C|tgG/tgT|rs758900805||-1||EntrezGene||||||1:g.11188975C>A|2.791e-05|0|0.0001739|0|0|0|0|0.0001633|0|0.0001739|gnomAD_AMR|uncertain_significance||1,A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_004958.4|protein_coding|41/58||NM_004958.4:c.5748G>T|NP_004949.1:p.Trp1916Cys|5869|5748|1916|W/C|tgG/tgT|rs758900805||-1||EntrezGene||||||1:g.11188975C>A|2.791e-05|0|0.0001739|0|0|0|0|0.0001633|0|0.0001739|gnomAD_AMR|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:627:0:0,0:279,347:626,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:129:2:1,1:56,71:127,2:0.0155:2,2:40.5:1:37:0:1:1.27:60:4:0.0156:0:1
    16. 

  16. 1	11190646	11190646	G	A	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon39:c.C5553T:p.S1851S	0.45	0.2823	0.4400	0.1360	0.3642	0.0712	0.2274	0.2359	0.2418	rs2275527	rs2275527	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63871083;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach),3(lung),1(thyroid),24(meninges),2(large_intestine)	364358	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU668989	LUSC-KR|3|170|0.0176471,COCA-CN|1|321|0.00311526	0.25	241	231	1	11190646	.	G	A	241	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1438;VD=1;AF=0.0007;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00091;LSEQ=TTCTCGGTGCTCTCGGCCTC;RSEQ=CTCTCACTGTTGCTGCCCTC;CSQ=A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|39/58||NM_001386500.1:c.5553C>T|NP_001373429.1:p.Ser1851%3D|5701|5553|1851|S|agC/agT|rs2275527&COSV63871083||-1||EntrezGene||YES||||1:g.11190646G>A|0.2155|0.4532|0.1182|0.3246|0.08024|0.2255|0.2351|0.229|0.1635|0.4532|gnomAD_AFR|benign|0&1|1&1,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|38/57||NM_001386501.1:c.4305C>T|NP_001373430.1:p.Ser1435%3D|5565|4305|1435|S|agC/agT|rs2275527&COSV63871083||-1||EntrezGene||||||1:g.11190646G>A|0.2155|0.4532|0.1182|0.3246|0.08024|0.2255|0.2351|0.229|0.1635|0.4532|gnomAD_AFR|benign|0&1|1&1,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|39/58||NM_004958.4:c.5553C>T|NP_004949.1:p.Ser1851%3D|5674|5553|1851|S|agC/agT|rs2275527&COSV63871083||-1||EntrezGene||||||1:g.11190646G>A|0.2155|0.4532|0.1182|0.3246|0.08024|0.2255|0.2351|0.229|0.1635|0.4532|gnomAD_AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1438:1:0,1:719,718:1437,1:0.0007:2,0:30:0:37:0:1:0:60:2:0.0007:0:1	0/1:231:101:58,43:63,67:130,101:0.4372:2,2:38.5:1:36.3:1:0.18663:1.43:60:100:0.4367:0:1
    17. 

  17. 1	11190807	11190807	A	T	exonic	MTOR	.	nonsynonymous SNV	MTOR:NM_004958:exon39:c.T5392A:p.F1798I	.	.	.	.	.	.	.	.	.	.	.	0.044	0.682	D	0.999	0.764	D	0.998	0.875	D	0.000	0.843	D	1	0.810	D	3.225	0.897	M	-0.66	0.724	T	-4.57	0.787	D	0.88	0.868	0.539	0.911	D	0.645	0.876	D	0.490	0.950	D	6.621	0.909	32	0.992	0.552	0.992	0.930	D	c	0.968	0.896	1.000	0.747	0.707	0.730	0	5.54	0.828	8.901	0.921	1.126	0.882	1.000	0.715	0.999	0.750	15.699	0.772	PIK-related kinase|PIK-related kinase, FAT	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	197	1	11190807	.	A	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2065;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00755;SOR=0;LSEQ=GTAGTGTAGCACAGCTTCGA;RSEQ=GTTCATCACTGCCCACGCAT;CSQ=T|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386500.1|protein_coding|39/58||NM_001386500.1:c.5392T>A|NP_001373429.1:p.Phe1798Ile|5540|5392|1798|F/I|Ttc/Atc|||-1||EntrezGene||YES||||1:g.11190807A>T||||||||||||||,T|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386501.1|protein_coding|38/57||NM_001386501.1:c.4144T>A|NP_001373430.1:p.Phe1382Ile|5404|4144|1382|F/I|Ttc/Atc|||-1||EntrezGene||||||1:g.11190807A>T||||||||||||||,T|missense_variant|MODERATE|MTOR|2475|Transcript|NM_004958.4|protein_coding|39/58||NM_004958.4:c.5392T>A|NP_004949.1:p.Phe1798Ile|5513|5392|1798|F/I|Ttc/Atc|||-1||EntrezGene||||||1:g.11190807A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2065:0:0,0:1072,992:2064,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:197:2:1,1:89,106:195,2:0.0102:2,2:58:1:37:0:1:1.19:60:4:0.0103:0:1
    18. 

  18. 1	11190847	11190847	A	G	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	197	1	11190847	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2204;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.0067;SOR=0;LSEQ=TGCCAGGCCTGGTTGGGGAG;RSEQ=AAGGCAAGGACAGACACTGG;CSQ=G|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding||38/57|NM_001386500.1:c.5365-13T>C|||||||||-1||EntrezGene||YES||||1:g.11190847A>G||||||||||||||,G|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding||37/56|NM_001386501.1:c.4117-13T>C|||||||||-1||EntrezGene||||||1:g.11190847A>G||||||||||||||,G|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding||38/57|NM_004958.4:c.5365-13T>C|||||||||-1||EntrezGene||||||1:g.11190847A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2204:0:0,0:1039,1165:2204,0:0:2,0:38.9:1:36.4:1:1:0:60:103.952:1:0:0.1	0/1:197:2:1,1:83,112:195,2:0.0102:2,2:48.5:1:37:0:1:1.35:60:4:0.0102:0:1
    19. 

  19. 1	11205058	11205058	C	T	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon33:c.G4731A:p.A1577A	0.82	0.5689	0.1535	0.7124	0.5530	0.8004	0.7093	0.7379	0.6735	rs1057079	rs1057079	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63875443;OCCURENCE=2(breast),1(thyroid)	497979	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4546849	COCA-CN|6|321|0.0186916	0.75	364	231	1	11205058	.	C	T	364	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1048;VD=1048;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CTGTAACTCTCTCCTGCCAT;RSEQ=GCAGTTAATTCAGCATCCAG;CSQ=T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|33/58||NM_001386500.1:c.4731G>A|NP_001373429.1:p.Ala1577%3D|4879|4731|1577|A|gcG/gcA|rs1057079&COSV63875443||-1||EntrezGene||YES||||1:g.11205058C>T|0.6859|0.1458|0.7285|0.5813|0.8135|0.7205|0.7407|0.6899|0.654|0.8165|EAS|benign|0&1|1&1,T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|32/57||NM_001386501.1:c.3483G>A|NP_001373430.1:p.Ala1161%3D|4743|3483|1161|A|gcG/gcA|rs1057079&COSV63875443||-1||EntrezGene||||||1:g.11205058C>T|0.6859|0.1458|0.7285|0.5813|0.8135|0.7205|0.7407|0.6899|0.654|0.8165|EAS|benign|0&1|1&1,T|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|33/58||NM_004958.4:c.4731G>A|NP_004949.1:p.Ala1577%3D|4852|4731|1577|A|gcG/gcA|rs1057079&COSV63875443||-1||EntrezGene||||||1:g.11205058C>T|0.6859|0.1458|0.7285|0.5813|0.8135|0.7205|0.7407|0.6899|0.654|0.8165|EAS|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|MTOR-AS1|100873935|Transcript|NR_046600.1|lncRNA||2/3|NR_046600.1:n.310+115C>T|||||||rs1057079&COSV63875443||1||EntrezGene||YES||||1:g.11205058C>T|0.6859|0.1458|0.7285|0.5813|0.8135|0.7205|0.7407|0.6899|0.654|0.8165|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1048:1048:515,533:0,0:0,1048:1:0,2:38:1:36.3:1:1:0:60:68.867:1:0:1.1	0/1:231:83:42,41:79,69:148,83:0.3593:2,2:42:1:36.9:1:0.78374:1.11713:60:166:0.3593:0:1.1
    20. 

  20. 1	11264675	11264675	G	A	exonic	MTOR	.	nonsynonymous SNV	MTOR:NM_004958:exon26:c.C3887T:p.S1296L	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.967	0.544	D	0.879	0.606	P	0.000	0.843	D	1	0.810	D	1.7	0.440	L	-0.14	0.650	T	-2.56	0.553	D	0.778	0.770	-0.336	0.740	T	0.372	0.731	T	0.041	0.597	D	5.274	0.713	25.7	0.999	0.971	0.992	0.920	D	c	0.771	0.790	1.000	0.747	0.732	0.924	0	5.79	0.917	9.502	0.969	1.048	0.713	1.000	0.715	0.716	0.313	20.041	0.976	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	154	1	11264675	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=273;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.12953;SOR=0;LSEQ=AGGAGCGCAGGGAGGGCGAT;RSEQ=ATGAGTCCTTCAGCAGCTCC;CSQ=A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386500.1|protein_coding|26/58||NM_001386500.1:c.3887C>T|NP_001373429.1:p.Ser1296Leu|4035|3887|1296|S/L|tCa/tTa|||-1||EntrezGene||YES||||1:g.11264675G>A||||||||||||||,A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386501.1|protein_coding|25/57||NM_001386501.1:c.2639C>T|NP_001373430.1:p.Ser880Leu|3899|2639|880|S/L|tCa/tTa|||-1||EntrezGene||||||1:g.11264675G>A||||||||||||||,A|missense_variant|MODERATE|MTOR|2475|Transcript|NM_004958.4|protein_coding|26/58||NM_004958.4:c.3887C>T|NP_004949.1:p.Ser1296Leu|4008|3887|1296|S/L|tCa/tTa|||-1||EntrezGene||||||1:g.11264675G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:273:0:0,0:135,138:273,0:0:2,0:38.5:1:36.8:1:1:0:60:272:1:0:0	0/1:154:2:1,1:87,65:152,2:0.013:2,2:27:1:37:0:1:1.33588:60:4:0.0131:0:1
    21. 

  21. 1	11270933	11270933	C	G	exonic	MTOR	.	nonsynonymous SNV	MTOR:NM_004958:exon24:c.G3592C:p.V1198L	.	.	.	.	.	.	.	.	.	.	.	0.06	0.373	T	0.841	0.445	P	0.846	0.587	P	0.008	0.313	N	1	0.810	D	2.155	0.604	M	-0.09	0.641	T	-2.25	0.503	N	0.662	0.674	-0.340	0.739	T	0.435	0.776	T	0.024	0.475	T	4.016	0.540	23.6	0.995	0.664	0.995	0.971	D	c	0.785	0.814	1.000	0.747	0.707	0.730	0	6.06	0.983	7.539	0.808	0.935	0.490	1.000	0.715	1.000	0.888	20.621	0.995	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	264	1	11270933	.	C	G	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=182;VD=2;AF=0.011;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.16598;SOR=inf;LSEQ=GATTCGGTGTCGCACCAGAA;RSEQ=TTTATTCACCATTGGAATGA;CSQ=G|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386500.1|protein_coding|24/58||NM_001386500.1:c.3592G>C|NP_001373429.1:p.Val1198Leu|3740|3592|1198|V/L|Gtt/Ctt|||-1||EntrezGene||YES||||1:g.11270933C>G||||||||||||||,G|missense_variant|MODERATE|MTOR|2475|Transcript|NM_001386501.1|protein_coding|23/57||NM_001386501.1:c.2344G>C|NP_001373430.1:p.Val782Leu|3604|2344|782|V/L|Gtt/Ctt|||-1||EntrezGene||||||1:g.11270933C>G||||||||||||||,G|missense_variant|MODERATE|MTOR|2475|Transcript|NM_004958.4|protein_coding|24/58||NM_004958.4:c.3592G>C|NP_004949.1:p.Val1198Leu|3713|3592|1198|V/L|Gtt/Ctt|||-1||EntrezGene||||||1:g.11270933C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:182:2:1,1:71,109:180,2:0.011:2,2:24:0:31:1:1:1.53:60:4:0.0112:0:1	0/0:264:0:0,0:122,142:264,0:0:2,0:39.9:1:35.8:1:1:0:60:51.8:1:0:0.1
    22. 

  22. 1	11270974	11270974	A	T	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	229	1	11270974	.	A	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=100;VD=2;AF=0.02;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.09174;SOR=inf;LSEQ=AAATTTGGTACTAAAACAGG;RSEQ=GGGGGAAGAGATGAGAAACT;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding||23/57|NM_001386500.1:c.3562-11T>A|||||||||-1||EntrezGene||YES||||1:g.11270974A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding||22/56|NM_001386501.1:c.2314-11T>A|||||||||-1||EntrezGene||||||1:g.11270974A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding||23/57|NM_004958.4:c.3562-11T>A|||||||||-1||EntrezGene||||||1:g.11270974A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:100:2:1,1:38,60:98,2:0.02:2,2:12:0:37:0:1:1.57:60:4:0.0206:0:2	0/0:229:0:0,0:87,142:229,0:0:2,0:37.8:1:35.6:1:1:0:60:37.167:1:0:0.1
    23. 

  23. 1	11288758	11288758	G	A	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon19:c.C2997T:p.N999N	0.92	0.6449	0.3858	0.8365	0.6126	0.9283	0.7467	0.7263	0.7157	rs1064261	rs1064261	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63873449;OCCURENCE=1(breast),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4552027	COCA-CN|5|321|0.0155763	0.75	386	520	1	11288758	.	G	A	386	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1850;VD=1841;AF=0.9951;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=232.298;LSEQ=CCATCACAGACTCGAATGAC;RSEQ=TTAAGGAACGTGGGCATGAC;CSQ=A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|19/58||NM_001386500.1:c.2997C>T|NP_001373429.1:p.Asn999%3D|3145|2997|999|N|aaC/aaT|rs1064261&COSV63873449||-1||EntrezGene||YES||||1:g.11288758G>A|0.7512|0.3732|0.8627|0.657|0.9191|0.7456|0.7334|0.7473|0.8271|0.9191|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|18/57||NM_001386501.1:c.1749C>T|NP_001373430.1:p.Asn583%3D|3009|1749|583|N|aaC/aaT|rs1064261&COSV63873449||-1||EntrezGene||||||1:g.11288758G>A|0.7512|0.3732|0.8627|0.657|0.9191|0.7456|0.7334|0.7473|0.8271|0.9191|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|19/58||NM_004958.4:c.2997C>T|NP_004949.1:p.Asn999%3D|3118|2997|999|N|aaC/aaT|rs1064261&COSV63873449||-1||EntrezGene||||||1:g.11288758G>A|0.7512|0.3732|0.8627|0.657|0.9191|0.7456|0.7334|0.7473|0.8271|0.9191|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1850:1841:953,888:0,0:0,1841:0.9951:0,2:38.7:1:35.6:1:1:0:60:40.841:0.9967:0:1.2	0/1:520:243:140,103:152,125:277,243:0.4673:2,2:37.5:1:36.2:1:0.53666:1.12:60:120.5:0.4707:0:1.2
    24. 

  24. 1	11294329	11294329	G	T	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	190	1	11294329	.	G	T	37	v3;f0.01;p8;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=616;VD=2;AF=0.0032;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.23758;SOR=0.30675;LSEQ=AACTCTGTCAAAATCTGTAG;RSEQ=GAAGAAAGGCTCATATGTTC;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding||13/57|NM_001386500.1:c.2209-7C>A|||||||||-1||EntrezGene||YES||||1:g.11294329G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding||12/56|NM_001386501.1:c.961-7C>A|||||||||-1||EntrezGene||||||1:g.11294329G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding||13/57|NM_004958.4:c.2209-7C>A|||||||||-1||EntrezGene||||||1:g.11294329G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:616:2:0,2:263,351:614,2:0.0032:2,0:7.5:1:11:0:0.50988:0:60:0:0:0:1	0/1:190:2:1,1:73,115:188,2:0.0105:2,2:55:1:37:0:1:1.57:60:4:0.0106:0:1.5
    25. 

  25. 1	11298113	11298113	A	T	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	181	1	11298113	.	A	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1376;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.01345;SOR=0;LSEQ=CGAATGTCAGGGTCTGCAAG;RSEQ=GCAATGGAGCCTTTGAACAT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding||12/57|NM_001386500.1:c.2003-8T>A|||||||||-1||EntrezGene||YES||||1:g.11298113A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding||11/56|NM_001386501.1:c.755-8T>A|||||||||-1||EntrezGene||||||1:g.11298113A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding||12/57|NM_004958.4:c.2003-8T>A|||||||||-1||EntrezGene||||||1:g.11298113A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1376:0:0,0:472,904:1376,0:0:2,0:36.8:1:36.5:1:1:0:60:104.846:1:0:0.1	0/1:181:2:1,1:52,127:179,2:0.011:2,2:58:1:37:0:0.50104:2.43:60:4:0.011:0:1.5
    26. 

  26. 1	11301714	11301714	A	G	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon10:c.T1437C:p.D479D	0.88	0.6129	0.2871	0.7751	0.6126	0.8837	0.7487	0.7263	0.7070	rs1135172	rs1135172	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63873456;OCCURENCE=1(breast),1(thyroid)	498006	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4552685	COCA-CN|5|321|0.0155763	0.75	368	202	1	11301714	.	A	G	368	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1058;VD=1055;AF=0.9972;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=377.029;LSEQ=ATGCAAGTGAAGACTGTGGC;RSEQ=TCCACCTGCATTGCCTTCTG;CSQ=G|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|10/58||NM_001386500.1:c.1437T>C|NP_001373429.1:p.Asp479%3D|1585|1437|479|D|gaT/gaC|rs1135172&COSV63873456||-1||EntrezGene||YES||||1:g.11301714A>G|0.7251|0.2779|0.7939|0.6568|0.8789|0.7468|0.7331|0.7287|0.7692|0.8789|gnomAD_EAS|benign|0&1|1&1,G|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding|9/57||NM_001386501.1:c.189T>C|NP_001373430.1:p.Asp63%3D|1449|189|63|D|gaT/gaC|rs1135172&COSV63873456||-1||EntrezGene||||||1:g.11301714A>G|0.7251|0.2779|0.7939|0.6568|0.8789|0.7468|0.7331|0.7287|0.7692|0.8789|gnomAD_EAS|benign|0&1|1&1,G|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|10/58||NM_004958.4:c.1437T>C|NP_004949.1:p.Asp479%3D|1558|1437|479|D|gaT/gaC|rs1135172&COSV63873456||-1||EntrezGene||||||1:g.11301714A>G|0.7251|0.2779|0.7939|0.6568|0.8789|0.7468|0.7331|0.7287|0.7692|0.8789|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1058:1055:501,554:0,0:0,1055:0.9972:0,2:38:1:36.7:1:1:0:60:174.833:0.999:0:1.1	0/1:202:97:42,55:49,56:105,97:0.4802:2,2:41.8:1:36.6:1:0.6724:1.14506:60:96:0.4776:0:1.1
    27. 

  27. 1	11308168	11308168	-	A	intronic	MTOR	.	.	.	0.0005	0.0001	0.0003	0.0012	0	0	0	0	0	rs759205492	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	108	144	1	11308168	.	G	GA	108	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=329;VD=7;AF=0.0213;SHIFT3=7;MSI=8;MSILEN=1;SSF=0.07723;SOR=inf;LSEQ=GACGCTATATATATGAGGAG;RSEQ=AAAAAAATCATCTTTACTTA;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding||6/57|NM_001386500.1:c.841-18dup|||||||rs759205492||-1||EntrezGene||YES||||1:g.11308175dup|6.167e-05|0.000461|0.0001148|0|0|0|3.022e-05|0|0|0.000461|gnomAD_AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_001386501.1|protein_coding||6/56|NM_001386501.1:c.-299-18dup|||||||rs759205492||-1||EntrezGene||||||1:g.11308175dup|6.167e-05|0.000461|0.0001148|0|0|0|3.022e-05|0|0|0.000461|gnomAD_AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding||6/57|NM_004958.4:c.841-18dup|||||||rs759205492||-1||EntrezGene||||||1:g.11308175dup|6.167e-05|0.000461|0.0001148|0|0|0|3.022e-05|0|0|0.000461|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:329:7:0,7:86,224:310,7:0.0213:2,0:23.5:1:38.5:0:0.19594:0:62.4:14:0.0224:0:0.1	0/0:144:0:0,0:41,103:144,0:0:2,0:32.7:1:35.5:1:1:0:60:19.571:1:0:0.2
    28. 

  28. 1	11316306	11316306	G	T	intronic	MTOR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	138	1	11316306	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=447;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05534;SOR=0;LSEQ=CCAGAGTTTTGTTCTCTCAG;RSEQ=AGTACAGTCTCTTGTCATCT;CSQ=T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386500.1|protein_coding||4/57|NM_001386500.1:c.505-57C>A|||||||||-1||EntrezGene||YES||||1:g.11316306G>T||||||||||||||,T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_001386501.1|protein_coding||4/56|NM_001386501.1:c.-635-57C>A|||||||||-1||EntrezGene||||||1:g.11316306G>T||||||||||||||,T|intron_variant|MODIFIER|MTOR|2475|Transcript|NM_004958.4|protein_coding||4/57|NM_004958.4:c.505-57C>A|||||||||-1||EntrezGene||||||1:g.11316306G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:447:0:0,0:120,327:447,0:0:2,0:33.8:1:36.6:1:1:0:60:222.5:1:0:0.1	0/1:138:2:1,1:33,103:136,2:0.0145:2,2:34.5:1:37:0:0.43341:3.09:60:4:0.0146:0:1
    29. 

  29. 1	11317005	11317005	G	A	exonic	MTOR	.	synonymous SNV	MTOR:NM_004958:exon4:c.C489T:p.G163G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	199	1	11317005	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1040;VD=0;AF=0;SHIFT3=3;MSI=3;MSILEN=1;SSF=0.02569;SOR=0;LSEQ=CTCACAGCTGCATGTCTCCG;RSEQ=CCCTCATTGCGGTCAGCACC;CSQ=A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_001386500.1|protein_coding|4/58||NM_001386500.1:c.489C>T|NP_001373429.1:p.Gly163%3D|637|489|163|G|ggC/ggT|||-1||EntrezGene||YES||||1:g.11317005G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MTOR|2475|Transcript|NM_001386501.1|protein_coding|4/57||NM_001386501.1:c.-651C>T||610|||||||-1||EntrezGene||||||1:g.11317005G>A||||||||||||||,A|synonymous_variant|LOW|MTOR|2475|Transcript|NM_004958.4|protein_coding|4/58||NM_004958.4:c.489C>T|NP_004949.1:p.Gly163%3D|610|489|163|G|ggC/ggT|||-1||EntrezGene||||||1:g.11317005G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1040:0:0,0:648,391:1039,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:199:2:1,1:143,54:197,2:0.0101:2,2:33:1:37:0:0.47739:2.63313:60:4:0.0101:0:2
    30. 

  30. 1	11854457	11854457	G	A	exonic	MTHFR	.	synonymous SNV	MTHFR:NM_001330358:exon8:c.C1428T:p.F476F,MTHFR:NM_005957:exon8:c.C1305T:p.F435F	1.	0.9091	0.6825	0.9809	0.9768	0.9988	1	0.9992	0.9867	rs4846051	rs4846051	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	177842	Homocystinuria_due_to_MTHFR_deficiency|not_specified	MedGen:C4017062|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	1	1	MU81691184	COCA-CN|5|321|0.0155763	1	401	269	1	11854457	.	G	A	401	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2180;VD=2172;AF=0.9963;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.64972;SOR=1.01306;LSEQ=TCTCCCGAGAGGTAAAGAAC;RSEQ=AAGACTTCAAAGACACTTTC;CSQ=A|downstream_gene_variant|MODIFIER|C1orf167|284498|Transcript|NM_001010881.2|protein_coding||||||||||rs4846051&CM044675|4815|1||EntrezGene||YES||||1:g.11854457G>A|0.9748|0.678|0.9819|0.9852|0.9991|1|0.9983|0.9839|0.9993|1|gnomAD_FIN|benign||1&1,A|synonymous_variant|LOW|MTHFR|4524|Transcript|NM_001330358.2|protein_coding|8/12||NM_001330358.2:c.1428C>T|NP_001317287.1:p.Phe476%3D|1451|1428|476|F|ttC/ttT|rs4846051&CM044675||-1||EntrezGene||YES||||1:g.11854457G>A|0.9748|0.678|0.9819|0.9852|0.9991|1|0.9983|0.9839|0.9993|1|gnomAD_FIN|benign||1&1,A|synonymous_variant|LOW|MTHFR|4524|Transcript|NM_005957.5|protein_coding|8/12||NM_005957.5:c.1305C>T|NP_005948.3:p.Phe435%3D|1395|1305|435|F|ttC/ttT|rs4846051&CM044675||-1||EntrezGene||||||1:g.11854457G>A|0.9748|0.678|0.9819|0.9852|0.9991|1|0.9983|0.9839|0.9993|1|gnomAD_FIN|benign||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2180:2172:1074,1098:0,0:0,2172:0.9963:0,2:38.7:1:36.2:1:1:0:60:89.5:0.9963:0:1.1	1/1:269:268:137,131:0,0:0,268:0.9963:0,2:36.8:1:36.6:1:1:0:60:133:0.9963:0:1.1
    31. 

  31. 1	11856321	11856321	T	A	exonic	MTHFR	.	nonsynonymous SNV	MTHFR:NM_001330358:exon5:c.A845T:p.K282M,MTHFR:NM_005957:exon5:c.A722T:p.K241M	.	.	.	.	.	.	.	.	.	.	.	0.013	0.586	D	0.539	0.516	P	0.427	0.576	B	0.000	0.491	D	1.000	0.548	D	3.06	0.872	M	-3.09	0.926	D	-3.29	0.657	D	0.465	0.518	0.798	0.944	D	0.817	0.938	D	0.293	0.907	D	5.544	0.754	26.4	0.995	0.667	0.945	0.611	D	c	0.386	0.366	1.000	0.747	0.722	0.854	0	5.08	0.682	5.586	0.670	1.061	0.807	1.000	0.715	0.488	0.269	14.347	0.661	FAD-linked oxidoreductase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	199	1	11856321	.	T	A	37	v3;f0.01;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1790;VD=2;AF=0.0011;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05218;SOR=0.11043;LSEQ=TGCCCATGTCGGTGCATGCC;RSEQ=TCACAAAGCGGAAGAATGTG;CSQ=A|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_001330358.2|protein_coding|5/12||NM_001330358.2:c.845A>T|NP_001317287.1:p.Lys282Met|868|845|282|K/M|aAg/aTg|||-1||EntrezGene||YES||||1:g.11856321T>A||||||||||||||,A|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_005957.5|protein_coding|5/12||NM_005957.5:c.722A>T|NP_005948.3:p.Lys241Met|812|722|241|K/M|aAg/aTg|||-1||EntrezGene||||||1:g.11856321T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1790:2:2,0:981,806:1787,2:0.0011:2,0:58.5:1:11:0:0.50462:0:60:0:0:0:1	0/1:199:2:1,1:105,92:197,2:0.0101:2,2:25:1:37:0:1:1.14054:60:4:0.0103:0:1.5
    32. 

  32. 1	11856378	11856378	G	A	exonic	MTHFR	.	nonsynonymous SNV	MTHFR:NM_001330358:exon5:c.C788T:p.A263V,MTHFR:NM_005957:exon5:c.C665T:p.A222V	0.51	0.2572	0.1131	0.4845	0.4470	0.2866	0.2351	0.3265	0.2633	rs1801133	rs1801133	0.002	0.721	D	0.998	0.764	D	0.941	0.759	D	0.000	0.843	D	0.000	0.588	P	2.965	0.855	M	-4.03	0.964	D	-3.76	0.712	D	0.955	0.952	-1.455	0.000	T	0.000	0.000	T	.	.	.	4.914	0.660	25.0	0.999	0.995	0.980	0.783	D	c	0.739	0.658	1.0	0.983	0.722	0.854	0	5.08	0.682	9.137	0.937	1.048	0.713	1.000	0.715	0.530	0.276	17.432	0.874	FAD-linked oxidoreductase-like	ENSG00000242349.1	Nerve_Tibial	ID=COSV64876755;OCCURENCE=1(breast),2(stomach),3(haematopoietic_and_lymphoid_tissue),1(urinary_tract),24(soft_tissue),1(prostate),1(lung)	18559	Neoplasm_of_stomach|Gastrointestinal_stromal_tumor|Thrombophilia_due_to_thrombin_defect|Homocystinuria_due_to_methylene_tetrahydrofolate_reductase_deficiency|Neural_tube_defects,_folate-sensitive|MTHFR_deficiency,_thermolabile_type|Homocystinuria_due_to_MTHFR_deficiency|not_specified|none_provided|carboplatin_response_-_Efficacy|cyclophosphamide_response_-_Toxicity/ADR|methotrexate_response_-_Dosage,_Efficacy,_Toxicity/ADR|not_provided	Human_Phenotype_Ontology:HP:0006753,MONDO:MONDO:0021085,MeSH:D013274,MedGen:C0038356,SNOMED_CT:126824007|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0008559,MedGen:C3160733,OMIM:188050|MONDO:MONDO:0009353,MedGen:C1856058,OMIM:236250,Orphanet:ORPHA395|MONDO:MONDO:0011120,MedGen:C1866558,OMIM:601634|MedGen:C1856059|MedGen:C4017062|MedGen:CN169374|MedGen:CN235283|MedGen:CN236495|MedGen:CN236519|MedGen:CN240598|MedGen:CN517202	reviewed_by_expert_panel	drug_response	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	MU580088	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.25	237	202	1	11856378	.	G	A	237	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1926;VD=3;AF=0.0016;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=0.00216;LSEQ=GCTGCGTGATGATGAAATCG;RSEQ=CTCCCGCAGACACCTTCTCC;CSQ=A|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_001330358.2|protein_coding|5/12||NM_001330358.2:c.788C>T|NP_001317287.1:p.Ala263Val|811|788|263|A/V|gCc/gTc|rs1801133&CM950819&COSV64876755||-1||EntrezGene||YES||||1:g.11856378G>A|0.3149|0.1076|0.5027|0.4569|0.2905|0.2307|0.3396|0.3297|0.1451|0.5027|gnomAD_AMR|uncertain_significance&_other&conflicting_interpretations_of_pathogenicity&pathogenic&uncertain_significance&not_provided&likely_benign&drug_response|0&0&1|1&1&1,A|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_005957.5|protein_coding|5/12||NM_005957.5:c.665C>T|NP_005948.3:p.Ala222Val|755|665|222|A/V|gCc/gTc|rs1801133&CM950819&COSV64876755||-1||EntrezGene||||||1:g.11856378G>A|0.3149|0.1076|0.5027|0.4569|0.2905|0.2307|0.3396|0.3297|0.1451|0.5027|gnomAD_AMR|uncertain_significance&_other&conflicting_interpretations_of_pathogenicity&pathogenic&uncertain_significance&not_provided&likely_benign&drug_response|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1926:3:1,2:937,986:1923,3:0.0016:2,2:27.7:1:37:0:1:1.89999:60:6:0.0016:0:1	0/1:202:85:41,44:53,64:117,85:0.4208:2,2:44.2:1:37:0:0.77521:1.12:60:170:0.4208:0:1.4
    33. 

  33. 1	11856420	11856420	T	C	exonic	MTHFR	.	nonsynonymous SNV	MTHFR:NM_001330358:exon5:c.A746G:p.E249G,MTHFR:NM_005957:exon5:c.A623G:p.E208G	.	.	.	.	.	.	.	.	.	.	.	0.019	0.501	D	0.738	0.455	P	0.574	0.523	P	0.000	0.629	D	1.000	0.506	D	2.74	0.803	M	-2.95	0.919	D	-4.22	0.758	D	0.594	0.625	0.838	0.949	D	0.829	0.943	D	0.112	0.791	D	3.444	0.472	23.0	0.999	0.980	0.952	0.635	D	c	0.567	0.557	1.0	0.983	0.732	0.924	0	5.08	0.682	5.535	0.667	1.061	0.807	1.000	0.715	0.979	0.486	14.000	0.638	FAD-linked oxidoreductase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	175	1	11856420	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1619;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00947;SOR=0;LSEQ=TCAAGTGCTTCAGGTCAGCC;RSEQ=CAAAGCTCCCTGCTTCGGGG;CSQ=C|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_001330358.2|protein_coding|5/12||NM_001330358.2:c.746A>G|NP_001317287.1:p.Glu249Gly|769|746|249|E/G|gAg/gGg|||-1||EntrezGene||YES||||1:g.11856420T>C||||||||||||||,C|missense_variant|MODERATE|MTHFR|4524|Transcript|NM_005957.5|protein_coding|5/12||NM_005957.5:c.623A>G|NP_005948.3:p.Glu208Gly|713|623|208|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.11856420T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1619:0:0,0:680,938:1618,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:175:2:1,1:73,100:173,2:0.0114:2,2:35:1:37:0:1:1.37:60:4:0.0115:0:2
    34. 

  34. 1	16199718	16199718	T	A	ncRNA_intronic	MIR5096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	88	1	16199718	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.27356;SOR=inf;LSEQ=TTAGGGGCCCCAGATGGATT;RSEQ=AAAGTTTTGGGCATTCTCAA;CSQ=A|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||2/14|NM_015001.3:c.404+87T>A|||||||||1||EntrezGene||YES||||1:g.16199718T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:12,83:95,2:0.0206:2,2:32:1:37:0:0.25129:6.69:60:4:0.0217:0:1	0/0:88:0:0,0:13,75:88,0:0:2,0:37.1:1:34.9:1:1:0:60:28.333:1:0:0.1
    35. 

  35. 1	16200730	16200730	T	-	ncRNA_intronic	MIR5096	.	.	.	0.0042	3.291e-05	0	0	0	0	0.0003	0	0	rs774258389	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	122	245	1	16200729	.	AT	A	122	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=24;VD=1;AF=0.0417;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.64956;SOR=1.02166;LSEQ=TATTTTGTCTGGTCACTAAG;RSEQ=TTTTTTTTTCTTGTGGTTCA;CSQ=-|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||2/14|NM_015001.3:c.404+1108del|||||||rs761626223||1||EntrezGene||YES||||1:g.16200739del|0.0001603|0|0|0.0003257|0|0.0007583|0.0001701|0|3.521e-05|0.0007583|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:24:1:0,1:12,11:23,1:0.0417:2,0:53:0:37:0:1:0:60:2:0.0417:0:0	0/1:245:10:4,6:110,125:235,10:0.0408:2,2:47:1:37:0:0.75493:1.31852:60:20:0.0417:0:0.4
    36. 

  36. 1	16200812	16200812	A	-	ncRNA_intronic	MIR5096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	149	1	16200811	.	CA	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=24;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.74109;SOR=0;LSEQ=ATTACCCCCATAAGAGGGGC;RSEQ=AAATTGGGGAAGTTATGTTC;CSQ=-|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||2/14|NM_015001.3:c.404+1184del|||||||||1||EntrezGene||YES||||1:g.16200815del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:24:0:0,0:12,12:24,0:0:2,0:37:1:37:0:1:0:60:48:1:0:0	0/1:149:2:1,1:53,94:147,2:0.0134:2,2:21.5:1:37:0:1:1.77:60:4:0.0134:0:0
    37. 

  37. 1	16237812	16237812	G	T	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	181	1	16237812	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=118;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.36565;SOR=0;LSEQ=TCCAGGTAAGACACAAGCAA;RSEQ=CTGAGTTTGAGTTACTCATC;CSQ=T|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||5/14|NM_015001.3:c.1243+16G>T|||||||||1||EntrezGene||YES||||1:g.16237812G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:118:0:0,0:51,67:118,0:0:2,0:44.5:1:36.6:1:1:0:60:58:1:0:0.1	0/1:181:2:1,1:55,124:179,2:0.011:2,2:35:1:37:0:0.52425:2.24:60:4:0.0112:0:1
    38. 

  38. 1	16242593	16242593	C	A	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	92	1	16242593	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=73;VD=2;AF=0.0274;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.19424;SOR=inf;LSEQ=GCATTAAAATACTGTCTTCT;RSEQ=TTTTTACTCGGCCCCCATTC;CSQ=A|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||5/14|NM_015001.3:c.1244-30C>A|||||||||1||EntrezGene||YES||||1:g.16242593C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:73:2:1,1:57,14:71,2:0.0274:2,2:15:1:37:0:0.371:3.96773:60:4:0.0278:0:1	0/0:92:0:0,0:68,24:92,0:0:2,0:38.7:1:35.5:1:1:0:60:29.667:1:0:0.5
    39. 

  39. 1	16242620	16242620	C	A	intronic	SPEN	.	.	.	0.33	0.1025	0.0371	0.2727	0.0629	0.2024	0.1631	0.1056	0.1227	rs12063905	rs12063905	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65357961;OCCURENCE=4(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU755355	LICA-CN|2|402|0.00497512,LAML-KR|2|205|0.0097561,COCA-CN|2|321|0.00623053	0.25	209	118	1	16242620	.	C	A	209	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCGGCCCCCATTCCACTTA;RSEQ=AGAAACAGAAAGTGAAAATG;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding||5/14|NM_015001.3:c.1244-3C>A|||||||rs12063905&COSV65357961||1||EntrezGene||YES||||1:g.16242620C>A|0.1401|0.04153|0.3215|0.08136|0.2301|0.1633|0.1|0.1262|0.09198|0.3215|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:123:0:0,0:88,35:123,0:0:2,0:29.6:1:36.1:1:1:0:60:60.5:1:0:0.1	0/1:118:53:37,16:45,20:65,53:0.4492:2,2:38.2:1:36.5:1:1:1.03:60:106:0.4649:0:1.1
    40. 

  40. 1	16242634	16242634	G	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon6:c.G1255A:p.E419K	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.996	0.832	D	.	.	.	1	0.810	D	0.345	0.112	N	3.02	0.090	T	-2.59	0.558	D	0.228	0.820	-1.071	0.092	T	0.043	0.184	T	0.008	0.203	T	7.030	0.939	33	0.999	0.967	0.989	0.881	D	c	0.718	0.784	1.0	0.983	0.732	0.924	0	5.87	0.942	9.478	0.968	0.998	0.613	1.000	0.715	1.000	0.888	20.215	0.983	.	.	.	ID=COSV65362348;OCCURENCE=1(cervix)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU29255861	CESC-US|1|289|0.00346021	0.25	31	147	1	16242634	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.24746;SOR=0;LSEQ=CACTTACAGAAACAGAAAGT;RSEQ=AAAATGAATTTCGCCCCTTG;CSQ=A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|6/15||NM_015001.3:c.1255G>A|NP_055816.2:p.Glu419Lys|1616|1255|419|E/K|Gaa/Aaa|COSV65362348||1||EntrezGene||YES||||1:g.16242634G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:148:0:0,0:97,51:148,0:0:2,0:34.3:1:36.1:1:1:0:60:48.333:1:0:0.1	0/1:147:2:1,1:94,51:145,2:0.0136:2,2:48.5:1:31:1:1:1.83508:60:4:0.0146:0:1
    41. 

  41. 1	16242706	16242706	G	C	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon6:c.G1327C:p.G443R	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	.	.	.	1	0.810	D	2.33	0.670	M	2.86	0.105	T	-7.14	0.941	D	0.392	0.932	-0.151	0.789	T	0.483	0.803	T	0.008	0.214	T	6.219	0.858	28.8	0.999	0.998	0.991	0.912	D	c	0.638	0.710	1.0	0.983	0.732	0.924	0	5.87	0.942	9.478	0.968	0.998	0.613	1.000	0.715	1.000	0.888	20.215	0.983	Nucleotide-binding alpha-beta plait domain|RNA recognition motif domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	189	1	16242706	.	G	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=218;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.21503;SOR=0;LSEQ=CAACAAGAACTCTCTTTATT;RSEQ=GCAACCTTGAAAAAACCACT;CSQ=C|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|6/15||NM_015001.3:c.1327G>C|NP_055816.2:p.Gly443Arg|1688|1327|443|G/R|Ggc/Cgc|||1||EntrezGene||YES||||1:g.16242706G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:218:0:0,0:107,111:218,0:0:2,0:41.5:1:35.1:1:1:0:60:26.25:1:0:0.1	0/1:189:2:1,1:97,90:187,2:0.0106:2,2:52:1:37:0:1:1.07733:60:4:0.0108:0:1
    42. 

  42. 1	16242732	16242732	C	T	exonic	SPEN	.	synonymous SNV	SPEN:NM_015001:exon6:c.C1353T:p.Y451Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	190	1	16242732	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=184;VD=2;AF=0.0109;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.24137;SOR=inf;LSEQ=CTTGAAAAAACCACTACTTA;RSEQ=CATGACCTTCGCAACATCTT;CSQ=T|synonymous_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding|6/15||NM_015001.3:c.1353C>T|NP_055816.2:p.Tyr451%3D|1714|1353|451|Y|taC/taT|||1||EntrezGene||YES||||1:g.16242732C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:184:2:1,1:76,106:182,2:0.0109:2,2:52:0:37:0:1:1.39:60:4:0.0115:0:1	0/0:190:0:0,0:86,103:189,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    43. 

  43. 1	16242813	16242813	G	A	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	98	1	16242813	.	G	A	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=2;AF=0.0465;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.09149;SOR=inf;LSEQ=GTAAACAATTTTAGGTCTTT;RSEQ=TCATAACACATAAAGCATAG;CSQ=A|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||6/14|NM_015001.3:c.1395+39G>A|||||||||1||EntrezGene||YES||||1:g.16242813G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:43:2:1,1:11,30:41,2:0.0465:2,2:63:0:31:1:0.48505:2.65:60:4:0.0476:0:1	0/0:98:0:0,0:26,72:98,0:0:2,0:36.7:1:35.3:1:1:0:60:23.5:1:0:0.1
    44. 

  44. 1	16245372	16245372	A	G	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	51	1	16245372	.	A	G	25	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGACTTGGTTCATTCTA;RSEQ=TTTATTTTCTTGGGCATATT;CSQ=G|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||6/14|NM_015001.3:c.1396-49A>G|||||||||1||EntrezGene||YES||||1:g.16245372A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:51:2:1,1:42,7:49,2:0.0392:2,2:30.5:1:25:0:0.29176:5.67896:60:4:0.04:0:1
    45. 

  45. 1	16245450	16245450	T	C	exonic	SPEN	.	synonymous SNV	SPEN:NM_015001:exon7:c.T1425C:p.V475V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	131	1	16245450	.	T	C	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.98485;SOR=0;LSEQ=ATTAAGAAAGTAAATGGAGT;RSEQ=CCTCAGTATGCGTTTCTGCA;CSQ=C|synonymous_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding|7/15||NM_015001.3:c.1425T>C|NP_055816.2:p.Val475%3D|1786|1425|475|V|gtT/gtC|||1||EntrezGene||YES||||1:g.16245450T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:37:0:1:0:60:2:1:0:1	0/1:131:2:1,1:77,52:129,2:0.0153:2,2:40:1:37:0:1:1.47619:60:4:0.0154:0:1.5
    46. 

  46. 1	16245465	16245465	T	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon7:c.T1440A:p.F480L	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.998	0.875	D	.	.	.	1	0.810	D	3.34	0.912	M	1.54	0.301	T	-5.31	0.844	D	0.447	0.763	-0.283	0.755	T	0.281	0.653	T	0.099	0.771	D	5.646	0.769	26.6	0.998	0.892	0.958	0.658	D	c	0.277	0.248	1.000	0.747	0.732	0.924	0	3.92	0.444	3.231	0.507	-0.351	0.070	1.000	0.715	0.929	0.403	12.471	0.549	Nucleotide-binding alpha-beta plait domain|RNA recognition motif domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	153	1	16245465	.	T	A	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.98701;SOR=0;LSEQ=GGAGTTCCTCAGTATGCGTT;RSEQ=CTGCAATACTGTGATATTGC;CSQ=A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|7/15||NM_015001.3:c.1440T>A|NP_055816.2:p.Phe480Leu|1801|1440|480|F/L|ttT/ttA|||1||EntrezGene||YES||||1:g.16245465T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:37:0:1:0:60:2:1:0:1	0/1:153:2:1,1:82,69:151,2:0.0131:2,2:8.5:1:37:0:1:1.18706:60:4:0.0132:0:1
    47. 

  47. 1	16245920	16245920	C	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon8:c.C1543T:p.P515S	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.999	0.916	D	.	.	.	1	0.810	D	2.725	0.800	M	3.36	0.059	T	-6.6	0.920	D	0.203	0.904	-0.950	0.410	T	0.101	0.375	T	0.025	0.479	T	6.520	0.898	31	0.999	0.988	0.975	0.750	D	c	0.996	0.950	1.0	0.983	0.742	0.980	0	5.98	0.971	7.520	0.806	0.935	0.490	1.000	0.715	1.000	0.888	20.450	0.991	Nucleotide-binding alpha-beta plait domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	301	1	16245920	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=184;VD=2;AF=0.0109;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.14344;SOR=inf;LSEQ=TGGGTTTTGGAAAGAGCATG;RSEQ=CTACAAACTGCGTGTGGCTA;CSQ=T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|8/15||NM_015001.3:c.1543C>T|NP_055816.2:p.Pro515Ser|1904|1543|515|P/S|Cct/Tct|||1||EntrezGene||YES||||1:g.16245920C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:184:2:1,1:108,74:182,2:0.0109:2,2:29:0:37:0:1:1.45636:60:4:0.0113:0:1	0/0:301:0:0,0:170,130:300,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    48. 

  48. 1	16255644	16255644	C	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.C2909T:p.A970V	0.33	0.1023	0.0367	0.2727	0.0629	0.2014	0.1628	0.1058	0.1222	rs848208	rs848208	0.098	0.308	T	0.006	0.126	B	0.005	0.104	B	.	.	.	1	0.090	P	2.25	0.640	M	0.65	0.527	T	-0.36	0.131	N	0.008	0.004	-1.063	0.110	T	0.000	0.000	T	.	.	.	-0.317	0.067	0.608	0.498	0.042	0.206	0.209	N	c	-0.760	-0.758	0.013	0.124	0.707	0.730	0	3.64	0.407	0.605	0.237	0.935	0.490	0.000	0.063	0.001	0.043	8.844	0.341	.	ENSG00000186510.7|ENSG00000179743.2|ENSG00000173641.13	Adrenal_Gland|Muscle_Skeletal|Thyroid	ID=COSV65357982;OCCURENCE=4(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU755381	LICA-CN|2|402|0.00497512,LAML-KR|3|205|0.0146341,COCA-CN|2|321|0.00623053	0.25	283	447	1	16255644	.	C	T	283	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1793;VD=2;AF=0.0011;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.001;LSEQ=CCTCAAGCCTGAGCAGCCTG;RSEQ=AGATGGGGTAAGTGCTGTGG;CSQ=T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.2909C>T|NP_055816.2:p.Ala970Val|3270|2909|970|A/V|gCa/gTa|rs848208&COSV65357982||1||EntrezGene||YES||||1:g.16255644C>T|0.1409|0.04142|0.3225|0.08161|0.2302|0.1634|0.1003|0.1265|0.09225|0.3225|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1793:2:1,1:929,862:1791,2:0.0011:2,2:39.5:1:37:0:1:1.07766:60:4:0.0011:0:1	1/0:447:237:122,115:99,110:209,237:0.5302:2,2:40.5:1:35.9:1:0.39473:1.18:60:38.5:0.5238:0:1.1
    49. 

  49. 1	16256007	16256007	T	C	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.T3272C:p.L1091P	0.98	0.6713	0.9243	0.7584	0.61	0.2983	0.6105	0.5802	0.5867	rs848209	rs848209	0.846	0.028	T	0.0	0.026	B	0.0	0.013	B	.	.	.	1.000	0.090	P	-0.895	0.014	N	3.2	0.073	T	0.6	0.025	N	0.012	0.012	-1.030	0.206	T	0.000	0.000	T	.	.	.	-0.797	0.040	0.043	0.776	0.115	0.020	0.059	N	c	-1.030	-0.892	0.097	0.163	0.707	0.730	0	3.51	0.391	1.064	0.300	-0.302	0.080	0.124	0.230	0.197	0.217	11.158	0.475	.	ENSG00000186510.7|ENSG00000186510.7|ENSG00000173641.13|ENSG00000186510.7|ENSG00000186510.7|ENSG00000186510.7|ENSG00000186510.7|ENSG00000173641.13|ENSG00000186510.7	Artery_Aorta|Brain_Cortex|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Lung|Muscle_Skeletal|Nerve_Tibial|Thyroid|Thyroid	ID=COSV65359297;OCCURENCE=3(haematopoietic_and_lymphoid_tissue),1(urinary_tract),1(lung),1(thyroid),1(biliary_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU4550099	LICA-CN|1|402|0.00248756,LAML-KR|4|205|0.0195122,COCA-CN|3|321|0.00934579	0.5	297	386	1	16256007	.	T	C	297	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1416;VD=284;AF=0.2006;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=0.2934;LSEQ=ACAAGCAAGACTGGGAGAAC;RSEQ=AGCAGGTGAATCTGTGGAAA;CSQ=C|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.3272T>C|NP_055816.2:p.Leu1091Pro|3633|3272|1091|L/P|cTa/cCa|rs848209&COSV65359297||1||EntrezGene||YES||||1:g.16256007T>C|0.6155|0.9246|0.754|0.6134|0.3278|0.6082|0.5748|0.6078|0.6272|0.9758|AFR||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1416:284:146,138:596,535:1131,284:0.2006:2,2:38.4:1:36.5:1:0.73975:1.05297:60:93.667:0.2007:0:1.1	0/1:386:178:95,83:100,108:208,178:0.4611:2,2:34.8:1:36.2:1:0.30899:1.24:60:88:0.4607:0:1.1
    50. 

  50. 1	16257080	16257080	G	T	exonic	SPEN	.	stopgain	SPEN:NM_015001:exon11:c.G4345T:p.E1449X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.093	0.989	41	0.997	0.811	0.996	0.980	D	c	1.173	1.025	1.000	0.747	0.707	0.730	0	5.14	0.699	9.312	0.953	1.048	0.713	1.000	0.715	1.000	0.888	16.960	0.861	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	291	1	16257080	.	G	T	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=238;VD=3;AF=0.0126;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.09044;SOR=inf;LSEQ=CAGACACTAAAGCTTTGCTT;RSEQ=AAAGAGCTAAATCCCTCTCT;CSQ=T|stop_gained|HIGH|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.4345G>T|NP_055816.2:p.Glu1449Ter|4706|4345|1449|E/*|Gaa/Taa|||1||EntrezGene||YES||||1:g.16257080G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:238:3:1,2:118,117:235,3:0.0126:2,2:40:1:28.3:1:1:2.01136:60:2:0.0087:0:3.3	0/0:291:0:0,0:140,151:291,0:0:2,0:1:0:11:0:1:0:60:0:0:0:7
    51. 

  51. 1	16259813	16259813	A	G	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.A7078G:p.N2360D	0.98	0.6706	0.9239	0.7590	0.6033	0.2976	0.6101	0.5793	0.5866	rs848210	rs848210	0.853	0.027	T	0.0	0.026	B	0.0	0.013	B	.	.	.	1	0.090	P	-0.625	0.021	N	3.13	0.080	T	0.77	0.020	N	0.001	0.000	-1.042	0.168	T	0.000	0.000	T	.	.	.	-1.105	0.028	0.010	0.538	0.049	0.094	0.150	N	c	-1.237	-1.093	0.230	0.184	0.707	0.730	0	3.1	0.346	3.586	0.534	0.076	0.183	0.665	0.281	0.006	0.095	7.596	0.271	.	ENSG00000186510.7|ENSG00000186510.7|ENSG00000173641.13|ENSG00000186510.7|ENSG00000186510.7|ENSG00000186510.7|ENSG00000186510.7|ENSG00000173641.13|ENSG00000186510.7	Artery_Aorta|Brain_Cortex|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Lung|Muscle_Skeletal|Nerve_Tibial|Thyroid|Thyroid	ID=COSV65359302;OCCURENCE=3(haematopoietic_and_lymphoid_tissue),2(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU4549778	LAML-KR|4|205|0.0195122,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579	0.5	332	340	1	16259813	.	A	G	332	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3059;VD=539;AF=0.1762;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.23239;LSEQ=AGAGCCATGTCCCTGAATCC;RSEQ=ACCAAGCTCAAGGTGAGAGT;CSQ=G|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.7078A>G|NP_055816.2:p.Asn2360Asp|7439|7078|2360|N/D|Aac/Gac|rs848210&COSV65359302||1||EntrezGene||YES||||1:g.16259813A>G|0.6156|0.9246|0.7539|0.6137|0.3278|0.6084|0.5749|0.6084|0.6269|0.9758|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3059:539:260,279:1232,1286:2518,539:0.1762:2,2:38.2:1:36.6:1:0.77598:1.02802:60:106.8:0.1772:0:1.1	0/1:340:163:81,82:83,92:175,163:0.4794:2,2:39:1:36.5:1:0.74399:1.09:60:80.5:0.4763:0:1.1
    52. 

  52. 1	16260060	16260060	A	G	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.A7325G:p.E2442G	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.002	0.090	B	0.002	0.063	B	.	.	.	1.000	0.205	N	0.345	0.112	N	3.01	0.091	T	-1.51	0.368	N	0.072	0.061	-0.966	0.381	T	0.017	0.071	T	0.004	0.092	T	0.297	0.123	5.662	0.238	0.010	0.973	0.738	D	c	-0.869	-0.786	0.654	0.222	0.707	0.730	0	2.83	0.320	3.664	0.540	0.058	0.164	0.998	0.411	0.022	0.137	9.314	0.369	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	108	1	16260060	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1367;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00532;SOR=0;LSEQ=CCAGCCAGCACCGGTGGATG;RSEQ=GGAGCCTCAAGCCAGGTTCA;CSQ=G|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.7325A>G|NP_055816.2:p.Glu2442Gly|7686|7325|2442|E/G|gAg/gGg|COSV65367946||1||EntrezGene||YES||||1:g.16260060A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1367:0:0,0:593,773:1366,0:0:2,0:34.2:1:35.9:1:1:0:60:47.786:1:0:0.1	0/1:108:2:1,1:51,55:106,2:0.0185:2,2:48.5:1:37:0:1:1.08:60:4:0.0189:0:1
    53. 

  53. 1	16260074	16260074	A	G	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.A7339G:p.R2447G	.	.	.	.	.	.	.	.	.	.	.	0.093	0.315	T	0.0	0.026	B	0.001	0.040	B	.	.	.	0.989	0.244	N	1.24	0.311	L	3.08	0.085	T	0.13	0.055	N	0.178	0.227	-0.996	0.311	T	0.016	0.066	T	0.008	0.221	T	2.976	0.418	22.2	0.674	0.081	0.865	0.455	D	c	-0.415	-0.271	0.682	0.225	0.707	0.730	0	4.04	0.461	2.155	0.417	1.088	0.866	0.998	0.411	0.996	0.625	8.319	0.311	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	117	1	16260074	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1340;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0064;SOR=0;LSEQ=TGGATGAGGAGCCTCAAGCC;RSEQ=GGTTCAGGGTGCATTCCATC;CSQ=G|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.7339A>G|NP_055816.2:p.Arg2447Gly|7700|7339|2447|R/G|Agg/Ggg|||1||EntrezGene||YES||||1:g.16260074A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1340:0:0,0:587,750:1337,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:117:2:1,1:60,55:115,2:0.0171:2,2:42.5:1:37:0:1:1.09009:60:4:0.0172:0:1
    54. 

  54. 1	16260124	16260124	C	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.C7389A:p.S2463R	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.996	0.670	D	0.979	0.728	D	.	.	.	0.982	0.249	N	1.76	0.459	L	3.01	0.091	T	-1.11	0.287	N	0.469	0.531	-1.078	0.077	T	0.049	0.209	T	0.009	0.228	T	1.320	0.223	12.37	0.827	0.139	0.753	0.366	D	c	-0.920	-1.130	0.999	0.392	0.707	0.730	0	-6.33	0.018	-0.219	0.092	-1.770	0.007	0.052	0.213	0.090	0.185	13.649	0.616	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	161	1	16260124	.	C	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1439;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01007;SOR=0;LSEQ=GACCCGGTGACCCCACCCAG;RSEQ=GATCCAAGCATCCCCATACC;CSQ=A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.7389C>A|NP_055816.2:p.Ser2463Arg|7750|7389|2463|S/R|agC/agA|||1||EntrezGene||YES||||1:g.16260124C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1439:0:0,0:735,704:1439,0:0:2,0:35.3:1:36.5:1:1:0:60:178.875:1:0:0.1	0/1:161:2:1,1:91,68:159,2:0.0124:2,2:35:1:31:1:1:1.33577:60:4:0.0124:0:1
    55. 

  55. 1	16260916	16260916	C	T	exonic	SPEN	.	synonymous SNV	SPEN:NM_015001:exon11:c.C8181T:p.A2727A	0.33	0.1034	0.0384	0.2757	0.0629	0.2062	0.1657	0.1055	0.1235	rs848211	rs848211	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65357526;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),3(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU11296748	LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|2|321|0.00623053	0.25	284	410	1	16260916	.	C	T	284	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3450;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCCCAGGCACAGTCAATGC;RSEQ=GCTGCGAGTGCAGTGAATGC;CSQ=T|synonymous_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.8181C>T|NP_055816.2:p.Ala2727%3D|8542|8181|2727|A|gcC/gcT|rs848211&COSV65357526||1||EntrezGene||YES||||1:g.16260916C>T|0.1413|0.043|0.3224|0.08156|0.2338|0.1646|0.1003|0.1263|0.09227|0.3224|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3450:0:0,0:1953,1495:3448,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:410:216:115,101:97,94:191,216:0.5268:2,2:35.9:1:36.7:1:0.69095:1.1:60:107:0.5284:0:1.1
    56. 

  56. 1	16262135	16262135	C	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.C9400A:p.P3134T	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.995	0.657	D	0.943	0.662	D	.	.	.	0.998	0.445	D	2.125	0.592	M	2.9	0.101	T	-2.09	0.476	N	0.458	0.510	-1.140	0.014	T	0.068	0.279	T	0.009	0.232	T	3.552	0.484	23.1	0.985	0.412	0.977	0.760	D	c	0.459	0.420	1.000	0.747	0.707	0.730	0	4.2	0.486	3.741	0.546	0.888	0.391	0.998	0.411	0.892	0.376	13.320	0.597	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	1	16262135	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1098;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01539;SOR=0;LSEQ=AGCAAATAGAGGTCAGGGCC;RSEQ=CACAGCGTGCCAGCACCCCG;CSQ=A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9400C>A|NP_055816.2:p.Pro3134Thr|9761|9400|3134|P/T|Cca/Aca|||1||EntrezGene||YES||||1:g.16262135C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1098:0:0,0:593,505:1098,0:0:2,0:37.1:1:36.8:1:1:0:60:218.6:1:0:0.1	0/1:156:2:1,1:84,70:154,2:0.0128:2,2:31:0:37:0:1:1.19859:60:4:0.013:0:1
    57. 

  57. 1	16262145	16262145	C	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.C9410T:p.A3137V	.	.	.	.	.	.	.	.	.	.	.	0.656	0.047	T	0.001	0.067	B	0.001	0.040	B	.	.	.	1	0.090	N	-0.69	0.019	N	3.22	0.070	T	-0.27	0.114	N	0.027	0.009	-0.924	0.450	T	0.012	0.047	T	0.006	0.166	T	2.416	0.352	18.92	0.965	0.296	0.883	0.479	D	c	-0.652	-0.537	0.999	0.380	0.707	0.730	0	1.97	0.252	3.120	0.499	0.046	0.159	0.754	0.289	0.091	0.185	6.683	0.222	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	159	1	16262145	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1114;VD=0;AF=0;SHIFT3=4;MSI=2;MSILEN=1;SSF=0.01551;SOR=0;LSEQ=GGTCAGGGCCCCACAGCGTG;RSEQ=CAGCACCCCGCAGCCAGCCC;CSQ=T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9410C>T|NP_055816.2:p.Ala3137Val|9771|9410|3137|A/V|gCc/gTc|||1||EntrezGene||YES||||1:g.16262145C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1114:0:0,0:600,514:1114,0:0:2,0:37.8:1:36.7:1:1:0:60:184.667:1:0:0.1	0/1:159:2:1,1:89,68:157,2:0.0126:2,2:19:0:37:0:1:1.30657:60:4:0.0126:0:1
    58. 

  58. 1	16262149	16262149	C	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.C9414A:p.S3138R	.	.	.	.	.	.	.	.	.	.	.	0.005	0.632	D	0.006	0.126	B	0.01	0.139	B	.	.	.	0.987	0.245	N	1.245	0.315	L	2.98	0.094	T	-1.4	0.346	N	0.123	0.174	-0.922	0.453	T	0.016	0.064	T	0.010	0.265	T	2.457	0.357	19.19	0.940	0.235	0.879	0.472	D	c	-0.772	-0.694	0.985	0.307	0.707	0.730	0	-0.512	0.113	0.435	0.211	0.888	0.391	0.993	0.376	0.107	0.192	6.722	0.224	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	159	1	16262149	.	C	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1126;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01523;SOR=0;LSEQ=AGGGCCCCACAGCGTGCCAG;RSEQ=ACCCCGCAGCCAGCCCCAGC;CSQ=A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9414C>A|NP_055816.2:p.Ser3138Arg|9775|9414|3138|S/R|agC/agA|||1||EntrezGene||YES||||1:g.16262149C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1126:0:0,0:609,515:1124,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:159:2:1,1:88,69:157,2:0.0126:2,2:5.5:1:37:0:1:1.27339:60:4:0.0126:0:1
    59. 

  59. 1	16262404	16262404	C	T	exonic	SPEN	.	synonymous SNV	SPEN:NM_015001:exon11:c.C9669T:p.S3223S	0.33	0.1025	0.0367	0.2745	0.0629	0.2062	0.1636	0.1052	0.1186	rs61749277	rs61749277	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU14665254	LICA-CN|1|402|0.00248756,COCA-CN|2|321|0.00623053	0.25	210	106	1	16262404	.	C	T	210	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=892;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGAAGGTGCCACCAGCCAG;RSEQ=AAGGCCCCTCAGCAGCCAGG;CSQ=T|synonymous_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9669C>T|NP_055816.2:p.Ser3223%3D|10030|9669|3223|S|agC/agT|rs61749277||1||EntrezGene||YES||||1:g.16262404C>T|0.1406|0.0398|0.3214|0.08037|0.2334|0.1609|0.09905|0.1256|0.09226|0.3214|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:892:0:0,0:306,586:892,0:0:2,0:34.2:1:36.8:1:1:0:60:445:1:0:0.3	1/0:106:53:15,38:17,36:53,53:0.5:2,2:37.5:1:36.8:1:0.83267:1.19427:60:106:0.5:0:1.2
    60. 

  60. 1	16262450	16262450	G	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.G9715T:p.A3239S	.	.	.	.	.	.	.	.	.	.	.	0.054	0.386	T	0.181	0.274	B	0.092	0.285	B	.	.	.	1	0.090	N	0.69	0.170	N	3.15	0.078	T	-0.33	0.125	N	0.061	0.045	-0.938	0.430	T	0.013	0.049	T	0.005	0.135	T	0.449	0.137	7.032	0.910	0.196	0.856	0.444	D	c	-0.599	-0.483	0.981	0.301	0.672	0.522	0	2.24	0.271	2.173	0.419	0.067	0.174	0.921	0.317	0.016	0.126	8.883	0.344	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	52	1	16262450	.	G	T	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=393;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.01342;SOR=0;LSEQ=AAGCTGCCAAGACACCAGAT;RSEQ=CCAAAGCTGCCCCCACCCCC;CSQ=T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9715G>T|NP_055816.2:p.Ala3239Ser|10076|9715|3239|A/S|Gcc/Tcc|||1||EntrezGene||YES||||1:g.16262450G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:393:0:0,0:121,271:392,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:52:2:0,2:8,42:50,2:0.0385:2,0:26:1:31:1:1:0:60:4:0.04:0:5
    61. 

  61. 1	16262458	16262458	-	GC	exonic	SPEN	.	frameshift insertion	SPEN:NM_015001:exon11:c.9723_9724insGC:p.T3244Pfs*41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	62	43	1	16262458	.	T	TGC	62	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=327;VD=5;AF=0.0153;SHIFT3=2;MSI=2;MSILEN=2;SSF=0.53725;SOR=inf;LSEQ=AAGACACCAGATGCCAAAGC;RSEQ=GCCCCCACCCCCACCCCTGC;CSQ=GC|frameshift_variant|HIGH|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9724_9725dup|NP_055816.2:p.Thr3244ProfsTer41|10084-10085|9723-9724|3241-3242|-/X|-/GC|||1||EntrezGene||YES|||2|1:g.16262459_16262460dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:327:5:5,0:91,231:322,5:0.0153:2,0:23:1:27:1:0.00202:0:60:10:0.0158:0.0061:1.8	0/0:43:0:0,0:8,35:43,0:0:2,0:28.1:1:33.2:1:1:0:60:13.333:1:0:0.7
    62. 

  62. 1	16262465	16262465	A	C	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.A9730C:p.T3244P	0.19	0.2146	0.1803	0.345	0.2241	0.0973	0.3227	0.2013	0.2194	rs776474446	.	0.024	0.477	D	0.004	0.112	B	0.001	0.040	B	.	.	.	1	0.090	N	-0.895	0.014	N	3.02	0.090	T	-0.22	0.105	N	0.132	0.152	-0.933	0.438	T	0.010	0.037	T	.	.	.	-0.920	0.035	0.023	0.170	0.005	0.253	0.225	N	c	-1.388	-1.386	0.929	0.269	0.672	0.522	0	-0.36	0.119	0.451	0.213	-0.551	0.047	0.000	0.063	0.002	0.062	3.298	0.065	.	.	.	ID=COSV65357150;OCCURENCE=1(lung)	389337	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	.	.	0.5	132	37	1	16262465	.	A	C	132	Bias	STATUS=AFDiff;SAMPLE=LibM078FTT;TYPE=SNV;DP=275;VD=55;AF=0.2;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.12953;SOR=2.05855;LSEQ=CAGATGCCAAAGCTGCCCCC;RSEQ=CCCCCACCCCTGCCCCCGTC;CSQ=C|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9730A>C|NP_055816.2:p.Thr3244Pro|10091|9730|3244|T/P|Acc/Ccc|rs776474446&COSV65357150||1||EntrezGene||YES||||1:g.16262465A>C|0.03952|0.03194|0.01075|0.01036|0.02162|0.1631|0.05134|0.01868|0.01123|0.1631|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:275:55:55,0:19,198:217,55:0.2:2,1:9:1:22.9:1:0:0:60:1.619:0.1411:0:2.2	0/1:37:4:4,0:1,32:33,4:0.1081:1,0:11:1:18:1:8e-05:0:60:1:0.0625:0:1.5
    63. 

  63. 1	16262471	16262471	A	C	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon11:c.A9736C:p.T3246P	0.26	0.2833	0.2653	0.3448	0.4	0.1944	0.3262	0.2701	0.2627	rs769360962	.	0.095	0.312	T	0.0	0.026	B	0.0	0.013	B	.	.	.	1	0.090	N	-0.205	0.041	N	3.0	0.092	T	-0.44	0.146	N	0.165	0.199	-0.947	0.416	T	0.013	0.048	T	.	.	.	-1.346	0.021	0.004	0.144	0.003	0.081	0.139	N	c	-1.698	-1.745	0.958	0.283	0.672	0.522	0	-0.922	0.099	-0.543	0.061	-0.755	0.034	0.000	0.063	0.001	0.043	5.183	0.144	.	.	.	ID=COSV65357339;OCCURENCE=4(thyroid)	389329	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU4562650	THCA-CN|1|50|0.02	0.25	141	31	1	16262471	.	A	C	141	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=211;VD=31;AF=0.1469;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01046;SOR=inf;LSEQ=CCAAAGCTGCCCCCACCCCC;RSEQ=CCCCTGCCCCCGTCCCTGTC;CSQ=C|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9736A>C|NP_055816.2:p.Thr3246Pro|10097|9736|3246|T/P|Acc/Ccc|rs769360962&COSV65357339||1||EntrezGene||YES||||1:g.16262471A>C|0.05275|0.04432|0.01697|0.01742|0.03271|0.1519|0.07746|0.02471|0.01759|0.1519|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:211:31:30,1:6,173:179,31:0.1469:1,1:8.9:1:28.5:1:0:763.36:60:5.2:0.13:0:2.6	0/0:31:0:0,0:2,29:31,0:0:2,0:27.9:1:31.6:1:1:0:60:5.2:1:0:0.7
    64. 

  64. 1	16262476	16262476	T	C	exonic	SPEN	.	synonymous SNV	SPEN:NM_015001:exon11:c.T9741C:p.P3247P	0.037	0.1265	0.1237	0.1579	0.1538	0.0811	0.2044	0.0933	0.1136	rs762175217	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65357343;OCCURENCE=1(thyroid)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	.	.	0.25	105	28	1	16262476	.	T	C	105	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=179;VD=18;AF=0.1006;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06462;SOR=inf;LSEQ=GCTGCCCCCACCCCCACCCC;RSEQ=GCCCCCGTCCCTGTCCCTGT;CSQ=C|synonymous_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding|11/15||NM_015001.3:c.9741T>C|NP_055816.2:p.Pro3247%3D|10102|9741|3247|P|ccT/ccC|rs762175217&COSV65357343||1||EntrezGene||YES||||1:g.16262476T>C|0.01505|0.01002|0.002722|0.004485|0.00598|0.04317|0.02354|0.008916|0.003859|0.04317|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:179:18:17,1:3,157:160,18:0.1006:1,1:9.3:1:25.2:1:0:709.22:60:3.5:0.0833:0:2.8	0/0:28:0:0,0:1,27:28,0:0:1,0:8:0:11:0:1:0:60:0:0:0:2
    65. 

  65. 1	16262856	16262856	C	T	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	29	1	16262856	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=179;VD=2;AF=0.0112;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.74001;SOR=inf;LSEQ=TGTGTGAAAGAAATCAGGGG;RSEQ=CAGGTGTGGTGGCTTATGCC;CSQ=T|intron_variant|MODIFIER|SPEN|23013|Transcript|NM_015001.3|protein_coding||11/14|NM_015001.3:c.10026+95C>T|||||||||1||EntrezGene||YES||||1:g.16262856C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:179:2:1,1:48,129:177,2:0.0112:2,2:64.5:1:37:0:0.47367:2.67:60:4:0.0112:0:1	0/0:29:0:0,0:8,21:29,0:0:2,0:28.2:1:37:0:1:0:60:58:1:0:0.1
    66. 

  66. 1	16263806	16263806	C	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon12:c.C10175T:p.A3392V	.	.	.	.	.	.	.	.	.	.	.	0.106	0.296	T	0.456	0.344	P	0.066	0.260	B	.	.	.	0.989	0.244	N	1.85	0.492	L	3.0	0.092	T	-1.27	0.320	N	0.087	0.086	-1.017	0.248	T	0.019	0.082	T	0.004	0.109	T	3.166	0.440	22.7	0.964	0.292	0.921	0.546	D	c	-0.032	0.110	0.999	0.390	0.722	0.854	0	4.32	0.507	4.872	0.625	0.852	0.362	0.959	0.333	0.997	0.653	14.742	0.689	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	180	1	16263806	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1191;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01715;SOR=0;LSEQ=GCCTCAAGTGTCCCAGGAGG;RSEQ=AAAGGGGACCCAGACGGGAG;CSQ=T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001242884.2|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||||||1:g.16263806C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287603.2|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||YES||||1:g.16263806C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287604.2|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||||||1:g.16263806C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324137.2|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||||||1:g.16263806C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324138.2|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||||||1:g.16263806C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_003443.3|protein_coding||||||||||rs1255647665|4558|-1||EntrezGene||||||1:g.16263806C>T||||||||||||||,T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|12/15||NM_015001.3:c.10175C>T|NP_055816.2:p.Ala3392Val|10536|10175|3392|A/V|gCa/gTa|rs1255647665||1||EntrezGene||YES||||1:g.16263806C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1191:0:0,0:631,560:1191,0:0:2,0:35.1:1:36.1:1:1:0:60:65.167:1:0:0.2	0/1:180:2:1,1:95,83:178,2:0.0111:2,2:37.5:1:37:0:1:1.14372:60:4:0.0111:0:1
    67. 

  67. 1	16263821	16263821	C	T	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon12:c.C10190T:p.T3397M	0.0002	3.236e-05	0.0001	0	0	0	0	0	0	rs756771983	.	0.0	0.912	D	0.999	0.764	D	0.95	0.671	D	.	.	.	0.516	0.316	N	1.39	0.351	L	2.99	0.093	T	-0.33	0.125	N	0.268	0.326	-1.069	0.097	T	0.078	0.312	T	0.031	0.533	D	5.164	0.697	25.5	0.991	0.512	0.967	0.701	D	c	0.537	0.490	1.000	0.747	0.722	0.854	0	5.38	0.772	3.639	0.538	0.852	0.362	0.980	0.350	0.992	0.562	19.484	0.950	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	188	1	16263821	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1296;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01597;SOR=0;LSEQ=GGAGGCAAAGGGGACCCAGA;RSEQ=GGGAGTAGAGCAGCCTCGCC;CSQ=T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001242884.2|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287603.2|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||YES||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287604.2|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324137.2|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324138.2|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_003443.3|protein_coding||||||||||rs756771983|4543|-1||EntrezGene||||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||,T|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|12/15||NM_015001.3:c.10190C>T|NP_055816.2:p.Thr3397Met|10551|10190|3397|T/M|aCg/aTg|rs756771983||1||EntrezGene||YES||||1:g.16263821C>T|1.195e-05|0.000185|0|0|0|0|0|0|0|0.000185|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1296:0:0,0:698,598:1296,0:0:2,0:34.4:1:36.5:1:1:0:60:98.692:1:0:0.2	0/1:188:2:1,1:97,89:186,2:0.0106:2,2:36.5:1:37:0:1:1.08938:60:4:0.0106:0:1
    68. 

  68. 1	16265775	16265775	T	C	intronic	SPEN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	147	1	16265775	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1054;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.01489;SOR=0;LSEQ=CAGACGGTCCCACTTTGCTC;RSEQ=CTATCCTGTCTCCAGCCTGC;CSQ=C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001242884.2|protein_coding|||||||||||2589|-1||EntrezGene||||||1:g.16265775T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287603.2|protein_coding|||||||||||2589|-1||EntrezGene||YES||||1:g.16265775T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287604.2|protein_coding|||||||||||2589|-1||EntrezGene||||||1:g.16265775T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324137.2|protein_coding|||||||||||2589|-1||EntrezGene||||||1:g.16265775T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324138.2|protein_coding|||||||||||2589|-1||EntrezGene||||||1:g.16265775T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_003443.3|protein_coding|||||||||||2589|-1||EntrezGene||||||1:g.16265775T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPEN|23013|Transcript|NM_015001.3|protein_coding||14/14|NM_015001.3:c.10864-16T>C|||||||||1||EntrezGene||YES||||1:g.16265775T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1054:0:0,0:592,459:1051,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:147:2:1,1:87,58:145,2:0.0136:2,2:63:1:37:0:1:1.49572:60:4:0.0137:0:1
    69. 

  69. 1	16265829	16265829	C	A	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon15:c.C10902A:p.F3634L	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.899	0.475	P	0.824	0.575	P	.	.	.	0.999	0.461	D	3.14	0.885	M	1.04	0.402	T	-4.29	0.764	D	0.885	0.873	-0.521	0.679	T	0.257	0.628	T	0.036	0.569	D	5.405	0.733	26.0	0.990	0.490	0.928	0.564	D	c	0.281	0.213	1.000	0.747	0.672	0.522	0	2.48	0.291	0.585	0.234	0.022	0.145	0.998	0.411	0.992	0.562	10.186	0.420	SPOC-like, C-terminal domain|Spen paralogue/orthologue C-terminal, metazoa	.	.	ID=COSV65268554;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	171	1	16265829	.	C	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1221;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.01501;SOR=0;LSEQ=ATCTTCCCGCCCTGTGAGTT;RSEQ=TCTGAGAGTCACCTGTCCCG;CSQ=A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001242884.2|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||||||1:g.16265829C>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287603.2|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||YES||||1:g.16265829C>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287604.2|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||||||1:g.16265829C>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324137.2|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||||||1:g.16265829C>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324138.2|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||||||1:g.16265829C>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_003443.3|protein_coding||||||||||COSV65268554&COSV65272201|2535|-1||EntrezGene||||||1:g.16265829C>A|||||||||||||1&1|1&1,A|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|15/15||NM_015001.3:c.10902C>A|NP_055816.2:p.Phe3634Leu|11263|10902|3634|F/L|ttC/ttA|COSV65268554&COSV65272201||1||EntrezGene||YES||||1:g.16265829C>A|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1221:0:0,0:616,604:1220,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:171:2:1,1:84,85:169,2:0.0117:2,2:47:1:37:0:1:1.01:60:4:0.0118:0:1
    70. 

  70. 1	16265845	16265845	T	C	exonic	SPEN	.	nonsynonymous SNV	SPEN:NM_015001:exon15:c.T10918C:p.S3640P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.908	0.481	P	0.696	0.522	P	.	.	.	1	0.810	D	2.045	0.562	M	2.94	0.098	T	-2.88	0.605	D	0.832	0.820	-1.195	0.002	T	0.056	0.236	T	0.004	0.112	T	5.634	0.767	26.6	0.997	0.783	0.983	0.810	D	c	0.650	0.696	1.000	0.747	0.672	0.522	0	5.93	0.959	8.017	0.886	1.061	0.807	1.000	0.715	0.998	0.697	16.387	0.833	SPOC-like, C-terminal domain|Spen paralogue/orthologue C-terminal, metazoa	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	167	1	16265845	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1219;VD=0;AF=0;SHIFT3=5;MSI=3;MSILEN=1;SSF=0.01444;SOR=0;LSEQ=AGTTCTCTGAGAGTCACCTG;RSEQ=CCCGCCTGGCCCCTGACCTC;CSQ=C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001242884.2|protein_coding|||||||||||2519|-1||EntrezGene||||||1:g.16265845T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287603.2|protein_coding|||||||||||2519|-1||EntrezGene||YES||||1:g.16265845T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001287604.2|protein_coding|||||||||||2519|-1||EntrezGene||||||1:g.16265845T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324137.2|protein_coding|||||||||||2519|-1||EntrezGene||||||1:g.16265845T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_001324138.2|protein_coding|||||||||||2519|-1||EntrezGene||||||1:g.16265845T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ZBTB17|7709|Transcript|NM_003443.3|protein_coding|||||||||||2519|-1||EntrezGene||||||1:g.16265845T>C||||||||||||||,C|missense_variant|MODERATE|SPEN|23013|Transcript|NM_015001.3|protein_coding|15/15||NM_015001.3:c.10918T>C|NP_055816.2:p.Ser3640Pro|11279|10918|3640|S/P|Tcc/Ccc|||1||EntrezGene||YES||||1:g.16265845T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1219:0:0,0:610,609:1219,0:0:2,0:36.5:1:36.5:1:1:0:60:100.583:1:0:0.1	0/1:167:2:1,1:82,82:164,2:0.012:2,2:18.5:1:37:0:1:1:60:4:0.012:0:1
    71. 

  71. 1	17355273	17355273	G	T	intronic	SDHB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	182	1	17355273	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1039;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.02211;SOR=0;LSEQ=CACATCCTCACCCATATCCG;RSEQ=AATCAGTCCTGCCCCAAATA;CSQ=T|intron_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding||3/7|NM_003000.3:c.287-42C>A|||||||||-1||EntrezGene||YES||||1:g.17355273G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1039:0:0,0:434,605:1039,0:0:2,0:37.7:1:36.2:1:1:0:60:68.267:1:0:0.2	0/1:182:2:1,1:58,121:179,2:0.011:2,2:43.5:1:37:0:0.5469:2.08:60:4:0.0111:0:1
    72. 

  72. 1	17359564	17359564	A	G	exonic	SDHB	.	nonsynonymous SNV	SDHB:NM_003000:exon3:c.T277C:p.C93R	.	.	.	.	.	.	.	.	.	rs727503415	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.585	0.992	H	-6.67	0.998	D	-11.03	0.993	D	0.96	0.958	0.979	0.968	D	0.994	0.999	D	0.481	0.949	D	4.601	0.616	24.4	0.976	0.344	0.995	0.971	D	c	0.584	0.368	0.146	0.174	0.707	0.730	0	3.32	0.370	8.192	0.896	1.199	0.960	1.000	0.715	0.998	0.697	7.531	0.267	2Fe-2S ferredoxin, iron-sulphur binding site|2Fe-2S ferredoxin-type iron-sulfur binding domain|Beta-grasp domain|Succinate dehydogenase/fumarate reductase N-terminal	.	.	.	172353	Pheochromocytoma|Gastrointestinal_stromal_tumor|Paragangliomas_4|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes|not_specified	Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0007273,MedGen:C1861848,OMIM:115310|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072|MedGen:CN169374	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	119	1	17359564	.	A	G	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=140;VD=2;AF=0.0143;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.29122;SOR=inf;LSEQ=GAAATGCTCACCTTCTCTGC;RSEQ=TGATCTTCGGAAGGTCAAAG;CSQ=G|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|3/8||NM_003000.3:c.277T>C|NP_002991.2:p.Cys93Arg|290|277|93|C/R|Tgc/Cgc|rs727503415&CM077221&CM1611286||-1||EntrezGene||YES||||1:g.17359564A>G||||||||||||uncertain_significance&pathogenic||1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:140:2:1,1:52,86:138,2:0.0143:2,2:6:0:37:0:1:1.65:60:4:0.0144:0:1	0/0:119:0:0,0:66,53:119,0:0:2,0:39.4:1:35.9:1:1:0:60:58.5:1:0:0.2
    73. 

  73. 1	17371223	17371223	C	T	intronic	SDHB	.	.	.	0.19	0.1138	0.1702	0.0467	0.0762	0.0576	0.1220	0.0913	0.0888	rs2647169	rs2647169	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64964759;OCCURENCE=1(liver),7(soft_tissue)	432987	none_provided	MedGen:CN235283	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU9328724	LICA-CN|1|402|0.00248756	0.5	276	118	1	17371223	.	C	T	276	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=207;VD=207;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=TAAATCAAATCAAGAACTCT;RSEQ=CTTCAATAGCTGGCTTTCAC;CSQ=T|intron_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding||2/7|NM_003000.3:c.200+33G>A|||||||rs2647169&COSV64964759||-1||EntrezGene||YES||||1:g.17371223C>T|0.08362|0.1773|0.0377|0.08707|0.07867|0.111|0.08266|0.08312|0.07209|0.1899|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:207:207:146,61:0,0:0,207:1:0,2:33.8:1:35.9:1:1:0:60:40.4:1:0:1.1	0/0:118:0:0,0:89,29:118,0:0:2,0:38.8:1:36.4:1:1:0:60:117:1:0:0
    74. 

  74. 1	17371412	17371412	A	-	intronic	SDHB	.	.	.	0.0048	0.0004	0.0004	0	0	0	0	0.0006	0	rs776876741	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	985915	Paragangliomas_4	MONDO:MONDO:0007273,MedGen:C1861848,OMIM:115310	criteria_provided,_single_submitter	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	121	1	17371411	.	GA	G	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=190;VD=3;AF=0.0158;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.22662;SOR=inf;LSEQ=TTTTTAAAGTTCACAAAAAG;RSEQ=AAAAAAAATTAGAAATACAA;CSQ=-|intron_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding||1/7|NM_003000.3:c.73-29del|||||||rs745905902&CD030618&COSV64965889||-1||EntrezGene||YES||||1:g.17371420del|0.0003939|0.0003437|0.0002796|0.0002102|0|0.0001712|0.0006486|0.0001766|0.0001044|0.00485|EA||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:190:3:0,3:57,130:187,3:0.0158:2,0:15.7:1:37:1:0.55532:0:60:6:0.0158:0.0053:0.3	0/0:121:0:0,0:36,85:121,0:0:2,0:35.3:1:36.1:1:1:0:60:39.333:1:0:0.2
    75. 

  75. 1	17380497	17380497	G	T	exonic	SDHB	.	synonymous SNV	SDHB:NM_003000:exon1:c.C18A:p.A6A	1.	0.9577	0.9069	0.9690	0.9371	0.9994	0.9823	0.9755	0.9785	rs2746462	rs2746462	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	53808	Carney-Stratakis_syndrome|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes|not_specified|none_provided	MONDO:MONDO:0011740,MedGen:C1847319,OMIM:606864,Orphanet:ORPHA97286|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU81693539	COCA-CN|5|321|0.0155763	1	288	32	1	17380497	.	G	T	288	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=237;VD=237;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCGGCGCCTCAAGGAGAG;RSEQ=GCGACCACCGCCGCCATCTT;CSQ=T|synonymous_variant|LOW|SDHB|6390|Transcript|NM_003000.3|protein_coding|1/8||NM_003000.3:c.18C>A|NP_002991.2:p.Ala6%3D|31|18|6|A|gcC/gcA|rs2746462||-1||EntrezGene||YES||||1:g.17380497G>T|0.9737|0.9129|0.9828|0.9545|0.9991|0.9786|0.9721|0.9723|0.9877|0.9991|gnomAD_EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:237:237:118,119:0,0:0,237:1:0,2:39.2:1:36.6:1:1:0:60:474:1:0:1	1/1:32:32:15,17:0,0:0,32:1:0,2:42.7:1:36.6:1:1:0:60:64:1:0:1.2
    76. 

  76. 1	17380534	17380534	C	A	UTR5	SDHB	NM_003000:c.-20G>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	21	1	17380534	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=196;VD=2;AF=0.0102;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.81541;SOR=inf;LSEQ=TCTTGGCTCCTGACGTCAGC;RSEQ=CCACCCCTTAACCCCGAGGT;CSQ=A|upstream_gene_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding|||||||||||7|-1||EntrezGene||YES||||1:g.17380534C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:196:2:1,1:81,113:194,2:0.0102:2,2:65:1:37:0:1:1.39:60:4:0.0102:0:2	0/0:21:0:0,0:9,12:21,0:0:2,0:29.6:1:34.6:1:1:0:60:20:1:0:1.4
    77. 

  77. 1	20915590	20915590	C	-	UTR5	CDA	NM_001785:c.-33del-	.	.	0.65	0.5557	0.6259	0.4593	0.6	0.4248	0.5335	0.5398	0.5378	rs3215400	rs3215400	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU115536000	ESAD-UK|1|409|0.00244499	0.5	310	69	1	20915589	.	TC	T	310	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=411;VD=348;AF=0.8467;SHIFT3=2;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGCTGGCCGGAGCTCCTGTT;RSEQ=CCGCTGCTCTGCTGCCTGCC;CSQ=-|5_prime_UTR_variant|MODIFIER|CDA|978|Transcript|NM_001785.3|protein_coding|1/4||NM_001785.3:c.-31del||1|||||rs3215400||1||EntrezGene||YES||||1:g.20915592del|0.5355|0.6232|0.4599|0.6069|0.4232|0.5389|0.56|0.5498|0.5229|0.6467|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:411:348:206,142:40,23:63,348:0.8467:2,2:39.1:1:36.8:1:0.57771:1.1983:60:696:0.8467:0.0803:0.2	0/0:69:0:0,0:45,24:69,0:0:2,0:38.5:1:36.3:1:1:0:60:68:1:0:0.1
    78. 

  78. 1	22405008	22405008	G	T	exonic	CDC42	.	nonsynonymous SNV	CDC42:NM_001791:exon2:c.G37T:p.A13S,CDC42:NM_044472:exon2:c.G37T:p.A13S,CDC42:NM_001039802:exon3:c.G37T:p.A13S	.	.	.	.	.	.	.	.	.	.	.	0.044	0.538	D	0.985	0.592	D	0.9	0.656	P	0.000	0.629	D	1	0.810	D	1.475	0.372	L	-0.43	0.697	T	-2.56	0.580	D	0.27	0.481	-0.180	0.782	T	0.416	0.763	T	0.078	0.730	D	2.861	0.405	21.7	0.995	0.705	0.988	0.868	D	c	0.382	0.393	1.000	0.747	0.707	0.730	0	4.0	0.455	7.451	0.796	0.948	0.535	1.000	0.715	1.000	0.888	11.967	0.521	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	188	1	22405008	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.89224;SOR=0;LSEQ=GTGTTGTTGTGGGCGATGGT;RSEQ=CTGTTGGTAAAACATGTCTC;CSQ=T|missense_variant|MODERATE|CDC42|998|Transcript|NM_001039802.2|protein_coding|3/7||NM_001039802.2:c.37G>T|NP_001034891.1:p.Ala13Ser|247|37|13|A/S|Gct/Tct|COSV100212661||1||EntrezGene||YES||||1:g.22405008G>T|||||||||||||1|1,T|missense_variant|MODERATE|CDC42|998|Transcript|NM_001791.4|protein_coding|2/6||NM_001791.4:c.37G>T|NP_001782.1:p.Ala13Ser|121|37|13|A/S|Gct/Tct|COSV100212661||1||EntrezGene||||||1:g.22405008G>T|||||||||||||1|1,T|missense_variant|MODERATE|CDC42|998|Transcript|NM_044472.3|protein_coding|2/6||NM_044472.3:c.37G>T|NP_426359.1:p.Ala13Ser|121|37|13|A/S|Gct/Tct|COSV100212661||1||EntrezGene||||||1:g.22405008G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:6,5:11,0:0:2,0:25.3:1:37:0:1:0:58.9:22:1:0:0.2	0/1:188:2:1,1:96,90:186,2:0.0106:2,2:23:0:37:0:1:1.06633:60:4:0.0107:0:1
    79. 

  79. 1	22405287	22405287	A	G	intronic	CDC42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	332	1	22405287	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=121;VD=2;AF=0.0165;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.07091;SOR=inf;LSEQ=GGTGACACAGGGTTTGCAAG;RSEQ=AGTGCTGGGAGGCAAAACTC;CSQ=G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||3/6|NM_001039802.2:c.105+211A>G|||||||||1||EntrezGene||YES||||1:g.22405287A>G||||||||||||||,G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||2/5|NM_001791.4:c.105+211A>G|||||||||1||EntrezGene||||||1:g.22405287A>G||||||||||||||,G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding||2/5|NM_044472.3:c.105+211A>G|||||||||1||EntrezGene||||||1:g.22405287A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:121:2:1,1:67,52:119,2:0.0165:2,2:57:0:37:0:1:1.28573:60:4:0.0185:0:1	0/0:332:0:0,0:157,173:330,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    80. 

  80. 1	22405309	22405309	A	G	intronic	CDC42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	305	1	22405309	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=2;AF=0.0156;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.0869;SOR=inf;LSEQ=GTGCTGGGAGGCAAAACTCC;RSEQ=GTAGACAAGATTCTAACGAG;CSQ=G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||3/6|NM_001039802.2:c.105+233A>G|||||||||1||EntrezGene||YES||||1:g.22405309A>G||||||||||||||,G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||2/5|NM_001791.4:c.105+233A>G|||||||||1||EntrezGene||||||1:g.22405309A>G||||||||||||||,G|intron_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding||2/5|NM_044472.3:c.105+233A>G|||||||||1||EntrezGene||||||1:g.22405309A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:128:2:1,1:68,58:126,2:0.0156:2,2:46:0:37:0:1:1.17095:60:4:0.0169:0:1	0/0:305:0:0,0:134,170:304,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    81. 

  81. 1	22405379	22405379	-	T	intronic	CDC42	.	.	.	0.5	0.1156	0.0934	0.1762	0.1212	0.0807	0.0888	0.1326	0.1203	rs752728353	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU9541222	BTCA-SG|1|71|0.0140845	0.5	148	145	1	22405379	.	C	CT	148	MSI12;MSI12	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=74;VD=23;AF=0.3108;SHIFT3=18;MSI=19;MSILEN=1;SSF=0;SOR=31.719;LSEQ=TACATCTTGGAATGAGGTGA;RSEQ=TTTTTTTTTTTTTTTTTTGA;CSQ=T|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||3/6|NM_001039802.2:c.105+321dup|||||||rs34952712||1||EntrezGene||YES||||1:g.22405397dup|0.07237|0.05989|0.1069|0.07351|0.05573|0.07282|0.07698|0.0884|0.03149|0.1069|gnomAD_AMR|||,T|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||2/5|NM_001791.4:c.105+321dup|||||||rs34952712||1||EntrezGene||||||1:g.22405397dup|0.07237|0.05989|0.1069|0.07351|0.05573|0.07282|0.07698|0.0884|0.03149|0.1069|gnomAD_AMR|||,T|intron_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding||2/5|NM_044472.3:c.105+321dup|||||||rs34952712||1||EntrezGene||||||1:g.22405397dup|0.07237|0.05989|0.1069|0.07351|0.05573|0.07282|0.07698|0.0884|0.03149|0.1069|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:74:23:11,12:18,24:42,23:0.3108:2,2:48.9:1:32.8:1:0.79616:1.22:60.4:10.5:0.4038:0.0135:1.2	0/1:145:2:1,1:40,84:124,2:0.0138:2,2:32.8:1:34.5:1:0.54667:2.09:66.8:4:0.0196:0:3.3
    82. 

  82. 1	22405398	22405398	G	A	intronic	CDC42	.	.	.	0.2	0.1533	0.1335	0.2347	0.1204	0.1303	0.1740	0.1613	0.1770	rs2072921	rs2072921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59662561;OCCURENCE=1(biliary_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU44235496	COCA-CN|1|321|0.00311526,BTCA-JP|1|239|0.0041841	0.25	169	106	1	22405398	.	G	A	169	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=34;AF=0.6071;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=ACTTTTTTTTTTTTTTTTTT;RSEQ=ATATTTTGGCCAATTATTGA;CSQ=A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||3/6|NM_001039802.2:c.105+322G>A|||||||rs2072921&COSV59662561||1||EntrezGene||YES||||1:g.22405398G>A|0.09557|0.08525|0.1449|0.08353|0.1061|0.0882|0.1007|0.1159|0.03279|0.2046|AMR||0&1|0&1,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||2/5|NM_001791.4:c.105+322G>A|||||||rs2072921&COSV59662561||1||EntrezGene||||||1:g.22405398G>A|0.09557|0.08525|0.1449|0.08353|0.1061|0.0882|0.1007|0.1159|0.03279|0.2046|AMR||0&1|0&1,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding||2/5|NM_044472.3:c.105+322G>A|||||||rs2072921&COSV59662561||1||EntrezGene||||||1:g.22405398G>A|0.09557|0.08525|0.1449|0.08353|0.1061|0.0882|0.1007|0.1159|0.03279|0.2046|AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:56:34:14,20:7,14:21,34:0.6071:2,2:31.6:1:33.4:1:0.77566:1.39:59.6:16:0.64:0:1.4	0/0:106:0:0,0:25,76:101,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    83. 

  83. 1	22412995	22412995	G	A	exonic	CDC42	.	nonsynonymous SNV	CDC42:NM_001791:exon4:c.G242A:p.C81Y,CDC42:NM_044472:exon4:c.G242A:p.C81Y,CDC42:NM_001039802:exon5:c.G242A:p.C81Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.985	0.749	D	0.000	0.843	D	1	0.810	D	5.22	1.000	H	-0.56	0.712	T	-10.13	0.991	D	0.691	0.984	0.925	0.960	D	0.770	0.922	D	0.233	0.884	D	6.076	0.837	28.1	0.998	0.852	0.991	0.904	D	c	1.198	1.073	1.000	0.747	0.722	0.854	0	5.4	0.779	7.917	0.868	1.048	0.713	1.000	0.715	0.998	0.697	18.107	0.894	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	161	1	22412995	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.9073;SOR=0;LSEQ=AACAGATGTATTTCTAGTCT;RSEQ=TTTTTCAGTGGTCTCTCCAT;CSQ=A|missense_variant|MODERATE|CDC42|998|Transcript|NM_001039802.2|protein_coding|5/7||NM_001039802.2:c.242G>A|NP_001034891.1:p.Cys81Tyr|452|242|81|C/Y|tGt/tAt|||1||EntrezGene||YES||||1:g.22412995G>A||||||||||||||,A|missense_variant|MODERATE|CDC42|998|Transcript|NM_001791.4|protein_coding|4/6||NM_001791.4:c.242G>A|NP_001782.1:p.Cys81Tyr|326|242|81|C/Y|tGt/tAt|||1||EntrezGene||||||1:g.22412995G>A||||||||||||||,A|missense_variant|MODERATE|CDC42|998|Transcript|NM_044472.3|protein_coding|4/6||NM_044472.3:c.242G>A|NP_426359.1:p.Cys81Tyr|326|242|81|C/Y|tGt/tAt|||1||EntrezGene||||||1:g.22412995G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:6,2:8,0:0:2,0:27.8:1:35.5:1:1:0:60:16:1:0:0	0/1:161:2:1,1:83,76:159,2:0.0124:2,2:44.5:1:37:0:1:1.0915:60:4:0.0125:0:1
    84. 

  84. 1	22413250	22413250	T	C	exonic	CDC42	.	nonsynonymous SNV	CDC42:NM_001791:exon5:c.T377C:p.I126T,CDC42:NM_044472:exon5:c.T377C:p.I126T,CDC42:NM_001039802:exon6:c.T377C:p.I126T	0.0001	.	.	.	.	.	.	.	.	rs773774873	.	0.029	0.477	D	0.012	0.170	B	0.05	0.239	B	0.000	0.843	N	1	0.810	D	1.835	0.484	L	-0.43	0.697	T	-2.85	0.627	D	0.252	0.810	-0.534	0.674	T	0.316	0.686	T	0.037	0.576	D	2.439	0.354	19.07	0.994	0.623	0.969	0.711	D	c	0.200	0.349	1.000	0.747	0.722	0.854	0	5.72	0.893	5.771	0.683	1.061	0.807	1.000	0.715	1.000	0.888	15.126	0.720	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	225	1	22413250	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=117;VD=2;AF=0.0171;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11638;SOR=inf;LSEQ=CAGAGATGACCCCTCTACTA;RSEQ=TGAGAAACTTGCCAAGAACA;CSQ=C|missense_variant|MODERATE|CDC42|998|Transcript|NM_001039802.2|protein_coding|6/7||NM_001039802.2:c.377T>C|NP_001034891.1:p.Ile126Thr|587|377|126|I/T|aTt/aCt|rs773774873||1||EntrezGene||YES||||1:g.22413250T>C|7.956e-06|0|2.891e-05|0|0|0|8.792e-06|0|0|2.891e-05|gnomAD_AMR|||,C|missense_variant|MODERATE|CDC42|998|Transcript|NM_001791.4|protein_coding|5/6||NM_001791.4:c.377T>C|NP_001782.1:p.Ile126Thr|461|377|126|I/T|aTt/aCt|rs773774873||1||EntrezGene||||||1:g.22413250T>C|7.956e-06|0|2.891e-05|0|0|0|8.792e-06|0|0|2.891e-05|gnomAD_AMR|||,C|missense_variant|MODERATE|CDC42|998|Transcript|NM_044472.3|protein_coding|5/6||NM_044472.3:c.377T>C|NP_426359.1:p.Ile126Thr|461|377|126|I/T|aTt/aCt|rs773774873||1||EntrezGene||||||1:g.22413250T>C|7.956e-06|0|2.891e-05|0|0|0|8.792e-06|0|0|2.891e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:117:2:1,1:68,47:115,2:0.0171:2,2:55:0:37:0:1:1.44212:60:4:0.0177:0:1	0/0:225:0:0,0:121,104:225,0:0:2,0:37.6:1:35.7:1:1:0:58.3:44:1:0:0.1
    85. 

  85. 1	22416414	22416414	T	A	intronic	CDC42	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	135	1	22416414	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=2;SSF=0.24184;SOR=0;LSEQ=CTAACCTGGCTGCTATTCTC;RSEQ=CTCCTCCCCTCTGTCTTGTA;CSQ=A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||6/6|NM_001039802.2:c.487-1507T>A|||||||||1||EntrezGene||YES||||1:g.22416414T>A||||||||||||||,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||5/5|NM_001791.4:c.487-1507T>A|||||||||1||EntrezGene||||||1:g.22416414T>A||||||||||||||,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding||5/5|NM_044472.3:c.487-22T>A|||||||||1||EntrezGene||||||1:g.22416414T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:139:0:0,0:77,62:139,0:0:2,0:36.4:1:36:1:1:0:60:68.5:1:0:0.1	0/1:135:2:1,1:79,52:131,2:0.0148:2,2:53.5:1:37:0:1:1.51428:60:4:0.0148:0:1
    86. 

  86. 1	22416479	22416479	T	C	exonic	CDC42	.	nonsynonymous SNV	CDC42:NM_044472:exon6:c.T530C:p.L177P	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	.	.	.	1	0.810	D	.	.	.	-0.56	0.712	T	-4.76	0.803	D	0.928	0.920	0.196	0.858	D	0.554	0.837	D	0.119	0.799	D	0.900	0.180	10.07	0.998	0.855	0.991	0.907	D	c	0.760	0.776	1.000	0.747	0.628	0.401	0	5.96	0.967	7.477	0.799	1.057	0.759	1.000	0.715	1.000	0.888	15.269	0.733	P-loop containing nucleoside triphosphate hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	197	1	22416479	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=181;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.27095;SOR=0;LSEQ=TGAGGCTATCCTAGCTGCCC;RSEQ=CGAGCCTCCGGAAACTCAAC;CSQ=C|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||6/6|NM_001039802.2:c.487-1442T>C|||||||||1||EntrezGene||YES||||1:g.22416479T>C||||||||||||||,C|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||5/5|NM_001791.4:c.487-1442T>C|||||||||1||EntrezGene||||||1:g.22416479T>C||||||||||||||,C|missense_variant|MODERATE|CDC42|998|Transcript|NM_044472.3|protein_coding|6/6||NM_044472.3:c.530T>C|NP_426359.1:p.Leu177Pro|614|530|177|L/P|cTc/cCc|||1||EntrezGene||||||1:g.22416479T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:181:0:0,0:86,95:181,0:0:2,0:38.9:1:36.7:1:1:0:60:180:1:0:0.1	0/1:197:2:1,1:94,101:195,2:0.0102:2,2:40:0:37:0:1:1.07:60:4:0.0102:0:1
    87. 

  87. 1	22416480	22416480	C	A	exonic	CDC42	.	synonymous SNV	CDC42:NM_044472:exon6:c.C531A:p.L177L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	196	1	22416480	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=181;VD=2;AF=0.011;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.22984;SOR=inf;LSEQ=GAGGCTATCCTAGCTGCCCT;RSEQ=GAGCCTCCGGAAACTCAACC;CSQ=A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||6/6|NM_001039802.2:c.487-1441C>A|||||||COSV100212610||1||EntrezGene||YES||||1:g.22416480C>A|||||||||||||1|1,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||5/5|NM_001791.4:c.487-1441C>A|||||||COSV100212610||1||EntrezGene||||||1:g.22416480C>A|||||||||||||1|1,A|synonymous_variant|LOW|CDC42|998|Transcript|NM_044472.3|protein_coding|6/6||NM_044472.3:c.531C>A|NP_426359.1:p.Leu177%3D|615|531|177|L|ctC/ctA|COSV100212610||1||EntrezGene||||||1:g.22416480C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:181:2:1,1:85,94:179,2:0.011:2,2:45:1:37:0:1:1.11:60:4:0.0112:0:1	0/0:196:0:0,0:94,102:196,0:0:2,0:37.4:1:36.6:1:1:0:60:195:1:0:0.1
    88. 

  88. 1	22416481	22416481	G	T	exonic	CDC42	.	stopgain	CDC42:NM_044472:exon6:c.G532T:p.E178X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.097	0.199	11.20	0.996	0.752	0.995	0.973	D	c	0.462	0.584	1.0	0.983	0.628	0.401	0	5.96	0.967	9.358	0.965	1.044	0.665	1.000	0.715	1.000	0.888	18.983	0.927	P-loop containing nucleoside triphosphate hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	194	1	22416481	.	G	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=178;VD=2;AF=0.0112;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.22828;SOR=inf;LSEQ=AGGCTATCCTAGCTGCCCTC;RSEQ=AGCCTCCGGAAACTCAACCC;CSQ=T|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||6/6|NM_001039802.2:c.487-1440G>T|||||||||1||EntrezGene||YES||||1:g.22416481G>T||||||||||||||,T|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||5/5|NM_001791.4:c.487-1440G>T|||||||||1||EntrezGene||||||1:g.22416481G>T||||||||||||||,T|stop_gained|HIGH|CDC42|998|Transcript|NM_044472.3|protein_coding|6/6||NM_044472.3:c.532G>T|NP_426359.1:p.Glu178Ter|616|532|178|E/*|Gag/Tag|||1||EntrezGene||||||1:g.22416481G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:178:2:1,1:82,94:176,2:0.0112:2,2:27.5:1:31:1:1:1.15:60:4:0.0113:0:1	0/0:194:0:0,0:93,101:194,0:0:2,0:37.7:1:36.9:1:1:0:60:388:1:0:0.1
    89. 

  89. 1	22416552	22416552	G	A	UTR3	CDC42	NM_044472:c.*27G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	126	1	22416552	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=3;SSF=0.34553;SOR=0;LSEQ=TTCTCCTTCCCTTCTTTGCT;RSEQ=CTGCTTCCTGTCCCACTACT;CSQ=A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001039802.2|protein_coding||6/6|NM_001039802.2:c.487-1369G>A|||||||||1||EntrezGene||YES||||1:g.22416552G>A||||||||||||||,A|intron_variant|MODIFIER|CDC42|998|Transcript|NM_001791.4|protein_coding||5/5|NM_001791.4:c.487-1369G>A|||||||||1||EntrezGene||||||1:g.22416552G>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding|6/6||NM_044472.3:c.*27G>A||687|||||||1||EntrezGene||||||1:g.22416552G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:88:0:0,0:33,55:88,0:0:2,0:35.4:1:36.5:1:1:0:60:176:1:0:0.1	0/1:126:2:1,1:45,79:124,2:0.0159:2,2:29:0:37:0:1:1.75:60:4:0.016:0:1
    90. 

  90. 1	22418004	22418004	G	A	exonic	CDC42	.	synonymous SNV	CDC42:NM_001791:exon6:c.G570A:p.L190L,CDC42:NM_001039802:exon7:c.G570A:p.L190L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	104	1	22418004	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=106;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.24406;SOR=0;LSEQ=AAGAGCCGCAGGTGTGTGCT;RSEQ=CTATGAACATCTCTCCAGAG;CSQ=A|synonymous_variant|LOW|CDC42|998|Transcript|NM_001039802.2|protein_coding|7/7||NM_001039802.2:c.570G>A|NP_001034891.1:p.Leu190%3D|780|570|190|L|ctG/ctA|||1||EntrezGene||YES||||1:g.22418004G>A||||||||||||||,A|synonymous_variant|LOW|CDC42|998|Transcript|NM_001791.4|protein_coding|6/6||NM_001791.4:c.570G>A|NP_001782.1:p.Leu190%3D|654|570|190|L|ctG/ctA|||1||EntrezGene||||||1:g.22418004G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CDC42|998|Transcript|NM_044472.3|protein_coding|||||||||||704|1||EntrezGene||||||1:g.22418004G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:106:0:0,0:47,59:106,0:0:2,0:44.3:1:36.4:1:1:0:53.2:105:1:0:0	0/1:104:2:1,1:44,58:102,2:0.0192:2,2:7:0:37:0:1:1.31:60:4:0.0198:0:1
    91. 

  91. 1	23885498	23885498	T	C	exonic	ID3	.	nonsynonymous SNV	ID3:NM_002167:exon2:c.A313G:p.T105A	0.99	0.8086	0.9543	0.7303	0.9040	0.9746	0.6847	0.7405	0.7541	rs11574	rs11574	0.865	0.026	T	0.0	0.026	B	0.0	0.013	B	0.902	0.086	N	1	0.090	P	-0.205	0.041	N	-0.56	0.712	T	0.23	0.046	N	0.016	0.003	-0.986	0.337	T	0.000	0.000	T	.	.	.	-2.559	0.003	0.001	0.525	0.047	0.009	0.034	N	c	-1.707	-1.664	1.000	0.747	0.628	0.401	0	-2.76	0.055	-0.496	0.065	-1.609	0.009	0.000	0.063	0.145	0.203	4.909	0.131	.	ENSG00000117318.8	Thyroid	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU81695702	COCA-CN|5|321|0.0155763	0.5	37	0	1	23885498	.	T	C	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGATGACAAGTTCCGGAG;RSEQ=GAGCTCGGCTGTCTGATTAG;CSQ=C|missense_variant|MODERATE|ID3|3399|Transcript|NM_002167.5|protein_coding|2/3||NM_002167.5:c.313A>G|NP_002158.3:p.Thr105Ala|388|313|105|T/A|Act/Gct|rs11574&CM102358||-1||EntrezGene||YES||||1:g.23885498T>C|0.7973|0.9527|0.7016|0.9008|0.9756|0.6867|0.7569|0.8005|0.9089|0.9894|AFR|||0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:0,2:0,0:0,2:1:0,0:36:1:37:0:1:0:60:4:1:0:1.5	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    92. 

  92. 1	27023377	27023379	CGC	-	exonic	ARID1A	.	nonframeshift deletion	ARID1A:NM_006015:exon1:c.483_485del:p.A167del,ARID1A:NM_139135:exon1:c.483_485del:p.A167del	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	36	1	27023376	.	TCGC	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=124;VD=3;AF=0.0242;SHIFT3=9;MSI=4;MSILEN=3;SSF=0.46293;SOR=inf;LSEQ=CGGCCGGAGCCCGTCTGCCG;RSEQ=CGCCGCCGCGGCCGCCGTCT;CSQ=-|inframe_deletion|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|1/20||NM_006015.6:c.492_494del|NP_006006.3:p.Ala167del|872-874|483-485|161-162|VA/V|gtCGCc/gtc|rs759913677||1||EntrezGene||YES|||9|1:g.27023386_27023388del|0.0002098|0|0|0|0|0|0.0003861|0|0.0008711|0.0008711|gnomAD_SAS|||1,-|inframe_deletion|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|1/20||NM_139135.4:c.492_494del|NP_624361.1:p.Ala167del|872-874|483-485|161-162|VA/V|gtCGCc/gtc|rs759913677||1||EntrezGene|||||9|1:g.27023386_27023388del|0.0002098|0|0|0|0|0|0.0003861|0|0.0008711|0.0008711|gnomAD_SAS|||1,-|upstream_gene_variant|MODIFIER|LOC101928728|101928728|Transcript|NR_135804.1|lncRNA||||||||||rs759913677|2755|-1||EntrezGene||YES||||1:g.27023386_27023388del|0.0002098|0|0|0|0|0|0.0003861|0|0.0008711|0.0008711|gnomAD_SAS|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:3:2,1:83,38:121,3:0.0242:2,2:29:1:37:1:1:1.09131:60:6:0.0244:0.0081:0.3	0/0:36:0:0,0:23,13:36,0:0:2,0:38:1:35.6:1:1:0:60:35:1:0:0.9
    93. 

  93. 1	27023391	27023391	C	T	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon1:c.C497T:p.A166V,ARID1A:NM_139135:exon1:c.C497T:p.A166V	0.0004	.	.	.	.	.	.	.	.	rs764556085	.	0.007	0.599	D	0.06	0.241	B	0.003	0.127	B	0.008	0.313	U	0.738	0.297	N	0	0.065	N	4.46	0.026	T	-0.53	0.164	N	0.332	0.395	-0.824	0.537	T	0.006	0.019	T	0.668	0.972	D	1.553	0.248	13.60	0.982	0.390	0.109	0.161	N	c	-0.403	-0.273	1.000	0.747	0.243	0.034	2	2.89	0.326	0.544	0.228	0.710	0.302	0.018	0.193	1.000	0.888	5.890	0.180	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	41	1	27023391	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.0509;SOR=0;LSEQ=TGCCGTCGCCGCCGCCGCGG;RSEQ=CGCCGTCTTCCACCAACAAC;CSQ=T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|1/20||NM_006015.6:c.497C>T|NP_006006.3:p.Ala166Val|886|497|166|A/V|gCc/gTc|rs764556085||1||EntrezGene||YES||||1:g.27023391C>T|2.688e-05|0|0|0|0|0|5.663e-05|0|0|5.663e-05|gnomAD_NFE|||,T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|1/20||NM_139135.4:c.497C>T|NP_624361.1:p.Ala166Val|886|497|166|A/V|gCc/gTc|rs764556085||1||EntrezGene||||||1:g.27023391C>T|2.688e-05|0|0|0|0|0|5.663e-05|0|0|5.663e-05|gnomAD_NFE|||,T|upstream_gene_variant|MODIFIER|LOC101928728|101928728|Transcript|NR_135804.1|lncRNA||||||||||rs764556085|2769|-1||EntrezGene||YES||||1:g.27023391C>T|2.688e-05|0|0|0|0|0|5.663e-05|0|0|5.663e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:139:0:0,0:84,55:139,0:0:2,0:36:1:36.6:1:1:0:60:138:1:0:0.3	0/1:41:2:1,1:23,16:39,2:0.0488:2,2:42:1:37:0:1:1.42455:60:4:0.05:0:1
    94. 

  94. 1	27024013	27024013	G	A	exonic	ARID1A	.	synonymous SNV	ARID1A:NM_006015:exon1:c.G1119A:p.P373P,ARID1A:NM_139135:exon1:c.G1119A:p.P373P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	17	1	27024013	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=32;VD=2;AF=0.0625;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.42177;SOR=inf;LSEQ=AGCGGCGGCGGGGGGCAGCC;RSEQ=CTCGCCCGGACCCCTCAGGT;CSQ=A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_006015.6|protein_coding|1/20||NM_006015.6:c.1119G>A|NP_006006.3:p.Pro373%3D|1508|1119|373|P|ccG/ccA|||1||EntrezGene||YES||||1:g.27024013G>A||||||||||||||,A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_139135.4|protein_coding|1/20||NM_139135.4:c.1119G>A|NP_624361.1:p.Pro373%3D|1508|1119|373|P|ccG/ccA|||1||EntrezGene||||||1:g.27024013G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|LOC101928728|101928728|Transcript|NR_135804.1|lncRNA|||||||||||3391|-1||EntrezGene||YES||||1:g.27024013G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:32:2:1,1:13,17:30,2:0.0625:2,2:24:0:37:0:1:1.3:60:4:0.0625:0:1	0/0:17:0:0,0:6,11:17,0:0:2,0:36.5:1:35.6:1:1:0:60:34:1:0:0.8
    95. 

  95. 1	27056332	27056332	G	A	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon2:c.G1328A:p.G443D,ARID1A:NM_139135:exon2:c.G1328A:p.G443D	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.986	0.629	D	0.655	0.569	P	0.000	0.843	D	1.000	0.491	D	1.32	0.331	L	3.74	0.566	T	-3.39	0.831	D	0.419	0.869	-0.867	0.508	T	0.197	0.552	T	0.006	0.152	T	4.380	0.586	24.1	0.978	0.353	0.999	0.999	D	c	0.629	0.706	1.000	0.747	0.722	0.854	0	5.73	0.897	9.246	0.945	1.048	0.713	1.000	0.715	0.997	0.653	18.099	0.894	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	141	1	27056332	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=259;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.12368;SOR=0;LSEQ=CCGGGCGCAGAGTGCCATGG;RSEQ=CGGCCTCTCTTATACACAGC;CSQ=A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|2/20||NM_006015.6:c.1328G>A|NP_006006.3:p.Gly443Asp|1717|1328|443|G/D|gGc/gAc|||1||EntrezGene||YES||||1:g.27056332G>A||||||||||||||,A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|2/20||NM_139135.4:c.1328G>A|NP_624361.1:p.Gly443Asp|1717|1328|443|G/D|gGc/gAc|||1||EntrezGene||||||1:g.27056332G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:259:0:0,0:79,180:259,0:0:2,0:33.5:1:36.5:1:1:0:60:128.5:1:0:0.2	0/1:141:2:1,1:38,101:139,2:0.0142:2,2:61:1:37:0:0.47812:2.64:60:4:0.0144:0:1
    96. 

  96. 1	27057732	27057732	G	A	exonic	ARID1A	.	synonymous SNV	ARID1A:NM_006015:exon3:c.G1440A:p.Q480Q,ARID1A:NM_139135:exon3:c.G1440A:p.Q480Q	0.	.	.	.	.	.	.	.	.	rs746775479	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100254040;OCCURENCE=1(endometrium)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129135002	UCEC-US|1|531|0.00188324	0.25	37	192	1	27057732	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=928;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=3;SSF=0.02926;SOR=0;LSEQ=CAAAGTCCTCACCCTCAGCA;RSEQ=CAGCAGCCACCCTACTCCCA;CSQ=A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_006015.6|protein_coding|3/20||NM_006015.6:c.1440G>A|NP_006006.3:p.Gln480%3D|1829|1440|480|Q|caG/caA|rs746775479&COSV100254040||1||EntrezGene||YES||||1:g.27057732G>A|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1,A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_139135.4|protein_coding|3/20||NM_139135.4:c.1440G>A|NP_624361.1:p.Gln480%3D|1829|1440|480|Q|caG/caA|rs746775479&COSV100254040||1||EntrezGene||||||1:g.27057732G>A|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:928:0:0,0:492,435:927,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:192:2:1,1:97,93:190,2:0.0104:2,2:41:1:37:0:1:1.0428:60:4:0.0106:0:1
    97. 

  97. 1	27057779	27057779	C	T	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon3:c.C1487T:p.A496V,ARID1A:NM_139135:exon3:c.C1487T:p.A496V	.	.	.	.	.	.	.	.	.	.	.	0.02	0.512	D	0.22	0.321	B	0.024	0.279	B	0.027	0.259	N	0.987	0.255	N	0.895	0.225	L	4.49	0.453	T	-1.26	0.375	N	0.179	0.281	-1.110	0.030	T	0.056	0.236	T	0.006	0.166	T	1.449	0.237	13.04	0.879	0.170	0.812	0.404	D	c	-0.533	-0.381	1.000	0.747	0.722	0.854	0	3.43	0.382	1.168	0.313	0.060	0.166	0.011	0.184	0.999	0.750	15.848	0.786	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	176	1	27057779	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=822;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.03095;SOR=0;LSEQ=ACCGTCCCAGACCCCTCATG;RSEQ=CCAACCTTCGTATCAGCAGC;CSQ=T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|3/20||NM_006015.6:c.1487C>T|NP_006006.3:p.Ala496Val|1876|1487|496|A/V|gCc/gTc|COSV99055512||1||EntrezGene||YES||||1:g.27057779C>T|||||||||||||1|1,T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|3/20||NM_139135.4:c.1487C>T|NP_624361.1:p.Ala496Val|1876|1487|496|A/V|gCc/gTc|COSV99055512||1||EntrezGene||||||1:g.27057779C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:822:0:0,0:381,440:821,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:176:2:1,1:81,93:174,2:0.0114:2,2:48.5:1:37:0:1:1.15:60:4:0.0114:0:1
    98. 

  98. 1	27087531	27087531	C	A	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon5:c.C2105A:p.S702Y,ARID1A:NM_139135:exon5:c.C2105A:p.S702Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.998	0.764	D	0.991	0.832	D	0.000	0.629	D	1	0.810	D	2.415	0.700	M	1.86	0.243	T	-4.98	0.839	D	0.703	0.771	-0.849	0.521	T	0.186	0.535	T	0.063	0.690	D	3.021	0.423	22.3	0.994	0.612	0.991	0.917	D	c	0.888	0.884	1.000	0.747	0.707	0.730	0	5.95	0.964	7.568	0.814	0.935	0.490	1.000	0.715	0.999	0.750	20.393	0.990	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	104	1	27087531	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=381;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.04563;SOR=0;LSEQ=TTCCCCGTCCCCTGTTGGCT;RSEQ=TCCCGCCAGTGTTGCTCAGT;CSQ=A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|5/20||NM_006015.6:c.2105C>A|NP_006006.3:p.Ser702Tyr|2494|2105|702|S/Y|tCt/tAt|||1||EntrezGene||YES||||1:g.27087531C>A||||||||||||||,A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|5/20||NM_139135.4:c.2105C>A|NP_624361.1:p.Ser702Tyr|2494|2105|702|S/Y|tCt/tAt|||1||EntrezGene||||||1:g.27087531C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:381:0:0,0:136,245:381,0:0:2,0:33.9:1:36.9:1:1:0:60:762:1:0:0.1	0/1:104:2:1,1:33,69:102,2:0.0192:2,2:23:1:37:0:0.5491:2.07:60:4:0.0194:0:1
    99. 

  99. 1	27087627	27087627	A	G	intronic	ARID1A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	50	1	27087627	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=141;VD=2;AF=0.0142;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.54395;SOR=inf;LSEQ=TTTAGGGAGAGGGAAAGGTG;RSEQ=CTGCCCCCAGTAATATTAAG;CSQ=G|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_006015.6|protein_coding||5/19|NM_006015.6:c.2161+40A>G|||||||||1||EntrezGene||YES||||1:g.27087627A>G||||||||||||||,G|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding||5/19|NM_139135.4:c.2161+40A>G|||||||||1||EntrezGene||||||1:g.27087627A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:141:2:1,1:50,89:139,2:0.0142:2,2:10:0:37:0:1:1.77:60:4:0.0143:0:1	0/0:50:0:0,0:19,31:50,0:0:2,0:37.4:1:37:0:1:0:60:100:1:0:0
    100. 

  100. 1	27087953	27087953	C	T	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon6:c.C2240T:p.A747V,ARID1A:NM_139135:exon6:c.C2240T:p.A747V	.	.	.	.	.	.	.	.	.	.	.	0.017	0.512	D	0.986	0.596	D	0.558	0.540	P	0.000	0.445	D	0.915	0.365	D	1.65	0.424	L	1.84	0.247	T	-2.24	0.501	N	0.47	0.547	-1.122	0.022	T	0.096	0.361	T	0.008	0.211	T	3.897	0.525	23.5	0.998	0.894	0.957	0.656	D	c	0.502	0.553	1.000	0.517	0.672	0.522	0	5.85	0.936	1.560	0.357	0.935	0.490	1.000	0.715	1.000	0.888	15.632	0.766	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	182	1	27087953	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=560;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.05991;SOR=0;LSEQ=CATGAACCAATCAAGCATTG;RSEQ=CCAAGATCGAGGTGAGAGCC;CSQ=T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|6/20||NM_006015.6:c.2240C>T|NP_006006.3:p.Ala747Val|2629|2240|747|A/V|gCc/gTc|rs1244463961||1||EntrezGene||YES||||1:g.27087953C>T|3.979e-06|0|0|0|0|0|8.801e-06|0|0|8.801e-06|gnomAD_NFE|||,T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|6/20||NM_139135.4:c.2240C>T|NP_624361.1:p.Ala747Val|2629|2240|747|A/V|gCc/gTc|rs1244463961||1||EntrezGene||||||1:g.27087953C>T|3.979e-06|0|0|0|0|0|8.801e-06|0|0|8.801e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:560:0:0,0:271,289:560,0:0:2,0:39.1:1:36.5:1:1:0:60:185.667:1:0:0.1	0/1:182:2:1,1:86,94:180,2:0.011:2,2:32.5:1:37:0:1:1.09:60:4:0.0112:0:1
    101. 

  101. 1	27088697	27088697	C	T	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon7:c.C2306T:p.S769L,ARID1A:NM_139135:exon7:c.C2306T:p.S769L	.	.	.	.	.	.	.	.	.	.	.	0.062	0.388	T	0.958	0.564	D	0.477	0.515	P	0.000	0.629	D	1.000	0.588	D	2.14	0.601	M	2.1	0.200	T	-3.57	0.690	D	0.629	0.767	-1.127	0.019	T	0.099	0.369	T	0.019	0.415	T	3.927	0.529	23.5	0.999	0.960	0.998	0.994	D	c	0.704	0.754	1.000	0.747	0.707	0.730	0	5.95	0.964	7.568	0.814	0.935	0.490	1.000	0.715	0.990	0.544	20.393	0.990	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	177	1	27088697	.	C	T	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=410;VD=2;AF=0.0049;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.35086;SOR=0.42961;LSEQ=CAGTTCCCCCCAGCCCGGCT;RSEQ=AGCCTTATCTCCGCGTCAGC;CSQ=T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|7/20||NM_006015.6:c.2306C>T|NP_006006.3:p.Ser769Leu|2695|2306|769|S/L|tCa/tTa|COSV61383777&COSV61384786||1||EntrezGene||YES||||1:g.27088697C>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|7/20||NM_139135.4:c.2306C>T|NP_624361.1:p.Ser769Leu|2695|2306|769|S/L|tCa/tTa|COSV61383777&COSV61384786||1||EntrezGene||||||1:g.27088697C>T|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:410:2:1,1:231,177:408,2:0.0049:2,2:62:1:37:0:1:1.30422:60:4:0.0049:0:1	0/1:177:2:1,1:91,84:175,2:0.0113:2,2:46:0:37:0:1:1.08283:60:4:0.0114:0:1
    102. 

  102. 1	27088716	27088716	G	T	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon7:c.G2325T:p.Q775H,ARID1A:NM_139135:exon7:c.G2325T:p.Q775H	.	.	.	.	.	.	.	.	.	.	.	0.093	0.315	T	0.996	0.715	D	0.986	0.807	D	0.000	0.843	D	1	0.810	D	1.875	0.501	L	2.05	0.207	T	-1.53	0.372	N	0.64	0.719	-1.073	0.087	T	0.133	0.447	T	0.027	0.504	D	2.999	0.421	22.2	0.997	0.774	0.997	0.988	D	c	0.783	0.802	1.000	0.747	0.707	0.730	0	5.95	0.964	5.531	0.666	1.048	0.713	1.000	0.715	1.000	0.888	20.393	0.990	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	181	1	27088716	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=408;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.09407;SOR=0;LSEQ=TCAGCCTTATCTCCGCGTCA;RSEQ=CCTTCCGGAGGACAGATACA;CSQ=T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|7/20||NM_006015.6:c.2325G>T|NP_006006.3:p.Gln775His|2714|2325|775|Q/H|caG/caT|||1||EntrezGene||YES||||1:g.27088716G>T||||||||||||||,T|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|7/20||NM_139135.4:c.2325G>T|NP_624361.1:p.Gln775His|2714|2325|775|Q/H|caG/caT|||1||EntrezGene||||||1:g.27088716G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:408:0:0,0:225,183:408,0:0:2,0:43:1:36.1:1:1:0:60:67:1:0:0.1	0/1:181:2:1,1:90,89:179,2:0.011:2,2:36.5:1:31:1:1:1.01117:60:4:0.0111:0:1
    103. 

  103. 1	27099798	27099798	A	T	intronic	ARID1A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	181	1	27099798	.	A	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=929;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02647;SOR=0;LSEQ=GTAGATTACCAGGCTTGTCA;RSEQ=CTTACCAGTTTGTTCACCGC;CSQ=T|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_006015.6|protein_coding||14/19|NM_006015.6:c.3716-39A>T|||||||||1||EntrezGene||YES||||1:g.27099798A>T||||||||||||||,T|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding||14/19|NM_139135.4:c.3716-39A>T|||||||||1||EntrezGene||||||1:g.27099798A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:929:0:0,0:655,274:929,0:0:2,0:33.6:1:36.2:1:1:0:60:91.9:1:0:0.1	0/1:181:2:1,1:134,45:179,2:0.011:2,2:36.5:1:37:0:0.44475:2.95614:60:4:0.0114:0:1
    104. 

  104. 1	27099806	27099806	G	T	intronic	ARID1A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	197	1	27099806	.	G	T	44	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1034;VD=1;AF=0.001;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01427;SOR=0.06282;LSEQ=CCAGGCTTGTCAACTTACCA;RSEQ=TTTGTTCACCGCTTGCCTTT;CSQ=T|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_006015.6|protein_coding||14/19|NM_006015.6:c.3716-31G>T|||||||||1||EntrezGene||YES||||1:g.27099806G>T||||||||||||||,T|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding||14/19|NM_139135.4:c.3716-31G>T|||||||||1||EntrezGene||||||1:g.27099806G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1034:1:0,1:719,314:1033,1:0.001:2,0:38:0:11:0:0.30464:0:60:0:0:0:7	0/1:197:3:1,2:145,49:194,3:0.0152:2,2:15.7:1:28.3:1:0.16493:5.85314:60:2:0.0106:0:1
    105. 

  105. 1	27100182	27100184	GCA	-	exonic	ARID1A	.	nonframeshift deletion	ARID1A:NM_006015:exon16:c.3978_3980del:p.Q1334del,ARID1A:NM_139135:exon16:c.3978_3980del:p.Q1334del	0.018	3.242e-05	0	0	0	0	0	0	0.0010	rs374564889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	707303	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU1662117	BRCA-EU|1|569|0.00175747,ORCA-IN|2|178|0.011236	0.5	164	231	1	27100181	.	CGCA	C	164	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1253;VD=22;AF=0.0176;SHIFT3=21;MSI=8;MSILEN=3;SSF=0.15166;SOR=0.57215;LSEQ=TTCTCCTAGCCGCTACCCCC;RSEQ=GCAGCAGCAGCAGCAGCAGC;CSQ=-|inframe_deletion|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|16/20||NM_006015.6:c.3999_4001del|NP_006006.3:p.Gln1334del|4367-4369|3978-3980|1326-1327|PQ/P|ccGCAg/ccg|rs374564889||1||EntrezGene||YES|||21|1:g.27100203_27100205del|0.0001805|0.0001282|5.927e-05|0.0003041|0.0002818|0.0002881|0.0002182|0.0001672|3.326e-05|0.0003041|gnomAD_ASJ|||1,-|inframe_deletion|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|16/20||NM_139135.4:c.3999_4001del|NP_624361.1:p.Gln1334del|4367-4369|3978-3980|1326-1327|PQ/P|ccGCAg/ccg|rs374564889||1||EntrezGene|||||21|1:g.27100203_27100205del|0.0001805|0.0001282|5.927e-05|0.0003041|0.0002818|0.0002881|0.0002182|0.0001672|3.326e-05|0.0003041|gnomAD_ASJ|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1253:22:10,12:635,591:1226,22:0.0176:2,2:42.1:1:37:1:0.66824:1.28907:60:44:0.0178:0.0008:0.1	0/1:231:7:5,2:116,108:224,7:0.0303:2,2:39.4:1:37:1:0.44972:2.32:60:14:0.0304:0.0087:0.1
    106. 

  106. 1	27100328	27100328	G	A	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon17:c.G4040A:p.G1347D,ARID1A:NM_139135:exon17:c.G4040A:p.G1347D	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.989	0.637	D	0.836	0.581	P	0.000	0.843	D	0.999	0.810	D	2.07	0.570	M	3.77	0.044	T	-4.82	0.808	D	0.38	0.663	-1.144	0.012	T	0.033	0.140	T	0.012	0.303	T	2.011	0.303	16.28	0.988	0.455	0.980	0.789	D	c	0.536	0.546	1.000	0.747	0.722	0.854	0	4.61	0.566	6.455	0.732	1.048	0.713	1.000	0.715	1.000	0.888	16.405	0.834	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	273	1	27100328	.	G	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1571;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00321;SOR=0;LSEQ=CAATCAGTTCTCCACCCAAG;RSEQ=CACCCCTTCTGGCAGCCCCT;CSQ=A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|17/20||NM_006015.6:c.4040G>A|NP_006006.3:p.Gly1347Asp|4429|4040|1347|G/D|gGc/gAc|||1||EntrezGene||YES||||1:g.27100328G>A||||||||||||||,A|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|17/20||NM_139135.4:c.4040G>A|NP_624361.1:p.Gly1347Asp|4429|4040|1347|G/D|gGc/gAc|||1||EntrezGene||||||1:g.27100328G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1571:0:0,0:715,855:1570,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:273:3:2,1:127,143:270,3:0.011:2,2:46:1:37:0:0.60399:2.25:60:6:0.0111:0:1
    107. 

  107. 1	27101381	27101381	T	G	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon18:c.T4663G:p.Y1555D	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.998	0.715	D	0.93	0.647	D	0.000	0.629	D	1.000	0.810	D	1.65	0.424	L	4.27	0.028	T	-5.35	0.847	D	0.478	0.880	-1.087	0.060	T	0.024	0.104	T	0.020	0.431	T	2.323	0.340	18.32	0.980	0.370	0.992	0.919	D	c	0.645	0.651	1.000	0.747	0.707	0.730	0	5.18	0.710	7.579	0.817	1.049	0.752	1.000	0.715	0.999	0.750	15.200	0.727	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	92	98	1	27101381	.	T	G	92	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=727;VD=11;AF=0.0151;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.24657;SOR=inf;LSEQ=ATGGCACACGCCAGCCCCCA;RSEQ=ATGGTCCCTCTGCCCCTGTG;CSQ=G|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|18/20||NM_006015.6:c.4663T>G|NP_006006.3:p.Tyr1555Asp|5052|4663|1555|Y/D|Tat/Gat|||1||EntrezGene||YES||||1:g.27101381T>G||||||||||||||,G|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding||17/19|NM_139135.4:c.4102-90T>G|||||||||1||EntrezGene||||||1:g.27101381T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:727:11:10,1:123,591:714,11:0.0151:2,2:12.8:1:26.6:1:0:47.71:60:2.667:0.0121:0:1.8	0/0:98:0:0,0:13,85:98,0:0:2,0:15:0:11:0:1:0:60:0:0:0:4
    108. 

  108. 1	27101453	27101453	C	T	exonic	ARID1A	.	stopgain	ARID1A:NM_006015:exon18:c.C4735T:p.Q1579X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.537	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.517	0.984	39	0.998	0.855	0.971	0.722	D	c	1.108	0.936	1.000	0.747	0.672	0.522	0	5.31	0.750	7.283	0.778	0.925	0.434	1.000	0.715	0.999	0.750	19.173	0.935	.	.	.	ID=COSV61371921;OCCURENCE=1(oesophagus),1(lung),1(endometrium)	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU131277494	LUAD-US|1|516|0.00193798	0.25	37	94	1	27101453	.	C	T	37	v3;f0.01;p8;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=644;VD=1;AF=0.0016;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0442;SOR=0.07202;LSEQ=ACCAGCCCCCACCAAGCATG;RSEQ=AGAATCACATTCCTCAGGTA;CSQ=T|stop_gained|HIGH|ARID1A|8289|Transcript|NM_006015.6|protein_coding|18/20||NM_006015.6:c.4735C>T|NP_006006.3:p.Gln1579Ter|5124|4735|1579|Q/*|Cag/Tag|COSV61371921||1||EntrezGene||YES||||1:g.27101453C>T|||||||||||||1|1,T|intron_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding||17/19|NM_139135.4:c.4102-18C>T|||||||COSV61371921||1||EntrezGene||||||1:g.27101453C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:644:1:0,1:294,349:643,1:0.0016:2,0:5:0:37:0:1:0:60:2:0.0016:0:2	0/1:94:2:1,1:34,58:92,2:0.0213:2,2:25.5:1:37:0:1:1.7:60:4:0.0217:0:1
    109. 

  109. 1	27101584	27101584	C	A	exonic	ARID1A	.	synonymous SNV	ARID1A:NM_006015:exon18:c.C4866A:p.A1622A,ARID1A:NM_139135:exon18:c.C4215A:p.A1405A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	190	1	27101584	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1328;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01559;SOR=0;LSEQ=GCAGGTCCCCCAGTACCTGC;RSEQ=TCGCACATAGCACCTGCCCC;CSQ=A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_006015.6|protein_coding|18/20||NM_006015.6:c.4866C>A|NP_006006.3:p.Ala1622%3D|5255|4866|1622|A|gcC/gcA|||1||EntrezGene||YES||||1:g.27101584C>A||||||||||||||,A|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_139135.4|protein_coding|18/20||NM_139135.4:c.4215C>A|NP_624361.1:p.Ala1405%3D|4604|4215|1405|A|gcC/gcA|||1||EntrezGene||||||1:g.27101584C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1328:0:0,0:696,632:1328,0:0:2,0:34.8:1:36.8:1:1:0:60:331:1:0:0.1	0/1:190:2:1,1:102,86:188,2:0.0105:2,2:51:0:37:0:1:1.18497:60:4:0.0105:0:1
    110. 

  110. 1	27101600	27101600	G	C	exonic	ARID1A	.	nonsynonymous SNV	ARID1A:NM_006015:exon18:c.G4882C:p.A1628P,ARID1A:NM_139135:exon18:c.G4231C:p.A1411P	.	.	.	.	.	.	.	.	.	rs893433709	.	0.639	0.070	T	0.007	0.135	B	0.01	0.139	B	0.001	0.398	N	0.707	0.810	D	-1.15	0.009	N	4.5	0.024	T	0.36	0.037	N	0.399	0.524	-1.100	0.041	T	0.050	0.214	T	0.004	0.102	T	1.144	0.204	11.45	0.819	0.135	0.791	0.389	D	c	-0.231	-0.137	0.901	0.261	0.672	0.522	0	1.9	0.247	0.528	0.225	0.154	0.240	0.985	0.357	0.999	0.750	7.361	0.258	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	201	1	27101600	.	G	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1367;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.01636;SOR=0;LSEQ=CTGCCTCGCACATAGCACCT;RSEQ=CCCCTGTGCAGCCCCCCATG;CSQ=C|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_006015.6|protein_coding|18/20||NM_006015.6:c.4882G>C|NP_006006.3:p.Ala1628Pro|5271|4882|1628|A/P|Gcc/Ccc|rs893433709||1||EntrezGene||YES||||1:g.27101600G>C||||||||||||||,C|missense_variant|MODERATE|ARID1A|8289|Transcript|NM_139135.4|protein_coding|18/20||NM_139135.4:c.4231G>C|NP_624361.1:p.Ala1411Pro|4620|4231|1411|A/P|Gcc/Ccc|rs893433709||1||EntrezGene||||||1:g.27101600G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1367:0:0,0:699,667:1366,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:201:2:1,1:104,95:199,2:0.01:2,2:39.5:1:37:0:1:1.09424:60:4:0.0101:0:1
    111. 

  111. 1	27107238	27107238	C	T	exonic	ARID1A	.	synonymous SNV	ARID1A:NM_006015:exon20:c.C6849T:p.G2283G,ARID1A:NM_139135:exon20:c.C6198T:p.G2066G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129136292	UCEC-US|1|531|0.00188324	0.25	85	153	1	27107238	.	C	T	85	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2037;VD=5;AF=0.0025;SHIFT3=6;MSI=2;MSILEN=1;SSF=0.08072;SOR=0.18606;LSEQ=GATGTACTGTTTTTGATTGG;RSEQ=CAGTCATGACAGCCGTGGGA;CSQ=T|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_006015.6|protein_coding|20/20||NM_006015.6:c.6849C>T|NP_006006.3:p.Gly2283%3D|7238|6849|2283|G|ggC/ggT|||1||EntrezGene||YES||||1:g.27107238C>T||||||||||||||,T|synonymous_variant|LOW|ARID1A|8289|Transcript|NM_139135.4|protein_coding|20/20||NM_139135.4:c.6198C>T|NP_624361.1:p.Gly2066%3D|6587|6198|2066|G|ggC/ggT|||1||EntrezGene||||||1:g.27107238C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2037:5:2,3:832,1198:2030,5:0.0025:2,2:34.8:1:37:0:1:1.04172:60:10:0.0025:0:1	0/1:153:2:1,1:54,97:151,2:0.0131:2,2:10.5:1:37:0:1:1.79:60:4:0.0131:0:1
    112. 

  112. 1	27107264	27107264	C	-	UTR3	ARID1A	NM_006015:c.*17delC;NM_139135:c.*17delC	.	.	0.089	0.0010	0.0030	0	0	0.0019	0	6.891e-05	0.0011	rs745390232	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU80409886	COCA-CN|1|321|0.00311526	0.25	181	127	1	27107263	.	TC	T	181	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1718;VD=30;AF=0.0175;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.35842;SOR=2.23863;LSEQ=CATGACAGCCGTGGGACACC;RSEQ=CCCCCCCCGTGTGTGTGTGC;CSQ=-|3_prime_UTR_variant|MODIFIER|ARID1A|8289|Transcript|NM_006015.6|protein_coding|20/20||NM_006015.6:c.*25del||7264|||||rs3841356&COSV100253736||1||EntrezGene||YES||||1:g.27107272del|0.002607|0.004085|0.004587|0.003527|0.003511|0.003204|0.001428|0.003305|0.002952|0.01618|AA||0&1|0&1,-|3_prime_UTR_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding|20/20||NM_139135.4:c.*25del||6613|||||rs3841356&COSV100253736||1||EntrezGene||||||1:g.27107272del|0.002607|0.004085|0.004587|0.003527|0.003511|0.003204|0.001428|0.003305|0.002952|0.01618|AA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1718:30:12,18:647,1038:1685,30:0.0175:2,2:41.4:1:37:0:0.85193:1.07:60:60:0.0181:0:0.6	0/0:127:1:1,0:41,85:126,1:0.0079:2,0:20:0:37:0:0.33071:0:60:2:0.0081:0:0
    113. 

  113. 1	27107274	27107278	TGTGT	GGGGG	UTR3	ARID1A	NM_006015:c.*27_*31delinsGGGGG;NM_139135:c.*27_*31delinsGGGGG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	160	124	1	27107274	.	TGTGT	GGGGG	160	Bias	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Complex;DP=1507;VD=37;AF=0.0246;SHIFT3=0;MSI=5;MSILEN=2;SSF=0.05183;SOR=inf;LSEQ=TGGGACACCTCCCCCCCCCG;RSEQ=GTGTGCGTGTGTGGAGAACT;CSQ=GGGGG|3_prime_UTR_variant|MODIFIER|ARID1A|8289|Transcript|NM_006015.6|protein_coding|20/20||NM_006015.6:c.*27_*31delinsGGGGG||7274-7278|||||||1||EntrezGene||YES||||1:g.27107274_27107278delinsGGGGG||||||||||||||,GGGGG|3_prime_UTR_variant|MODIFIER|ARID1A|8289|Transcript|NM_139135.4|protein_coding|20/20||NM_139135.4:c.*27_*31delinsGGGGG||6623-6627|||||||1||EntrezGene||||||1:g.27107274_27107278delinsGGGGG||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1507:37:36,1:401,997:1398,37:0.0246:2,1:25.3:1:30.8:1:0:89.13:60:74:0.031:0.0232:0.8	0/0:124:0:0,0:32,85:117,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    114. 

  114. 1	32757783	32757783	C	T	exonic	HDAC1	.	stopgain	HDAC1:NM_004964:exon1:c.C13T:p.Q5X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.990	0.971	37	0.997	0.835	0.935	0.582	D	c	0.881	0.709	1.000	0.747	0.726	0.872	0	4.36	0.515	2.868	0.479	0.935	0.490	1.000	0.715	1.000	0.888	15.958	0.796	Histone deacetylase domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	108	1	32757783	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=444;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.03799;SOR=0;LSEQ=CGAGCAAGATGGCGCAGACG;RSEQ=AGGGCACCCGGAGGAAAGTC;CSQ=T|stop_gained|HIGH|HDAC1|3065|Transcript|NM_004964.3|protein_coding|1/14||NM_004964.3:c.13C>T|NP_004955.2:p.Gln5Ter|100|13|5|Q/*|Cag/Tag|||1||EntrezGene||YES||||1:g.32757783C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:444:0:0,0:264,180:444,0:0:2,0:36.2:1:36.7:1:1:0:60:443:1:0:0.2	0/1:108:2:1,1:53,53:106,2:0.0185:2,2:44:1:37:0:1:1:60:4:0.0187:0:1
    115. 

  115. 1	32793115	32793115	C	T	intronic	HDAC1	.	.	.	.	.	.	.	.	.	.	.	.	rs1053139692	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	156	1	32793115	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1547;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00834;SOR=0;LSEQ=CCCCAAAGAGCCCCCAGACC;RSEQ=CTGACCCCCTTCTGATCCTA;CSQ=T|intron_variant|MODIFIER|HDAC1|3065|Transcript|NM_004964.3|protein_coding||5/13|NM_004964.3:c.495-22C>T|||||||rs1053139692||1||EntrezGene||YES||||1:g.32793115C>T|4.007e-06|0|0|0|0|0|8.921e-06|0|0|8.921e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1547:0:0,0:842,705:1547,0:0:2,0:33.4:1:36.4:1:1:0:60:102.133:1:0:1.2	0/1:156:2:1,1:102,52:154,2:0.0128:2,2:49:1:37:0:1:1.95251:60:4:0.0128:0:1
    116. 

  116. 1	36807481	36807481	C	T	exonic	STK40	.	nonsynonymous SNV	STK40:NM_001282546:exon11:c.G1198A:p.A400T,STK40:NM_001282547:exon11:c.G1183A:p.A395T,STK40:NM_032017:exon12:c.G1183A:p.A395T	0.25	0.2186	0.1975	0.1122	0.1821	0.1067	0.2064	0.2516	0.2331	rs3795498	rs3795498	0.114	0.324	T	0.04	0.198	B	0.005	0.104	B	0.000	0.629	D	0.000	0.810	P	0.895	0.225	L	-0.02	0.629	T	-0.06	0.079	N	0.061	0.045	-1.106	0.034	T	0.000	0.000	T	.	.	.	3.937	0.530	23.5	0.998	0.879	0.960	0.667	D	c	-0.102	0.112	1.000	0.747	0.707	0.730	0	5.11	0.691	5.743	0.681	0.919	0.430	1.000	0.715	0.979	0.486	17.506	0.876	.	ENSG00000214193.5	Colon_Transverse	ID=COSV63734648;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(urinary_tract),3(prostate),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU3888830	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.25	74	0	1	36807481	.	C	T	74	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=4;AF=0.6667;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGTACCCAGCTCCGGG;RSEQ=GTCATGGATGGAGCTCTTCT;CSQ=T|missense_variant|MODERATE|STK40|83931|Transcript|NM_001282546.2|protein_coding|11/11||NM_001282546.2:c.1198G>A|NP_001269475.1:p.Ala400Thr|1408|1198|400|A/T|Gcc/Acc|rs3795498&COSV63734648||-1||EntrezGene||YES||||1:g.36807481C>T|0.2072|0.1917|0.1285|0.1694|0.1181|0.1966|0.2491|0.213|0.2228|0.2531|EA||0&1|0&1,T|missense_variant|MODERATE|STK40|83931|Transcript|NM_001282547.2|protein_coding|11/11||NM_001282547.2:c.1183G>A|NP_001269476.1:p.Ala395Thr|1393|1183|395|A/T|Gcc/Acc|rs3795498&COSV63734648||-1||EntrezGene||||||1:g.36807481C>T|0.2072|0.1917|0.1285|0.1694|0.1181|0.1966|0.2491|0.213|0.2228|0.2531|EA||0&1|0&1,T|missense_variant|MODERATE|STK40|83931|Transcript|NM_032017.3|protein_coding|12/12||NM_032017.3:c.1183G>A|NP_114406.1:p.Ala395Thr|1630|1183|395|A/T|Gcc/Acc|rs3795498&COSV63734648||-1||EntrezGene||||||1:g.36807481C>T|0.2072|0.1917|0.1285|0.1694|0.1181|0.1966|0.2491|0.213|0.2228|0.2531|EA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:6:4:2,2:1,1:2,4:0.6667:2,2:43:1:37:0:1:1:60:8:0.6667:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    117. 

  117. 1	40363054	40363054	G	C	exonic	MYCL	.	nonsynonymous SNV	MYCL:NM_001033081:exon2:c.C1085G:p.T362S,MYCL:NM_001033082:exon3:c.C1175G:p.T392S	1.	0.9116	0.9750	0.8568	0.8477	0.9975	0.8808	0.8796	0.8707	rs3134614	rs3134614	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.000	0.629	N	1.000	0.090	P	-0.77	0.017	N	-0.9	0.773	T	0.17	0.051	N	0.057	0.048	-0.955	0.401	T	0.000	0.000	T	.	.	.	0.145	0.108	4.091	0.818	0.134	0.109	0.161	N	c	-0.624	-0.369	1.000	0.747	0.646	0.442	0	4.53	0.548	2.284	0.429	0.012	0.140	1.000	0.715	0.999	0.750	5.637	0.167	.	ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11|ENSG00000043514.11	Adipose_Subcutaneous|Adrenal_Gland|Artery_Aorta|Artery_Tibial|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Colon_Transverse|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Thyroid	ID=COSV65693710;OCCURENCE=1(prostate)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU3888723	COCA-CN|5|321|0.0155763	1	381	118	1	40363054	.	G	C	381	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1423;VD=1420;AF=0.9979;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.78729;SOR=0;LSEQ=TTTTGGTCAGTTAGTAGCCA;RSEQ=TGAGGTATGCAATTCTTTTC;CSQ=C|missense_variant|MODERATE|MYCL|4610|Transcript|NM_001033081.3|protein_coding|2/2||NM_001033081.3:c.1085C>G|NP_001028253.1:p.Thr362Ser|1568|1085|362|T/S|aCt/aGt|rs3134614&COSV65693710||-1||EntrezGene||||||1:g.40363054G>C|0.8851|0.9773|0.872|0.8561|0.9993|0.8943|0.8732|0.885|0.8261|1|EAS||0&1|0&1,C|missense_variant|MODERATE|MYCL|4610|Transcript|NM_001033082.3|protein_coding|3/3||NM_001033082.3:c.1175C>G|NP_001028254.2:p.Thr392Ser|1204|1175|392|T/S|aCt/aGt|rs3134614&COSV65693710||-1||EntrezGene||YES||||1:g.40363054G>C|0.8851|0.9773|0.872|0.8561|0.9993|0.8943|0.8732|0.885|0.8261|1|EAS||0&1|0&1,C|downstream_gene_variant|MODIFIER|MYCL|4610|Transcript|NM_005376.5|protein_coding||||||||||rs3134614&COSV65693710|2230|-1||EntrezGene||||||1:g.40363054G>C|0.8851|0.9773|0.872|0.8561|0.9993|0.8943|0.8732|0.885|0.8261|1|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1423:1420:817,603:0,0:0,1420:0.9979:0,2:39.3:1:36.4:1:1:0:60:128.091:1:0:1.1	1/1:118:118:79,39:0,0:0,118:1:0,2:40.5:1:36.3:1:1:0:60:236:1:0:1
    118. 

  118. 1	40363694	40363694	A	G	intronic	MYCL	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	113	1	40363694	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=674;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02046;SOR=0;LSEQ=ACATCCCATGAGAAACACAA;RSEQ=CATAGACCCTACAGCTTTAG;CSQ=G|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_001033081.3|protein_coding||1/1|NM_001033081.3:c.497-52T>C|||||||||-1||EntrezGene||||||1:g.40363694A>G||||||||||||||,G|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_001033082.3|protein_coding||2/2|NM_001033082.3:c.587-52T>C|||||||||-1||EntrezGene||YES||||1:g.40363694A>G||||||||||||||,G|downstream_gene_variant|MODIFIER|MYCL|4610|Transcript|NM_005376.5|protein_coding|||||||||||1590|-1||EntrezGene||||||1:g.40363694A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:674:0:0,0:144,528:672,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:113:2:1,1:18,93:111,2:0.0177:2,2:44:1:37:0:0.30926:5.06:60:4:0.0187:0:1
    119. 

  119. 1	40366573	40366573	G	T	exonic	MYCL	.	synonymous SNV	MYCL:NM_005376:exon2:c.C624A:p.P208P	.	.	.	.	.	.	.	.	.	rs1034750343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	99	1	40366573	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=700;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01522;SOR=0;LSEQ=CAGAGCTTTGGCCACCCATG;RSEQ=GGTGGCCCCCTCTTGGATGG;CSQ=T|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_001033081.3|protein_coding||1/1|NM_001033081.3:c.496+38C>A|||||||rs1034750343||-1||EntrezGene||||||1:g.40366573G>T|8.821e-06|0|0|0|0|0|2.19e-05|0|0|2.19e-05|gnomAD_NFE|||,T|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_001033082.3|protein_coding||2/2|NM_001033082.3:c.586+38C>A|||||||rs1034750343||-1||EntrezGene||YES||||1:g.40366573G>T|8.821e-06|0|0|0|0|0|2.19e-05|0|0|2.19e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|MYCL|4610|Transcript|NM_005376.5|protein_coding|2/2||NM_005376.5:c.624C>A|NP_005367.2:p.Pro208%3D|653|624|208|P|ccC/ccA|rs1034750343||-1||EntrezGene||||||1:g.40366573G>T|8.821e-06|0|0|0|0|0|2.19e-05|0|0|2.19e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:700:0:0,0:265,435:700,0:0:2,0:34.9:1:36.3:1:1:0:60:62.636:1:0:0.5	0/1:99:2:1,1:46,51:97,2:0.0202:2,2:38:1:37:0:1:1.11:60:4:0.0206:0:1
    120. 

  120. 1	40366691	40366691	T	G	exonic	MYCL	.	nonsynonymous SNV	MYCL:NM_001033081:exon1:c.A416C:p.N139T,MYCL:NM_001033082:exon2:c.A506C:p.N169T,MYCL:NM_005376:exon2:c.A506C:p.N169T	.	.	.	.	.	.	.	.	.	.	.	0.369	0.371	T	0.001	0.236	B	0.002	0.246	B	0.003	0.363	N	0.766	0.295	N	1.78	0.463	L	-0.92	0.779	T	-1.06	0.309	N	0.019	0.018	-0.747	0.581	T	0.262	0.633	T	0.203	0.869	D	-0.445	0.059	0.300	0.928	0.218	0.558	0.297	D	c	-0.819	-0.699	1.000	0.747	0.726	0.872	0	-0.102	0.129	0.429	0.210	-0.282	0.084	0.951	0.329	0.836	0.349	7.606	0.271	Transcription regulator Myc, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	62	61	1	40366691	.	T	G	62	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=303;VD=5;AF=0.0165;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.39745;SOR=inf;LSEQ=AGGGGGCGGCGGGCGCCGGG;RSEQ=TGCCGGCTTCGAGGCTGGGA;CSQ=G|missense_variant|MODERATE|MYCL|4610|Transcript|NM_001033081.3|protein_coding|1/2||NM_001033081.3:c.416A>C|NP_001028253.1:p.Asn139Thr|899|416|139|N/T|aAc/aCc|||-1||EntrezGene||||||1:g.40366691T>G||||||||||||||,G|missense_variant|MODERATE|MYCL|4610|Transcript|NM_001033082.3|protein_coding|2/3||NM_001033082.3:c.506A>C|NP_001028254.2:p.Asn169Thr|535|506|169|N/T|aAc/aCc|||-1||EntrezGene||YES||||1:g.40366691T>G||||||||||||||,G|missense_variant|MODERATE|MYCL|4610|Transcript|NM_005376.5|protein_coding|2/2||NM_005376.5:c.506A>C|NP_005367.2:p.Asn169Thr|535|506|169|N/T|aAc/aCc|||-1||EntrezGene||||||1:g.40366691T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:303:5:4,1:103,195:298,5:0.0165:2,2:26:1:27:1:0.05429:7.52:60:4:0.0144:0:4.2	0/0:61:0:0,0:24,37:61,0:0:2,2:27.5:1:11:0:1:0:60:0:0:0:3.5
    121. 

  121. 1	40367177	40367177	G	T	UTR5	MYCL	NM_001033081:c.-71C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	68	29	1	40367177	.	G	T	68	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=243;VD=4;AF=0.0165;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.63532;SOR=inf;LSEQ=GGGCGAAGGAGGTGTCCCCG;RSEQ=GTCCCTCGGCACAGTCGGCT;CSQ=T|5_prime_UTR_variant|MODIFIER|MYCL|4610|Transcript|NM_001033081.3|protein_coding|1/2||NM_001033081.3:c.-71C>A||413|||||||-1||EntrezGene||||||1:g.40367177G>T||||||||||||||,T|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_001033082.3|protein_coding||1/2|NM_001033082.3:c.82-62C>A|||||||||-1||EntrezGene||YES||||1:g.40367177G>T||||||||||||||,T|intron_variant|MODIFIER|MYCL|4610|Transcript|NM_005376.5|protein_coding||1/1|NM_005376.5:c.82-62C>A|||||||||-1||EntrezGene||||||1:g.40367177G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:243:4:2,2:61,178:239,4:0.0165:2,2:25:1:34:1:0.27664:2.9:60:8:0.0165:0:1	0/0:29:0:0,0:7,22:29,0:0:2,0:27.6:1:35.8:1:1:0:60:58:1:0:0.2
    122. 

  122. 1	43803793	43803793	T	A	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon2:c.T103A:p.S35T	.	.	.	.	.	.	.	.	.	.	.	0.717	0.040	T	0.007	0.154	B	0.007	0.149	B	0.035	0.247	N	1.000	0.195	N	1.5	0.380	L	-0.3	0.679	T	-0.33	0.168	N	0.13	0.149	-1.020	0.238	T	0.113	0.403	T	0.006	0.172	T	0.250	0.118	5.194	0.412	0.029	0.415	0.264	N	c	-0.605	-0.431	0.007	0.113	0.487	0.133	0	1.74	0.235	-0.260	0.087	0.086	0.193	0.720	0.286	0.992	0.562	2.991	0.056	Fibronectin type III|Growth hormone/erythropoietin receptor, ligand binding|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	196	1	43803793	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1998;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00794;SOR=0;LSEQ=TCTCCTTGCTGGCATCAGAC;RSEQ=CAGAGCCCCTGAAGTGTTTC;CSQ=A|missense_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|2/12||NM_005373.3:c.103T>A|NP_005364.1:p.Ser35Thr|134|103|35|S/T|Tca/Aca|||1||EntrezGene||YES||||1:g.43803793T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1998:0:0,0:1052,946:1998,0:0:2,0:37.6:1:36.4:1:1:0:60:110:1:0:0.1	0/1:196:2:1,1:102,92:194,2:0.0102:2,2:68:1:37:0:1:1.10811:60:4:0.0102:0:1
    123. 

  123. 1	43805002	43805002	A	G	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon4:c.A452G:p.Q151R	.	.	.	.	.	.	.	.	.	.	.	0.342	0.126	T	0.274	0.375	B	0.056	0.316	B	0.002	0.370	N	0.980	0.251	N	1.93	0.516	L	-1.96	0.851	D	-0.96	0.264	N	0.225	0.276	-0.808	0.547	T	0.282	0.655	T	0.031	0.530	D	1.107	0.200	11.25	0.981	0.381	0.459	0.274	N	c	-0.334	-0.187	0.021	0.133	0.487	0.133	0	3.23	0.360	1.170	0.313	1.199	0.960	1.000	0.715	1.000	0.888	4.318	0.104	Fibronectin type III|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	184	1	43805002	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1605;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01053;SOR=0;LSEQ=GAGCCAGCCAGGGGAACTTC;RSEQ=GATCAGCTGGGAGGAGCCAG;CSQ=G|missense_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|4/12||NM_005373.3:c.452A>G|NP_005364.1:p.Gln151Arg|483|452|151|Q/R|cAg/cGg|||1||EntrezGene||YES||||1:g.43805002A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1605:0:0,0:994,611:1605,0:0:2,0:35.4:1:36.4:1:1:0:60:106:1:0:0.1	0/1:184:2:1,1:117,65:182,2:0.0109:2,2:47:1:37:0:1:1.79383:60:4:0.0109:0:1
    124. 

  124. 1	43805269	43805269	T	C	intronic	MPL	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	175	1	43805269	.	T	C	37	v3;f0.01;p8;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1413;VD=2;AF=0.0014;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.06238;SOR=0.12293;LSEQ=ACCTTCTTCTGCCCCACCTC;RSEQ=TATCTCCTACCTTCAATCTT;CSQ=C|intron_variant|MODIFIER|MPL|4352|Transcript|NM_005373.3|protein_coding||4/11|NM_005373.3:c.690+29T>C|||||||||1||EntrezGene||YES||||1:g.43805269T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1413:2:0,2:493,914:1407,2:0.0014:2,0:1:0:37:0:0.54474:0:60:4:0.0015:0:1	0/1:175:2:1,1:48,124:172,2:0.0114:2,2:40.5:1:37:0:0.48508:2.57:60:4:0.0123:0:1
    125. 

  125. 1	43805650	43805650	G	A	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon5:c.G706A:p.A236T	.	.	.	.	.	.	.	.	.	.	.	0.303	0.143	T	0.001	0.126	B	0.002	0.080	B	0.394	0.045	N	1	0.090	N	0	0.065	N	-1.39	0.804	T	-0.17	0.096	N	0.013	0.003	-0.874	0.503	T	0.240	0.608	T	0.021	0.443	T	1.023	0.192	10.79	0.961	0.282	0.094	0.150	N	c	-0.787	-0.677	0.296	0.191	0.487	0.133	0	2.8	0.317	1.318	0.330	1.048	0.713	0.069	0.218	0.321	0.241	4.571	0.115	Fibronectin type III|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	150	1	43805650	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=967;VD=1;AF=0.001;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04903;SOR=0.07692;LSEQ=CCAAGGCTTCAGCTCTGACA;RSEQ=CAGAGGGTGGAAGCTGCCTC;CSQ=A|missense_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|5/12||NM_005373.3:c.706G>A|NP_005364.1:p.Ala236Thr|737|706|236|A/T|Gca/Aca|||1||EntrezGene||YES||||1:g.43805650G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:967:1:1,0:563,403:966,1:0.001:2,0:26:0:37:0:1:0:60:2:0.001:0:1	0/1:150:2:1,1:95,53:148,2:0.0133:2,2:25.5:1:37:0:1:1.78501:60:4:0.0133:0:1
    126. 

  126. 1	43805659	43805659	G	A	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon5:c.G715A:p.G239R	.	.	.	.	.	.	.	.	.	.	.	0.01	0.564	D	0.999	0.764	D	0.946	0.666	D	0.264	0.152	N	0.774	0.294	N	1.91	0.513	L	-1.93	0.849	D	-0.99	0.262	N	0.325	0.405	0.204	0.860	D	0.691	0.893	D	0.059	0.676	D	2.150	0.320	17.18	0.999	0.982	0.842	0.430	D	c	0.448	0.415	0.998	0.361	0.487	0.133	0	4.66	0.577	1.343	0.333	0.998	0.613	0.993	0.376	0.765	0.326	10.355	0.429	Fibronectin type III|Immunoglobulin-like fold	.	.	ID=COSV100991634;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129152649	SKCM-US|1|466|0.00214592	0.25	37	154	1	43805659	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1038;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0166;SOR=0;LSEQ=CAGCTCTGACAGCAGAGGGT;RSEQ=GAAGCTGCCTCATCTCAGGA;CSQ=A|missense_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|5/12||NM_005373.3:c.715G>A|NP_005364.1:p.Gly239Arg|746|715|239|G/R|Gga/Aga|COSV100991634||1||EntrezGene||YES||||1:g.43805659G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1038:0:0,0:584,454:1038,0:0:2,0:36.9:1:36.7:1:1:0:60:172:1:0:0.1	0/1:154:2:1,1:96,56:152,2:0.013:2,2:39:1:37:0:1:1.70793:60:4:0.013:0:1
    127. 

  127. 1	43814491	43814491	C	A	intronic	MPL	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	14	1	43814491	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=158;VD=2;AF=0.0127;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.8434;SOR=inf;LSEQ=ATCGAAGCCCCGACGCCGGG;RSEQ=CACCGCACGCTTCTTTGCTC;CSQ=A|intron_variant|MODIFIER|MPL|4352|Transcript|NM_005373.3|protein_coding||8/11|NM_005373.3:c.1309-23C>A|||||||||1||EntrezGene||YES||||1:g.43814491C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:158:2:1,1:109,47:156,2:0.0127:2,2:42:1:37:0:0.51665:2.30539:60:4:0.0127:0:1	0/0:14:0:0,0:13,1:14,0:0:1,0:26.2:1:37:0:1:0:60:28:1:0:0.1
    128. 

  128. 1	43815029	43815029	A	G	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon10:c.A1564G:p.R522G	.	.	.	.	.	.	.	.	.	.	.	0.008	0.912	D	0.919	0.715	P	0.395	0.759	B	0.143	0.029	N	1	0.810	D	2.135	0.597	M	-1.86	0.853	D	-3.2	0.647	D	0.551	0.647	-0.239	0.767	T	0.747	0.914	D	0.519	0.954	D	5.299	0.717	25.7	0.998	0.921	0.867	0.457	D	c	0.369	0.385	1.000	0.747	0.0	0.000	3	4.93	0.643	4.646	0.609	1.062	0.847	1.000	0.715	0.972	0.466	10.988	0.466	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	109	1	43815029	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1095;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00813;SOR=0;LSEQ=GGCAGTTTCCTGCACACTAC;RSEQ=GGTACCGCCCCCGCCAGGCA;CSQ=G|missense_variant&splice_region_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|10/12||NM_005373.3:c.1564A>G|NP_005364.1:p.Arg522Gly|1595|1564|522|R/G|Agg/Ggg|||1||EntrezGene||YES||||1:g.43815029A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1095:0:0,0:495,584:1079,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:109:2:1,1:52,53:105,2:0.0183:2,2:43:1:37:0:1:1.02:60:4:0.0225:0:4.5
    129. 

  129. 1	43818344	43818344	C	A	exonic	MPL	.	synonymous SNV	MPL:NM_005373:exon12:c.C1809A:p.P603P	0.0001	.	.	.	.	.	.	.	.	rs374553815	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	173	1	43818344	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1673;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00874;SOR=0;LSEQ=TCTTGCCTGGGGACCATGCC;RSEQ=CTGTCTGTGTGCCCACCCAT;CSQ=A|synonymous_variant|LOW|MPL|4352|Transcript|NM_005373.3|protein_coding|12/12||NM_005373.3:c.1809C>A|NP_005364.1:p.Pro603%3D|1840|1809|603|P|ccC/ccA|rs374553815||1||EntrezGene||YES||||1:g.43818344C>A||||||||||0.0001163|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1673:0:0,0:801,872:1673,0:0:2,0:37:1:36.6:1:1:0:60:151.091:1:0:0.1	0/1:173:2:1,1:81,90:171,2:0.0116:2,2:39:1:37:0:1:1.11:60:4:0.0116:0:1
    130. 

  130. 1	43818396	43818396	A	G	exonic	MPL	.	nonsynonymous SNV	MPL:NM_005373:exon12:c.A1861G:p.I621V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.803	0.537	P	0.847	0.647	P	.	.	.	0.820	0.289	N	2.135	0.597	M	-1.74	0.834	D	-0.25	0.110	N	0.248	0.303	0.213	0.861	D	0.606	0.860	D	0.286	0.904	D	3.397	0.467	23.0	0.996	0.744	0.908	0.519	D	c	0.222	0.107	1.000	0.480	0.554	0.283	0	3.43	0.382	4.573	0.604	1.015	0.643	1.000	0.715	0.907	0.385	9.334	0.370	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	161	1	43818396	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1577;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00853;SOR=0;LSEQ=GGTCCTGCTGTACCACCCAC;RSEQ=TTGCCAACCATTCCTACCTA;CSQ=G|missense_variant|MODERATE|MPL|4352|Transcript|NM_005373.3|protein_coding|12/12||NM_005373.3:c.1861A>G|NP_005364.1:p.Ile621Val|1892|1861|621|I/V|Att/Gtt|||1||EntrezGene||YES||||1:g.43818396A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1577:0:0,0:731,846:1577,0:0:2,0:37.2:1:35.7:1:1:0:60:40.5:1:0:0.1	0/1:161:2:1,1:69,89:158,2:0.0124:2,2:29:1:37:0:1:1.29:60:4:0.0131:0:1
    131. 

  131. 1	45796846	45796846	G	T	intronic	MUTYH	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	236	1	45796846	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1629;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.002;SOR=0;LSEQ=AGTACAACAAAGACAACAAA;RSEQ=GTAGTGCCTTTTTCATGGCG;CSQ=T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048171.2|protein_coding||14/15|NM_001048171.2:c.1392+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048172.2|protein_coding||14/15|NM_001048172.2:c.1395+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048173.2|protein_coding||14/15|NM_001048173.2:c.1392+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048174.2|protein_coding||14/15|NM_001048174.2:c.1392+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001128425.2|protein_coding||14/15|NM_001128425.2:c.1476+8C>A|||||||||-1||EntrezGene||YES||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293190.2|protein_coding||14/15|NM_001293190.2:c.1437+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293191.2|protein_coding||14/15|NM_001293191.2:c.1425+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||14/15|NM_001293192.2:c.1116+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293195.2|protein_coding||15/16|NM_001293195.2:c.1392+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||14/15|NM_001293196.2:c.1116+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001350650.2|protein_coding||13/14|NM_001350650.2:c.1047+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||13/14|NM_001350651.2:c.1047+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_012222.3|protein_coding||14/15|NM_012222.3:c.1467+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding|||||||||||2464|1||EntrezGene||YES||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|MUTYH|4595|Transcript|NR_146882.2|misc_RNA||14/16|NR_146882.2:n.1620+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||,T|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|MUTYH|4595|Transcript|NR_146883.2|misc_RNA||13/15|NR_146883.2:n.1469+8C>A|||||||||-1||EntrezGene||||||1:g.45796846G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1629:0:0,0:1145,484:1629,0:0:2,0:28.7:1:36.1:1:1:0:60:64.16:1:0:0.1	0/1:236:3:1,2:166,67:233,3:0.0127:2,2:51.7:1:28.3:1:0.20536:4.91663:60:2:0.0087:0:2
    132. 

  132. 1	45797156	45797156	A	T	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001350650:exon12:c.T830A:p.L277Q,MUTYH:NM_001350651:exon12:c.T830A:p.L277Q,MUTYH:NM_001048171:exon13:c.T1217A:p.L406Q,MUTYH:NM_001048172:exon13:c.T1178A:p.L393Q,MUTYH:NM_001048173:exon13:c.T1175A:p.L392Q,MUTYH:NM_001048174:exon13:c.T1175A:p.L392Q,MUTYH:NM_001128425:exon13:c.T1259A:p.L420Q,MUTYH:NM_001293190:exon13:c.T1220A:p.L407Q,MUTYH:NM_001293191:exon13:c.T1208A:p.L403Q,MUTYH:NM_001293192:exon13:c.T899A:p.L300Q,MUTYH:NM_001293196:exon13:c.T899A:p.L300Q,MUTYH:NM_012222:exon13:c.T1250A:p.L417Q,MUTYH:NM_001293195:exon14:c.T1175A:p.L392Q	.	.	.	.	.	.	.	.	.	.	.	0.005	0.654	D	0.999	0.764	D	0.999	0.916	D	0.000	0.843	D	1.000	0.810	D	2.62	0.769	M	-2.82	0.912	D	-2.7	0.585	D	0.862	0.854	0.921	0.960	D	0.858	0.953	D	0.377	0.929	D	5.247	0.709	25.6	0.995	0.701	0.998	0.996	D	c	0.612	0.609	1.000	0.747	0.672	0.522	0	5.4	0.779	6.753	0.745	1.199	0.960	1.000	0.715	0.918	0.393	15.435	0.748	MutY, C-terminal|NUDIX hydrolase domain|NUDIX hydrolase domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	158	1	45797156	.	A	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1550;VD=0;AF=0;SHIFT3=4;MSI=3;MSILEN=1;SSF=0.00851;SOR=0;LSEQ=AACGCTGTAGTTCCTGCAGC;RSEQ=GGGCCTTGCGCTGAAGCTGC;CSQ=T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|13/16||NM_001048171.2:c.1175T>A|NP_001041636.2:p.Leu392Gln|1403|1175|392|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|13/16||NM_001048172.2:c.1178T>A|NP_001041637.1:p.Leu393Gln|1329|1178|393|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|13/16||NM_001048173.2:c.1175T>A|NP_001041638.1:p.Leu392Gln|1326|1175|392|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|13/16||NM_001048174.2:c.1175T>A|NP_001041639.1:p.Leu392Gln|1253|1175|392|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|13/16||NM_001128425.2:c.1259T>A|NP_001121897.1:p.Leu420Gln|1445|1259|420|L/Q|cTg/cAg|||-1||EntrezGene||YES||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|13/16||NM_001293190.2:c.1220T>A|NP_001280119.1:p.Leu407Gln|1406|1220|407|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|13/16||NM_001293191.2:c.1208T>A|NP_001280120.1:p.Leu403Gln|1286|1208|403|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|13/16||NM_001293192.2:c.899T>A|NP_001280121.1:p.Leu300Gln|1339|899|300|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|14/17||NM_001293195.2:c.1175T>A|NP_001280124.1:p.Leu392Gln|1403|1175|392|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|13/16||NM_001293196.2:c.899T>A|NP_001280125.1:p.Leu300Gln|1262|899|300|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|12/15||NM_001350650.2:c.830T>A|NP_001337579.1:p.Leu277Gln|1329|830|277|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|12/15||NM_001350651.2:c.830T>A|NP_001337580.1:p.Leu277Gln|1265|830|277|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|13/16||NM_012222.3:c.1250T>A|NP_036354.1:p.Leu417Gln|1436|1250|417|L/Q|cTg/cAg|||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding|||||||||||2774|1||EntrezGene||YES||||1:g.45797156A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|13/17||NR_146882.2:n.1403T>A||1403|||||||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|12/16||NR_146883.2:n.1252T>A||1252|||||||-1||EntrezGene||||||1:g.45797156A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1550:0:0,0:608,942:1550,0:0:2,0:35.8:1:36.3:1:1:0:60:118.231:1:0:0.9	0/1:158:2:1,1:56,100:156,2:0.0127:2,2:67.5:1:37:0:1:1.78:60:4:0.0127:0:4
    133. 

  133. 1	45797348	45797348	G	A	exonic	MUTYH	.	stopgain	MUTYH:NM_001350650:exon11:c.C742T:p.Q248X,MUTYH:NM_001350651:exon11:c.C742T:p.Q248X,MUTYH:NM_001048171:exon12:c.C1129T:p.Q377X,MUTYH:NM_001048172:exon12:c.C1090T:p.Q364X,MUTYH:NM_001048173:exon12:c.C1087T:p.Q363X,MUTYH:NM_001048174:exon12:c.C1087T:p.Q363X,MUTYH:NM_001128425:exon12:c.C1171T:p.Q391X,MUTYH:NM_001293190:exon12:c.C1132T:p.Q378X,MUTYH:NM_001293191:exon12:c.C1120T:p.Q374X,MUTYH:NM_001293192:exon12:c.C811T:p.Q271X,MUTYH:NM_001293196:exon12:c.C811T:p.Q271X,MUTYH:NM_012222:exon12:c.C1162T:p.Q388X,MUTYH:NM_001293195:exon13:c.C1087T:p.Q363X	0.	.	.	.	.	.	.	.	.	rs587783057	.	.	.	.	.	.	.	.	.	.	0.000	0.629	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.838	0.978	38	0.994	0.633	0.997	0.988	D	c	0.986	0.836	1.000	0.747	0.672	0.522	0	4.9	0.635	7.723	0.836	1.048	0.713	1.000	0.715	0.986	0.517	14.639	0.682	MutY, C-terminal|NUDIX hydrolase domain|NUDIX hydrolase domain-like;NUDIX hydrolase domain-like;NUDIX hydrolase domain|NUDIX hydrolase domain-like	.	.	ID=COSV58344049;OCCURENCE=1(large_intestine),1(skin)	166274	Carcinoma_of_colon|MYH-associated_polyposis|Hereditary_cancer-predisposing_syndrome|not_provided	MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0012041,MedGen:C1837991,OMIM:608456,Orphanet:ORPHA247798|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Pathogenic	Pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	MU58433980	MELA-AU|1|183|0.00546448	0.25	37	164	1	45797348	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1649;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00814;SOR=0;LSEQ=GGTACCTGAGTTGGGCCTCT;RSEQ=CACCAGCAGAATTTGGGCCC;CSQ=A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|12/16||NM_001048171.2:c.1087C>T|NP_001041636.2:p.Gln363Ter|1315|1087|363|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|12/16||NM_001048172.2:c.1090C>T|NP_001041637.1:p.Gln364Ter|1241|1090|364|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|12/16||NM_001048173.2:c.1087C>T|NP_001041638.1:p.Gln363Ter|1238|1087|363|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|12/16||NM_001048174.2:c.1087C>T|NP_001041639.1:p.Gln363Ter|1165|1087|363|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|12/16||NM_001128425.2:c.1171C>T|NP_001121897.1:p.Gln391Ter|1357|1171|391|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||YES||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|12/16||NM_001293190.2:c.1132C>T|NP_001280119.1:p.Gln378Ter|1318|1132|378|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|12/16||NM_001293191.2:c.1120C>T|NP_001280120.1:p.Gln374Ter|1198|1120|374|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|12/16||NM_001293192.2:c.811C>T|NP_001280121.1:p.Gln271Ter|1251|811|271|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|13/17||NM_001293195.2:c.1087C>T|NP_001280124.1:p.Gln363Ter|1315|1087|363|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|12/16||NM_001293196.2:c.811C>T|NP_001280125.1:p.Gln271Ter|1174|811|271|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|11/15||NM_001350650.2:c.742C>T|NP_001337579.1:p.Gln248Ter|1241|742|248|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|11/15||NM_001350651.2:c.742C>T|NP_001337580.1:p.Gln248Ter|1177|742|248|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|stop_gained|HIGH|MUTYH|4595|Transcript|NM_012222.3|protein_coding|12/16||NM_012222.3:c.1162C>T|NP_036354.1:p.Gln388Ter|1348|1162|388|Q/*|Cag/Tag|rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs587783057&CM053335&COSV58344049|2966|1||EntrezGene||YES||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|12/17||NR_146882.2:n.1315C>T||1315|||||rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|11/16||NR_146883.2:n.1164C>T||1164|||||rs587783057&CM053335&COSV58344049||-1||EntrezGene||||||1:g.45797348G>A|1.202e-05|0|0|0|0|0|2.652e-05|0|0|2.652e-05|gnomAD_NFE|pathogenic|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1649:0:0,0:1013,636:1649,0:0:2,0:39.2:1:36.7:1:1:0:60:182.222:1:0:0.1	0/1:164:2:1,1:102,60:162,2:0.0122:2,2:24.5:1:37:0:1:1.69418:60:4:0.0123:0:1
    134. 

  134. 1	45797505	45797505	C	G	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001350650:exon11:c.G585C:p.Q195H,MUTYH:NM_001350651:exon11:c.G585C:p.Q195H,MUTYH:NM_001048171:exon12:c.G972C:p.Q324H,MUTYH:NM_001048172:exon12:c.G933C:p.Q311H,MUTYH:NM_001048173:exon12:c.G930C:p.Q310H,MUTYH:NM_001048174:exon12:c.G930C:p.Q310H,MUTYH:NM_001128425:exon12:c.G1014C:p.Q338H,MUTYH:NM_001293190:exon12:c.G975C:p.Q325H,MUTYH:NM_001293191:exon12:c.G963C:p.Q321H,MUTYH:NM_001293192:exon12:c.G654C:p.Q218H,MUTYH:NM_001293196:exon12:c.G654C:p.Q218H,MUTYH:NM_012222:exon12:c.G1005C:p.Q335H,MUTYH:NM_001293195:exon13:c.G930C:p.Q310H	0.53	0.2584	0.2696	0.4353	0.3013	0.4143	0.2278	0.2327	0.2382	rs3219489	rs3219489	0.168	0.284	T	0.343	0.386	B	0.086	0.342	B	0.038	0.243	N	0.743	0.588	P	2.665	0.782	M	3.23	0.229	T	-1.03	0.270	N	0.056	0.088	-0.933	0.437	T	0.000	0.000	T	.	.	.	0.336	0.126	6.039	0.797	0.124	0.147	0.184	N	c	-0.583	-0.613	0.998	0.361	0.732	0.924	0	1.26	0.204	-0.265	0.086	0.935	0.490	0.000	0.063	0.732	0.317	2.473	0.043	DNA glycosylase|Helix-turn-helix, base-excision DNA repair, C-terminal	ENSG00000117450.9|ENSG00000117450.9|ENSG00000117450.9|ENSG00000236624.4|ENSG00000236624.4|ENSG00000117450.9|ENSG00000236624.4|ENSG00000070759.12|ENSG00000117450.9|ENSG00000236624.4|ENSG00000070759.12	Adipose_Subcutaneous|Artery_Tibial|Cells_Transformed_fibroblasts|Esophagus_Mucosa|Lung|Lung|Skin_Not_Sun_Exposed_Suprapubic|Testis|Thyroid|Whole_Blood|Whole_Blood	ID=COSV58343790;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),19(soft_tissue),5(prostate),1(lung)	50206	Carcinoma_of_colon|MYH-associated_polyposis|Hereditary_cancer-predisposing_syndrome|Familial_multiple_polyposis_syndrome|not_specified|none_provided|not_provided	MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0012041,MedGen:C1837991,OMIM:608456,Orphanet:ORPHA247798|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0021055,MedGen:C0032580,OMIM:PS175100,Orphanet:ORPHA733,SNOMED_CT:72900001|MedGen:CN169374|MedGen:CN235283|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	0	MU120737	ESAD-UK|1|409|0.00244499,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|5|321|0.0155763	0.25	372	239	1	45797505	.	C	G	372	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2184;VD=1136;AF=0.5201;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGAGGCAGGCACAGGTGGCA;RSEQ=TGTCCAGTGTTGGGAGCTGG;CSQ=G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|12/16||NM_001048171.2:c.930G>C|NP_001041636.2:p.Gln310His|1158|930|310|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|12/16||NM_001048172.2:c.933G>C|NP_001041637.1:p.Gln311His|1084|933|311|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|12/16||NM_001048173.2:c.930G>C|NP_001041638.1:p.Gln310His|1081|930|310|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|12/16||NM_001048174.2:c.930G>C|NP_001041639.1:p.Gln310His|1008|930|310|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|12/16||NM_001128425.2:c.1014G>C|NP_001121897.1:p.Gln338His|1200|1014|338|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||YES||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|12/16||NM_001293190.2:c.975G>C|NP_001280119.1:p.Gln325His|1161|975|325|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|12/16||NM_001293191.2:c.963G>C|NP_001280120.1:p.Gln321His|1041|963|321|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|12/16||NM_001293192.2:c.654G>C|NP_001280121.1:p.Gln218His|1094|654|218|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|13/17||NM_001293195.2:c.930G>C|NP_001280124.1:p.Gln310His|1158|930|310|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|12/16||NM_001293196.2:c.654G>C|NP_001280125.1:p.Gln218His|1017|654|218|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|11/15||NM_001350650.2:c.585G>C|NP_001337579.1:p.Gln195His|1084|585|195|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|11/15||NM_001350651.2:c.585G>C|NP_001337580.1:p.Gln195His|1020|585|195|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|12/16||NM_012222.3:c.1005G>C|NP_036354.1:p.Gln335His|1191|1005|335|Q/H|caG/caC|rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs3219489&CM083726&COSV58343790|3123|1||EntrezGene||YES||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|12/17||NR_146882.2:n.1158G>C||1158|||||rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1,G|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|11/16||NR_146883.2:n.1007G>C||1007|||||rs3219489&CM083726&COSV58343790||-1||EntrezGene||||||1:g.45797505C>G|0.29|0.263|0.4881|0.2631|0.3974|0.2205|0.2444|0.2882|0.2371|0.4881|gnomAD_AMR|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2184:1136:502,634:469,575:1044,1136:0.5201:2,2:36.7:1:36.7:1:0.76272:1.03013:60:283:0.5212:0:1.1	0/0:239:0:0,0:108,131:239,0:0:2,0:37.8:1:36.9:1:1:0:60:478:1:0:0.1
    135. 

  135. 1	45798555	45798555	T	C	intronic	MUTYH	.	.	.	0.98	0.9393	0.9665	0.9390	0.8940	0.8926	0.9731	0.9218	0.9357	rs3219487	rs3219487	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58343750;OCCURENCE=1(biliary_tract)	249965	not_specified|none_provided	MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU22808742	COCA-CN|5|321|0.0155763	0.75	420	272	1	45798555	.	T	C	420	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2810;VD=2792;AF=0.9936;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=210.583;LSEQ=TCACCCGTCAGTCCCTCTAT;RSEQ=GTTCCTATTTCCCCTACCCT;CSQ=C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048171.2|protein_coding||6/15|NM_001048171.2:c.420+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048172.2|protein_coding||6/15|NM_001048172.2:c.423+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048173.2|protein_coding||6/15|NM_001048173.2:c.420+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048174.2|protein_coding||6/15|NM_001048174.2:c.420+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001128425.2|protein_coding||6/15|NM_001128425.2:c.504+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||YES||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293190.2|protein_coding||6/15|NM_001293190.2:c.465+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293191.2|protein_coding||6/15|NM_001293191.2:c.453+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||6/15|NM_001293192.2:c.144+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293195.2|protein_coding||7/16|NM_001293195.2:c.420+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||6/15|NM_001293196.2:c.144+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding||5/14|NM_001350650.2:c.75+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||5/14|NM_001350651.2:c.75+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_012222.3|protein_coding||6/15|NM_012222.3:c.495+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs3219487&COSV58343750|4173|1||EntrezGene||YES||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant&non_coding_transcript_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA||6/16|NR_146882.2:n.648+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1,C|intron_variant&non_coding_transcript_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA||5/15|NR_146883.2:n.497+35A>G|||||||rs3219487&COSV58343750||-1||EntrezGene||||||1:g.45798555T>C|0.9262|0.9677|0.953|0.8912|0.8902|0.9777|0.9134|0.9211|0.919|0.9777|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2810:2792:1516,1276:1,1:2,2792:0.9936:2,2:33.7:1:36.7:1:1:1.19:60:213.769:0.9957:0:1.1	0/1:272:115:57,58:90,67:157,115:0.4228:2,2:35.6:1:36.7:1:0.21975:1.36525:60:114:0.4254:0:1
    136. 

  136. 1	45798995	45798995	G	A	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001048171:exon4:c.C308T:p.A103V,MUTYH:NM_001048172:exon4:c.C269T:p.A90V,MUTYH:NM_001048173:exon4:c.C266T:p.A89V,MUTYH:NM_001048174:exon4:c.C266T:p.A89V,MUTYH:NM_001128425:exon4:c.C350T:p.A117V,MUTYH:NM_001293190:exon4:c.C311T:p.A104V,MUTYH:NM_001293191:exon4:c.C299T:p.A100V,MUTYH:NM_012222:exon4:c.C341T:p.A114V,MUTYH:NM_001293195:exon5:c.C266T:p.A89V	.	.	.	.	.	.	.	.	.	.	.	0.215	0.217	T	0.044	0.238	B	0.006	0.190	B	0.000	0.491	N	1.000	0.810	D	1.395	0.354	L	3.2	0.456	T	-1.61	0.446	N	0.255	0.311	-1.087	0.061	T	0.076	0.305	T	0.010	0.261	T	0.941	0.184	10.32	0.953	0.261	0.331	0.245	N	c	-0.743	-0.697	0.992	0.328	0.707	0.730	0	1.71	0.233	1.247	0.322	0.135	0.219	0.911	0.315	0.035	0.152	5.805	0.176	DNA glycosylase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	169	1	45798995	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1583;VD=1;AF=0.0006;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.026;SOR=0.05298;LSEQ=CCAGGTCCATCTCATCTTCT;RSEQ=CCTGTCAATGCAACCCCAGA;CSQ=A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|4/16||NM_001048171.2:c.266C>T|NP_001041636.2:p.Ala89Val|494|266|89|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|4/16||NM_001048172.2:c.269C>T|NP_001041637.1:p.Ala90Val|420|269|90|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|4/16||NM_001048173.2:c.266C>T|NP_001041638.1:p.Ala89Val|417|266|89|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|4/16||NM_001048174.2:c.266C>T|NP_001041639.1:p.Ala89Val|344|266|89|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|4/16||NM_001128425.2:c.350C>T|NP_001121897.1:p.Ala117Val|536|350|117|A/V|gCa/gTa|||-1||EntrezGene||YES||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|4/16||NM_001293190.2:c.311C>T|NP_001280119.1:p.Ala104Val|497|311|104|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|4/16||NM_001293191.2:c.299C>T|NP_001280120.1:p.Ala100Val|377|299|100|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&5_prime_UTR_variant|LOW|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|4/16||NM_001293192.2:c.-11C>T||430|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|5/17||NM_001293195.2:c.266C>T|NP_001280124.1:p.Ala89Val|494|266|89|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&5_prime_UTR_variant|LOW|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|4/16||NM_001293196.2:c.-11C>T||353|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&5_prime_UTR_variant|LOW|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|4/15||NM_001350650.2:c.-6C>T||494|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&5_prime_UTR_variant|LOW|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|4/15||NM_001350651.2:c.-6C>T||430|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|4/16||NM_012222.3:c.341C>T|NP_036354.1:p.Ala114Val|527|341|114|A/V|gCa/gTa|||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding|||||||||||4613|1||EntrezGene||YES||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&non_coding_transcript_exon_variant|LOW|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|4/17||NR_146882.2:n.494C>T||494|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||,A|splice_region_variant&non_coding_transcript_exon_variant|LOW|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|4/16||NR_146883.2:n.417C>T||417|||||||-1||EntrezGene||||||1:g.45798995G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1583:1:1,0:784,798:1582,1:0.0006:2,0:12:0:37:0:0.49589:0:60:2:0.0006:0:1	0/1:169:2:1,1:74,93:167,2:0.0118:2,2:47.5:1:37:0:1:1.26:60:4:0.0119:0:1
    137. 

  137. 1	45799227	45799227	G	A	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001048171:exon3:c.C164T:p.A55V,MUTYH:NM_001048172:exon3:c.C125T:p.A42V,MUTYH:NM_001048173:exon3:c.C122T:p.A41V,MUTYH:NM_001048174:exon3:c.C122T:p.A41V,MUTYH:NM_001128425:exon3:c.C206T:p.A69V,MUTYH:NM_001293190:exon3:c.C167T:p.A56V,MUTYH:NM_001293191:exon3:c.C155T:p.A52V,MUTYH:NM_012222:exon3:c.C197T:p.A66V,MUTYH:NM_001293195:exon4:c.C122T:p.A41V	.	.	.	.	.	.	.	.	.	rs786203354	.	0.056	0.390	T	0.002	0.139	B	0.003	0.139	B	0.001	0.434	N	1	0.090	N	1.005	0.253	L	3.11	0.507	T	-1.35	0.354	N	0.065	0.203	-0.987	0.334	T	0.100	0.373	T	0.011	0.283	T	2.591	0.373	20.1	0.992	0.558	0.197	0.206	N	c	-0.640	-0.655	0.998	0.356	0.719	0.830	0	-0.19	0.125	1.490	0.350	1.048	0.713	0.015	0.189	0.604	0.289	7.299	0.254	.	.	.	.	181733	MYH-associated_polyposis|Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0012041,MedGen:C1837991,OMIM:608456,Orphanet:ORPHA247798|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	162	1	45799227	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1313;VD=1;AF=0.0008;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03338;SOR=0.06121;LSEQ=CCACCTCTTCCGGCTGCCTG;RSEQ=CCAGGCCTGCTGGGGCCCCA;CSQ=A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|3/16||NM_001048171.2:c.122C>T|NP_001041636.2:p.Ala41Val|350|122|41|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|3/16||NM_001048172.2:c.125C>T|NP_001041637.1:p.Ala42Val|276|125|42|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|3/16||NM_001048173.2:c.122C>T|NP_001041638.1:p.Ala41Val|273|122|41|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|3/16||NM_001048174.2:c.122C>T|NP_001041639.1:p.Ala41Val|200|122|41|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|3/16||NM_001128425.2:c.206C>T|NP_001121897.1:p.Ala69Val|392|206|69|A/V|gCc/gTc|rs786203354||-1||EntrezGene||YES||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|3/16||NM_001293190.2:c.167C>T|NP_001280119.1:p.Ala56Val|353|167|56|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|3/16||NM_001293191.2:c.155C>T|NP_001280120.1:p.Ala52Val|233|155|52|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||2/15|NM_001293192.2:c.-97-58C>T|||||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|4/17||NM_001293195.2:c.122C>T|NP_001280124.1:p.Ala41Val|350|122|41|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||2/15|NM_001293196.2:c.-97-58C>T|||||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|3/15||NM_001350650.2:c.-150C>T||350|||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||2/14|NM_001350651.2:c.-92-58C>T|||||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|3/16||NM_012222.3:c.197C>T|NP_036354.1:p.Ala66Val|383|197|66|A/V|gCc/gTc|rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs786203354|4845|1||EntrezGene||YES||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|3/17||NR_146882.2:n.350C>T||350|||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|3/16||NR_146883.2:n.273C>T||273|||||rs786203354||-1||EntrezGene||||||1:g.45799227G>A||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1313:1:1,0:584,727:1311,1:0.0008:2,0:14:0:37:0:0.44588:0:60:2:0.0008:0:1	0/1:162:2:1,1:71,89:160,2:0.0123:2,2:27:0:37:0:1:1.25:60:4:0.0125:0:1
    138. 

  138. 1	45799229	45799229	C	T	exonic	MUTYH	.	synonymous SNV	MUTYH:NM_001048171:exon3:c.G162A:p.L54L,MUTYH:NM_001048172:exon3:c.G123A:p.L41L,MUTYH:NM_001048173:exon3:c.G120A:p.L40L,MUTYH:NM_001048174:exon3:c.G120A:p.L40L,MUTYH:NM_001128425:exon3:c.G204A:p.L68L,MUTYH:NM_001293190:exon3:c.G165A:p.L55L,MUTYH:NM_001293191:exon3:c.G153A:p.L51L,MUTYH:NM_012222:exon3:c.G195A:p.L65L,MUTYH:NM_001293195:exon4:c.G120A:p.L40L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	472436	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	163	1	45799229	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1301;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01233;SOR=0;LSEQ=ACCTCTTCCGGCTGCCTGGC;RSEQ=AGGCCTGCTGGGGCCCCAGG;CSQ=T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|3/16||NM_001048171.2:c.120G>A|NP_001041636.2:p.Leu40%3D|348|120|40|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|3/16||NM_001048172.2:c.123G>A|NP_001041637.1:p.Leu41%3D|274|123|41|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|3/16||NM_001048173.2:c.120G>A|NP_001041638.1:p.Leu40%3D|271|120|40|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|3/16||NM_001048174.2:c.120G>A|NP_001041639.1:p.Leu40%3D|198|120|40|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|3/16||NM_001128425.2:c.204G>A|NP_001121897.1:p.Leu68%3D|390|204|68|L|ctG/ctA|rs1553130454||-1||EntrezGene||YES||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|3/16||NM_001293190.2:c.165G>A|NP_001280119.1:p.Leu55%3D|351|165|55|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|3/16||NM_001293191.2:c.153G>A|NP_001280120.1:p.Leu51%3D|231|153|51|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||2/15|NM_001293192.2:c.-97-60G>A|||||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|4/17||NM_001293195.2:c.120G>A|NP_001280124.1:p.Leu40%3D|348|120|40|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||2/15|NM_001293196.2:c.-97-60G>A|||||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|3/15||NM_001350650.2:c.-152G>A||348|||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||2/14|NM_001350651.2:c.-92-60G>A|||||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|MUTYH|4595|Transcript|NM_012222.3|protein_coding|3/16||NM_012222.3:c.195G>A|NP_036354.1:p.Leu65%3D|381|195|65|L|ctG/ctA|rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs1553130454|4847|1||EntrezGene||YES||||1:g.45799229C>T||||||||||||likely_benign||1,T|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|3/17||NR_146882.2:n.348G>A||348|||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1,T|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|3/16||NR_146883.2:n.271G>A||271|||||rs1553130454||-1||EntrezGene||||||1:g.45799229C>T||||||||||||likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1301:0:0,0:579,722:1301,0:0:2,0:37.9:1:36.3:1:1:0:60:85.733:1:0:0.1	0/1:163:2:1,1:71,90:161,2:0.0123:2,2:12:1:31:1:1:1.27:60:4:0.0123:0:2.5
    139. 

  139. 1	45799237	45799237	C	T	exonic;splicing	MUTYH;MUTYH	NM_001293190:exon3:c.158-1G>A;NM_001048172:exon3:c.116-1G>A	nonsynonymous SNV	MUTYH:NM_001128425:exon3:c.G196A:p.A66T,MUTYH:NM_001293191:exon3:c.G145A:p.A49T,MUTYH:NM_012222:exon3:c.G187A:p.A63T	.	.	.	.	.	.	.	.	.	rs1064793421	.	0.114	0.318	T	0.003	0.102	B	0.005	0.104	B	0.172	0.031	N	1	0.230	N	0.55	0.145	N	3.23	0.453	T	-0.28	0.121	N	0.051	0.191	-1.052	0.139	T	0.098	0.367	T	0.002	0.041	T	0.504	0.142	7.462	0.731	0.099	0.176	0.197	N	c	-0.886	-0.872	0.998	0.364	0.707	0.730	0	1.6	0.226	0.115	0.153	-0.328	0.075	0.061	0.216	0.050	0.164	5.546	0.162	.	.	.	.	405208	MYH-associated_polyposis|Hereditary_cancer-predisposing_syndrome|not_provided	MONDO:MONDO:0012041,MedGen:C1837991,OMIM:608456,Orphanet:ORPHA247798|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	162	1	45799237	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1245;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01318;SOR=0;LSEQ=CGGCTGCCTGGCCAGGCCTG;RSEQ=TGGGGCCCCAGGACACTCAG;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048171.2|protein_coding||2/15|NM_001048171.2:c.116-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_acceptor_variant|HIGH|MUTYH|4595|Transcript|NM_001048172.2|protein_coding||2/15|NM_001048172.2:c.116-1G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048173.2|protein_coding||2/15|NM_001048173.2:c.116-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048174.2|protein_coding||2/15|NM_001048174.2:c.116-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|3/16||NM_001128425.2:c.196G>A|NP_001121897.1:p.Ala66Thr|382|196|66|A/T|Gca/Aca|rs1064793421||-1||EntrezGene||YES||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_acceptor_variant|HIGH|MUTYH|4595|Transcript|NM_001293190.2|protein_coding||2/15|NM_001293190.2:c.158-1G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|3/16||NM_001293191.2:c.145G>A|NP_001280120.1:p.Ala49Thr|223|145|49|A/T|Gca/Aca|rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||2/15|NM_001293192.2:c.-97-68G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293195.2|protein_coding||3/16|NM_001293195.2:c.116-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||2/15|NM_001293196.2:c.-97-68G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001350650.2|protein_coding||2/14|NM_001350650.2:c.-156-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||2/14|NM_001350651.2:c.-92-68G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|3/16||NM_012222.3:c.187G>A|NP_036354.1:p.Ala63Thr|373|187|63|A/T|Gca/Aca|rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|downstream_gene_variant|MODIFIER|HPDL|84842|Transcript|NM_032756.4|protein_coding||||||||||rs1064793421|4855|1||EntrezGene||YES||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|MUTYH|4595|Transcript|NR_146882.2|misc_RNA||2/16|NR_146882.2:n.344-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|MUTYH|4595|Transcript|NR_146883.2|misc_RNA||2/15|NR_146883.2:n.267-4G>A|||||||rs1064793421||-1||EntrezGene||||||1:g.45799237C>T||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1245:0:0,0:524,721:1245,0:0:2,0:37.7:1:36.7:1:1:0:60:414:1:0:0.1	0/1:162:2:1,1:69,91:160,2:0.0123:2,2:54.5:1:37:0:1:1.32:60:4:0.0127:0:1
    140. 

  140. 1	45800131	45800131	G	A	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001048171:exon2:c.C89T:p.A30V,MUTYH:NM_001048172:exon2:c.C47T:p.A16V,MUTYH:NM_001048173:exon2:c.C47T:p.A16V,MUTYH:NM_001048174:exon2:c.C47T:p.A16V,MUTYH:NM_001128425:exon2:c.C89T:p.A30V,MUTYH:NM_001293190:exon2:c.C89T:p.A30V,MUTYH:NM_001293191:exon2:c.C47T:p.A16V,MUTYH:NM_012222:exon2:c.C89T:p.A30V,MUTYH:NM_001293195:exon3:c.C47T:p.A16V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.004	0.316	B	0.018	0.250	B	0.080	0.209	N	1	0.090	N	1.625	0.417	L	2.22	0.588	T	-0.44	0.734	N	0.115	0.301	-0.294	0.752	T	0.579	0.849	D	0.022	0.450	T	1.951	0.295	15.90	0.994	0.642	0.093	0.149	N	c	-0.598	-0.626	1.000	0.747	0.719	0.830	0	1.42	0.214	0.314	0.190	0.143	0.228	0.000	0.063	0.584	0.286	6.093	0.191	NUDIX hydrolase domain	.	.	.	628107	MYH-associated_polyposis	MONDO:MONDO:0012041,MedGen:C1837991,OMIM:608456,Orphanet:ORPHA247798	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	116	1	45800131	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1789;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00368;SOR=0;LSEQ=GCCTCCCTTCCTGGCTGGCT;RSEQ=CCTGCTTCCTGTGACCACTT;CSQ=A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|2/16||NM_001048171.2:c.47C>T|NP_001041636.2:p.Ala16Val|275|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|2/16||NM_001048172.2:c.47C>T|NP_001041637.1:p.Ala16Val|198|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|2/16||NM_001048173.2:c.47C>T|NP_001041638.1:p.Ala16Val|198|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|2/16||NM_001048174.2:c.47C>T|NP_001041639.1:p.Ala16Val|125|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|2/16||NM_001128425.2:c.89C>T|NP_001121897.1:p.Ala30Val|275|89|30|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||YES||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|2/16||NM_001293190.2:c.89C>T|NP_001280119.1:p.Ala30Val|275|89|30|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|2/16||NM_001293191.2:c.47C>T|NP_001280120.1:p.Ala16Val|125|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|2/16||NM_001293192.2:c.-166C>T||275|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|3/17||NM_001293195.2:c.47C>T|NP_001280124.1:p.Ala16Val|275|47|16|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|2/16||NM_001293196.2:c.-166C>T||198|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|2/15||NM_001350650.2:c.-225C>T||275|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|2/15||NM_001350651.2:c.-161C>T||275|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|2/16||NM_012222.3:c.89C>T|NP_036354.1:p.Ala30Val|275|89|30|A/V|gCa/gTa|rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|2/17||NR_146882.2:n.275C>T||275|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|2/16||NR_146883.2:n.198C>T||198|||||rs1570465480||-1||EntrezGene||||||1:g.45800131G>A||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1789:0:0,0:899,889:1788,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:116:2:1,1:61,53:114,2:0.0172:2,2:29:1:37:0:1:1.14954:60:4:0.0174:0:1
    141. 

  141. 1	45800141	45800141	T	A	exonic	MUTYH	.	nonsynonymous SNV	MUTYH:NM_001048171:exon2:c.A79T:p.R27W,MUTYH:NM_001048172:exon2:c.A37T:p.R13W,MUTYH:NM_001048173:exon2:c.A37T:p.R13W,MUTYH:NM_001048174:exon2:c.A37T:p.R13W,MUTYH:NM_001128425:exon2:c.A79T:p.R27W,MUTYH:NM_001293190:exon2:c.A79T:p.R27W,MUTYH:NM_001293191:exon2:c.A37T:p.R13W,MUTYH:NM_012222:exon2:c.A79T:p.R27W,MUTYH:NM_001293195:exon3:c.A37T:p.R13W	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.995	0.689	D	0.847	0.619	P	0.012	0.292	N	1.000	0.090	N	1.7	0.440	L	1.96	0.682	T	-0.76	0.965	N	0.384	0.524	0.019	0.826	D	0.743	0.912	D	0.072	0.716	D	5.917	0.812	27.5	0.996	0.763	0.329	0.245	N	c	-0.016	-0.155	1.000	0.747	0.719	0.830	0	1.95	0.250	0.548	0.229	1.061	0.807	0.206	0.242	0.544	0.278	4.474	0.111	NUDIX hydrolase domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	118	1	45800141	.	T	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1803;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.00374;SOR=0;LSEQ=CTGGCTGGCTGCCTGCTTCC;RSEQ=GTGACCACTTCCCACGGCTG;CSQ=A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048171.2|protein_coding|2/16||NM_001048171.2:c.37A>T|NP_001041636.2:p.Arg13Trp|265|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|2/16||NM_001048172.2:c.37A>T|NP_001041637.1:p.Arg13Trp|188|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|2/16||NM_001048173.2:c.37A>T|NP_001041638.1:p.Arg13Trp|188|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|2/16||NM_001048174.2:c.37A>T|NP_001041639.1:p.Arg13Trp|115|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001128425.2|protein_coding|2/16||NM_001128425.2:c.79A>T|NP_001121897.1:p.Arg27Trp|265|79|27|R/W|Agg/Tgg|||-1||EntrezGene||YES||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293190.2|protein_coding|2/16||NM_001293190.2:c.79A>T|NP_001280119.1:p.Arg27Trp|265|79|27|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|2/16||NM_001293191.2:c.37A>T|NP_001280120.1:p.Arg13Trp|115|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding|2/16||NM_001293192.2:c.-176A>T||265|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|3/17||NM_001293195.2:c.37A>T|NP_001280124.1:p.Arg13Trp|265|37|13|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|2/16||NM_001293196.2:c.-176A>T||188|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding|2/15||NM_001350650.2:c.-235A>T||265|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding|2/15||NM_001350651.2:c.-171A>T||265|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|missense_variant|MODERATE|MUTYH|4595|Transcript|NM_012222.3|protein_coding|2/16||NM_012222.3:c.79A>T|NP_036354.1:p.Arg27Trp|265|79|27|R/W|Agg/Tgg|||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA|2/17||NR_146882.2:n.265A>T||265|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|2/16||NR_146883.2:n.188A>T||188|||||||-1||EntrezGene||||||1:g.45800141T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1803:0:0,0:866,935:1801,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:118:2:1,1:59,57:116,2:0.0169:2,2:30:0:37:0:1:1.03479:60:4:0.0171:0:1
    142. 

  142. 1	45805566	45805566	G	C	UTR5	TOE1	NM_025077:c.-359G>C	.	.	1.	0.9899	0.9971	0.9881	0.9867	1	0.9931	0.9843	0.9867	rs3219468	rs3219468	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	360	97	1	45805566	.	G	C	360	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=920;VD=890;AF=0.9674;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.41018;SOR=1.27565;LSEQ=ACCCAGCCACCCCACTACCC;RSEQ=CTACCCGCGGCCCACGCTGA;CSQ=C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048171.2|protein_coding||1/15|NM_001048171.2:c.-7+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048172.2|protein_coding||1/15|NM_001048172.2:c.-7+82C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048173.2|protein_coding||1/15|NM_001048173.2:c.-7+82C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|splice_donor_5th_base_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001048174.2|protein_coding||1/15|NM_001048174.2:c.-7+5C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001128425.2|protein_coding||1/15|NM_001128425.2:c.36+325C>G|||||||rs3219468||-1||EntrezGene||YES||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293190.2|protein_coding||1/15|NM_001293190.2:c.36+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|splice_donor_5th_base_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293191.2|protein_coding||1/15|NM_001293191.2:c.-7+5C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||1/15|NM_001293192.2:c.-219+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|splice_donor_5th_base_variant&intron_variant|LOW|MUTYH|4595|Transcript|NM_001293195.2|protein_coding||1/16|NM_001293195.2:c.-157+5C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding||1/15|NM_001293196.2:c.-219+82C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|downstream_gene_variant|MODIFIER|TESK2|10420|Transcript|NM_001320800.2|protein_coding||||||||||rs3219468|3989|-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding||1/14|NM_001350650.2:c.-278+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||1/14|NM_001350651.2:c.-214+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|downstream_gene_variant|MODIFIER|TESK2|10420|Transcript|NM_007170.3|protein_coding||||||||||rs3219468|3989|-1||EntrezGene||YES||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_012222.3|protein_coding||1/15|NM_012222.3:c.36+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|upstream_gene_variant|MODIFIER|TOE1|114034|Transcript|NM_025077.4|protein_coding||||||||||rs3219468|276|1||EntrezGene||YES||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA||1/16|NR_146882.2:n.222+325C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||,C|intron_variant&non_coding_transcript_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA||1/15|NR_146883.2:n.145+82C>G|||||||rs3219468||-1||EntrezGene||||||1:g.45805566G>C|0.9897|0.9966|0.9914|0.994|1|0.991|0.9838|0.9863|0.9961|1|EAS&gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:920:890:452,438:0,0:0,890:0.9674:0,2:41.5:1:36.8:1:1:0:60:221.5:0.9672:0:1.1	1/1:97:93:60,33:0,0:0,93:0.9588:0,2:42.2:1:36.9:1:1:0:60:186:0.9588:0:1.2
    143. 

  143. 1	45805820	45805820	C	A	UTR5	TOE1	NM_025077:c.-105C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	158	1	45805820	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1398;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01025;SOR=0;LSEQ=AGTTCGACCCATCGGCGACC;RSEQ=GACGGCGAGACCCCGCCCCA;CSQ=A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048171.2|protein_coding||1/15|NM_001048171.2:c.-7+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048172.2|protein_coding|||||||||||28|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048173.2|protein_coding|||||||||||28|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001048174.2|protein_coding|||||||||||178|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001128425.2|protein_coding||1/15|NM_001128425.2:c.36+71G>T|||||||||-1||EntrezGene||YES||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293190.2|protein_coding||1/15|NM_001293190.2:c.36+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293191.2|protein_coding|||||||||||178|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293192.2|protein_coding||1/15|NM_001293192.2:c.-219+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293195.2|protein_coding|||||||||||178|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NM_001293196.2|protein_coding|||||||||||28|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|downstream_gene_variant|MODIFIER|TESK2|10420|Transcript|NM_001320800.2|protein_coding|||||||||||3735|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350650.2|protein_coding||1/14|NM_001350650.2:c.-278+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_001350651.2|protein_coding||1/14|NM_001350651.2:c.-214+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|downstream_gene_variant|MODIFIER|TESK2|10420|Transcript|NM_007170.3|protein_coding|||||||||||3735|-1||EntrezGene||YES||||1:g.45805820C>A||||||||||||||,A|intron_variant|MODIFIER|MUTYH|4595|Transcript|NM_012222.3|protein_coding||1/15|NM_012222.3:c.36+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|TOE1|114034|Transcript|NM_025077.4|protein_coding|||||||||||22|1||EntrezGene||YES||||1:g.45805820C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|MUTYH|4595|Transcript|NR_146882.2|misc_RNA||1/16|NR_146882.2:n.222+71G>T|||||||||-1||EntrezGene||||||1:g.45805820C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|MUTYH|4595|Transcript|NR_146883.2|misc_RNA|||||||||||28|-1||EntrezGene||||||1:g.45805820C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1398:0:0,0:847,551:1398,0:0:2,0:36.9:1:36.7:1:1:0:60:698:1:0:0.1	0/1:158:2:1,1:88,68:156,2:0.0127:2,2:20:0:37:0:1:1.29197:60:4:0.0127:0:1
    144. 

  144. 1	46740312	46740312	G	A	exonic	RAD54L	.	nonsynonymous SNV	RAD54L:NM_003579:exon16:c.G1792A:p.A598T,RAD54L:NM_001142548:exon17:c.G1792A:p.A598T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.995	0.971	D	0.000	0.843	D	1	0.810	D	2.84	0.828	M	-0.84	0.743	T	-3.65	0.699	D	0.68	0.701	0.341	0.882	D	0.615	0.864	D	0.073	0.717	D	7.006	0.937	33	0.999	0.998	0.972	0.731	D	c	0.895	0.856	1.000	0.747	0.672	0.522	0	5.19	0.713	9.633	0.978	1.038	0.658	1.000	0.715	0.999	0.750	18.777	0.918	Helicase, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	0	1	46740312	.	G	A	37	v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=2;AF=0.4;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGACCCTGACTGGAACCCA;RSEQ=CCAATGATGAACAAGCCATG;CSQ=A|missense_variant|MODERATE|RAD54L|8438|Transcript|NM_001142548.2|protein_coding|17/19||NM_001142548.2:c.1792G>A|NP_001136020.1:p.Ala598Thr|1913|1792|598|A/T|Gcc/Acc|||1||EntrezGene||||||1:g.46740312G>A||||||||||||||,A|missense_variant|MODERATE|RAD54L|8438|Transcript|NM_001370766.1|protein_coding|16/18||NM_001370766.1:c.1252G>A|NP_001357695.1:p.Ala418Thr|1848|1252|418|A/T|Gcc/Acc|||1||EntrezGene||||||1:g.46740312G>A||||||||||||||,A|missense_variant|MODERATE|RAD54L|8438|Transcript|NM_003579.4|protein_coding|16/18||NM_003579.4:c.1792G>A|NP_003570.2:p.Ala598Thr|2435|1792|598|A/T|Gcc/Acc|||1||EntrezGene||YES||||1:g.46740312G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRC41|10489|Transcript|NM_006369.5|protein_coding|||||||||||2822|-1||EntrezGene||YES||||1:g.46740312G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:5:2:1,1:1,2:3,2:0.4:2,2:53:1:37:0:1:1.73:60:4:0.4:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    145. 

  145. 1	47279175	47279175	C	T	exonic	CYP4B1	.	nonsynonymous SNV	CYP4B1:NM_001319162:exon3:c.C28T:p.R10W,CYP4B1:NM_001319163:exon3:c.C28T:p.R10W,CYP4B1:NM_001319161:exon4:c.C472T:p.R158W,CYP4B1:NM_000779:exon5:c.C517T:p.R173W,CYP4B1:NM_001099772:exon5:c.C517T:p.R173W	0.26	0.1445	0.1886	0.1301	0.1093	0.1963	0.1113	0.1229	0.1388	rs4646487	rs4646487	0.01	0.586	D	0.991	0.715	D	0.394	0.568	B	0.167	0.031	N	1.000	0.090	P	2.08	0.576	M	-0.37	0.689	T	-1.75	0.526	N	0.091	0.383	-1.098	0.043	T	0.001	0.003	T	.	.	.	5.046	0.679	25.2	0.998	0.894	0.105	0.158	N	c	-0.317	-0.481	0.000	0.038	0.554	0.246	0	0.775	0.176	0.973	0.288	-0.027	0.127	0.191	0.240	0.361	0.248	5.297	0.150	.	.	.	ID=COSV54721701;OCCURENCE=1(liver),1(large_intestine),2(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU9798988	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|3|170|0.0176471,COCA-CN|1|321|0.00311526	0.25	371	311	1	47279175	.	C	T	371	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=3004;VD=1414;AF=0.4707;SHIFT3=3;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=ACAAGTGGGAAGAGAAAGCT;RSEQ=GGGAGGGTAAGTCCTTTGAC;CSQ=T|missense_variant|MODERATE|CYP4B1|1580|Transcript|NM_000779.4|protein_coding|5/12||NM_000779.4:c.517C>T|NP_000770.2:p.Arg173Trp|553|517|173|R/W|Cgg/Tgg|rs4646487&COSV54721701||1||EntrezGene||||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1,T|missense_variant|MODERATE|CYP4B1|1580|Transcript|NM_001099772.2|protein_coding|5/12||NM_001099772.2:c.517C>T|NP_001093242.1:p.Arg173Trp|553|517|173|R/W|Cgg/Tgg|rs4646487&COSV54721701||1||EntrezGene||YES||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1,T|missense_variant|MODERATE|CYP4B1|1580|Transcript|NM_001319161.2|protein_coding|4/11||NM_001319161.2:c.472C>T|NP_001306090.1:p.Arg158Trp|508|472|158|R/W|Cgg/Tgg|rs4646487&COSV54721701||1||EntrezGene||||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1,T|missense_variant|MODERATE|CYP4B1|1580|Transcript|NM_001319162.2|protein_coding|3/10||NM_001319162.2:c.28C>T|NP_001306091.1:p.Arg10Trp|366|28|10|R/W|Cgg/Tgg|rs4646487&COSV54721701||1||EntrezGene||||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1,T|missense_variant|MODERATE|CYP4B1|1580|Transcript|NM_001319163.2|protein_coding|3/10||NM_001319163.2:c.28C>T|NP_001306092.1:p.Arg10Trp|366|28|10|R/W|Cgg/Tgg|rs4646487&COSV54721701||1||EntrezGene||||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1,T|non_coding_transcript_exon_variant|MODIFIER|CYP4B1|1580|Transcript|NR_135003.2|misc_RNA|5/12||NR_135003.2:n.553C>T||553|||||rs4646487&COSV54721701||1||EntrezGene||||||1:g.47279175C>T|0.1489|0.1896|0.1247|0.106|0.1978|0.114|0.1231|0.1328|0.2625|0.2625|gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3004:1414:798,616:862,724:1586,1414:0.4707:2,2:38.1:1:35.5:1:0.25437:1.09:60:29.739:0.4637:0:1.1	0/0:311:0:0,0:166,145:311,0:0:2,0:36.2:1:36.8:1:1:0:60:622:1:0:0
    146. 

  146. 1	59248124	59248126	GCT	-	exonic	JUN	.	nonframeshift deletion	JUN:NM_002228:exon1:c.617_619del:p.Q206del	0.011	3.239e-05	0	0	0	0	0	6.681e-05	0	rs781350994	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU121066967	GACA-JP|2|585|0.0034188	0.5	111	112	1	59248123	.	GGCT	G	111	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=619;VD=8;AF=0.0129;SHIFT3=13;MSI=5;MSILEN=3;SSF=0.23001;SOR=0.47633;LSEQ=GCTGGGGCAGGTGGTGCGGC;RSEQ=GCTGCTGCTGCTGGGGTTGC;CSQ=-|inframe_deletion|MODERATE|JUN|3725|Transcript|NM_002228.4|protein_coding|1/1||NM_002228.4:c.617_619del|NP_002219.1:p.Gln206del|1594-1596|617-619|206-207|QP/P|cAGCcg/ccg|rs748534142||-1||EntrezGene||YES||||1:g.59248137_59248139del|0.001006|0.0005632|0.0007579|0.00147|0.0005665|0.002336|0.0008779|0.001429|0.00121|0.002336|gnomAD_FIN|||,-|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034014.1|lncRNA||||||||||rs748534142|2697|1||EntrezGene||YES||||1:g.59248137_59248139del|0.001006|0.0005632|0.0007579|0.00147|0.0005665|0.002336|0.0008779|0.001429|0.00121|0.002336|gnomAD_FIN|||,-|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034015.1|lncRNA||||||||||rs748534142|2697|1||EntrezGene||||||1:g.59248137_59248139del|0.001006|0.0005632|0.0007579|0.00147|0.0005665|0.002336|0.0008779|0.001429|0.00121|0.002336|gnomAD_FIN|||,-|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_108106.1|lncRNA||||||||||rs748534142|2697|1||EntrezGene||||||1:g.59248137_59248139del|0.001006|0.0005632|0.0007579|0.00147|0.0005665|0.002336|0.0008779|0.001429|0.00121|0.002336|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:619:8:4,4:284,328:612,8:0.0129:2,2:32.4:1:37:1:1:1.15:60:16:0.013:0.0016:0	0/1:112:3:2,1:47,61:108,3:0.0268:2,2:54:1:37:0:0.58227:2.57:60:6:0.0278:0:0
    147. 

  147. 1	59248719	59248719	G	A	exonic	JUN	.	synonymous SNV	JUN:NM_002228:exon1:c.C24T:p.T8T	0.0001	3.231e-05	0	0	0	0.0006	0	0	0	rs762524747	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	68	196	1	59248719	.	G	A	68	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3184;VD=4;AF=0.0013;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.04299;SOR=0.12218;LSEQ=TTGAGGGCATCGTCATAGAA;RSEQ=GTCGTTTCCATCTTTGCAGT;CSQ=A|synonymous_variant|LOW|JUN|3725|Transcript|NM_002228.4|protein_coding|1/1||NM_002228.4:c.24C>T|NP_002219.1:p.Thr8%3D|1001|24|8|T|acC/acT|rs762524747||-1||EntrezGene||YES||||1:g.59248719G>A|1.594e-05|0|0|0|0.0002175|0|0|0|0|0.0002175|gnomAD_EAS|||,A|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034014.1|lncRNA||||||||||rs762524747|2104|1||EntrezGene||YES||||1:g.59248719G>A|1.594e-05|0|0|0|0.0002175|0|0|0|0|0.0002175|gnomAD_EAS|||,A|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034015.1|lncRNA||||||||||rs762524747|2104|1||EntrezGene||||||1:g.59248719G>A|1.594e-05|0|0|0|0.0002175|0|0|0|0|0.0002175|gnomAD_EAS|||,A|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_108106.1|lncRNA||||||||||rs762524747|2104|1||EntrezGene||||||1:g.59248719G>A|1.594e-05|0|0|0|0.0002175|0|0|0|0|0.0002175|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3184:4:0,4:1349,1830:3179,4:0.0013:2,0:12:1:34:1:0.14224:0:60:8:0.0013:0:1.8	0/1:196:2:1,1:76,118:194,2:0.0102:2,2:55:1:31:1:1:1.55:60:4:0.0102:0:2
    148. 

  148. 1	59248813	59248813	G	C	UTR5	JUN	NM_002228:c.-71C>G	.	.	1.	0.9554	0.8443	0.9893	1	1	1	0.9992	0.9969	rs2760499	rs2760499	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	368	68	1	59248813	.	G	C	368	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1060;VD=1058;AF=0.9981;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.88302;SOR=0;LSEQ=TTCGGGGCCGCAACAGGGCT;RSEQ=TGGCAAGCGGGGGACACCCG;CSQ=C|5_prime_UTR_variant|MODIFIER|JUN|3725|Transcript|NM_002228.4|protein_coding|1/1||NM_002228.4:c.-71C>G||907|||||rs2760499||-1||EntrezGene||YES||||1:g.59248813G>C||||||||||1|EAS&SAS|||,C|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034014.1|lncRNA||||||||||rs2760499|2010|1||EntrezGene||YES||||1:g.59248813G>C||||||||||1|EAS&SAS|||,C|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_034015.1|lncRNA||||||||||rs2760499|2010|1||EntrezGene||||||1:g.59248813G>C||||||||||1|EAS&SAS|||,C|upstream_gene_variant|MODIFIER|LINC01135|100131060|Transcript|NR_108106.1|lncRNA||||||||||rs2760499|2010|1||EntrezGene||||||1:g.59248813G>C||||||||||1|EAS&SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1060:1058:233,825:0,0:0,1058:0.9981:0,2:31.9:1:36.7:1:1:0:60:263.5:0.9981:0:1.1	1/1:68:68:11,57:0,0:0,68:1:0,2:32.8:1:37:0:1:0:60:136:1:0:1
    149. 

  149. 1	65304165	65304165	C	T	exonic	JAK1	.	nonsynonymous SNV	JAK1:NM_001321852:exon21:c.G2950A:p.A984T,JAK1:NM_001321856:exon21:c.G2950A:p.A984T,JAK1:NM_001321857:exon21:c.G2947A:p.A983T,JAK1:NM_002227:exon21:c.G2950A:p.A984T,JAK1:NM_001320923:exon22:c.G2950A:p.A984T,JAK1:NM_001321854:exon22:c.G2950A:p.A984T,JAK1:NM_001321855:exon22:c.G2950A:p.A984T,JAK1:NM_001321853:exon23:c.G2950A:p.A984T	.	.	.	.	.	.	.	.	.	.	.	0.23	0.183	T	0.978	0.568	D	0.664	0.511	P	.	.	.	1.000	0.548	D	1.27	0.322	L	-2.66	0.903	D	-2.65	0.567	D	0.67	0.680	0.268	0.870	D	0.677	0.888	D	0.083	0.741	D	6.078	0.837	28.2	0.999	0.943	0.934	0.579	D	c	0.559	0.590	1.000	0.747	0.706	0.609	0	5.38	0.772	2.967	0.487	0.935	0.490	0.994	0.380	0.996	0.625	19.333	0.943	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	121	1	65304165	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=98;VD=2;AF=0.0204;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.19911;SOR=inf;LSEQ=TACCTTACAAATCTGAACGG;RSEQ=ATATTTTAGCTGCTGTTTGA;CSQ=T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001320923.2|protein_coding|22/26||NM_001320923.2:c.2950G>A|NP_001307852.1:p.Ala984Thr|3167|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321852.2|protein_coding|21/25||NM_001321852.2:c.2950G>A|NP_001308781.1:p.Ala984Thr|3170|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321853.2|protein_coding|23/27||NM_001321853.2:c.2950G>A|NP_001308782.1:p.Ala984Thr|3429|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||YES||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321854.2|protein_coding|22/26||NM_001321854.2:c.2950G>A|NP_001308783.1:p.Ala984Thr|3345|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321855.2|protein_coding|22/26||NM_001321855.2:c.2950G>A|NP_001308784.1:p.Ala984Thr|3328|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321856.2|protein_coding|21/25||NM_001321856.2:c.2950G>A|NP_001308785.1:p.Ala984Thr|3083|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_001321857.2|protein_coding|21/25||NM_001321857.2:c.2947G>A|NP_001308786.1:p.Ala983Thr|3241|2947|983|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||,T|missense_variant|MODERATE|JAK1|3716|Transcript|NM_002227.4|protein_coding|21/25||NM_002227.4:c.2950G>A|NP_002218.2:p.Ala984Thr|3244|2950|984|A/T|Gcc/Acc|||-1||EntrezGene||||||1:g.65304165C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:98:2:2,0:69,27:96,2:0.0204:2,0:8.5:1:37:0:1:0:60:4:0.0208:0:1	0/0:121:0:0,0:84,37:121,0:0:2,0:33.2:1:36.3:1:1:0:60:59.5:1:0:0
    150. 

  150. 1	65304319	65304319	A	C	intronic	JAK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	17	133	1	65304319	.	A	C	17	f0.01;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=683;VD=3;AF=0.0044;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.18877;SOR=0.28959;LSEQ=TGAGGCTGCCAAATGAGGGA;RSEQ=CCATGGGAGAGGCAAGGGCA;CSQ=C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001320923.2|protein_coding||21/25|NM_001320923.2:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321852.2|protein_coding||20/24|NM_001321852.2:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321853.2|protein_coding||22/26|NM_001321853.2:c.2843-47T>G|||||||||-1||EntrezGene||YES||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321854.2|protein_coding||21/25|NM_001321854.2:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321855.2|protein_coding||21/25|NM_001321855.2:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321856.2|protein_coding||20/24|NM_001321856.2:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321857.2|protein_coding||20/24|NM_001321857.2:c.2840-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||,C|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_002227.4|protein_coding||20/24|NM_002227.4:c.2843-47T>G|||||||||-1||EntrezGene||||||1:g.65304319A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:683:3:3,0:361,319:680,3:0.0044:2,0:54.7:1:11:0:0.25216:0:60:0:0:0:1	0/1:133:2:2,0:53,78:131,2:0.015:2,0:28.5:1:25:0:0.16917:0:60:4:0.0182:0:1
    151. 

  151. 1	65311262	65311262	G	A	exonic	JAK1	.	synonymous SNV	JAK1:NM_001321852:exon15:c.C2049T:p.S683S,JAK1:NM_001321856:exon15:c.C2049T:p.S683S,JAK1:NM_001321857:exon15:c.C2046T:p.S682S,JAK1:NM_002227:exon15:c.C2049T:p.S683S,JAK1:NM_001320923:exon16:c.C2049T:p.S683S,JAK1:NM_001321854:exon16:c.C2049T:p.S683S,JAK1:NM_001321855:exon16:c.C2049T:p.S683S,JAK1:NM_001321853:exon17:c.C2049T:p.S683S	0.32	0.1514	0.1953	0.1599	0.1225	0.3181	0.1246	0.1155	0.1316	rs2230587	rs2230587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61087573;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),1(urinary_tract),6(soft_tissue),1(thyroid),2(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU99745	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|5|321|0.0155763	0.75	415	223	1	65311262	.	G	A	415	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2752;VD=2748;AF=0.9985;SHIFT3=3;MSI=1;MSILEN=1;SSF=0;SOR=774.745;LSEQ=CATGGTGTGGTAAGGACATC;RSEQ=CTTTTCCGGTGCATGAAGAG;CSQ=A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001320923.2|protein_coding|16/26||NM_001320923.2:c.2049C>T|NP_001307852.1:p.Ser683%3D|2266|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321852.2|protein_coding|15/25||NM_001321852.2:c.2049C>T|NP_001308781.1:p.Ser683%3D|2269|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321853.2|protein_coding|17/27||NM_001321853.2:c.2049C>T|NP_001308782.1:p.Ser683%3D|2528|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||YES||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321854.2|protein_coding|16/26||NM_001321854.2:c.2049C>T|NP_001308783.1:p.Ser683%3D|2444|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321855.2|protein_coding|16/26||NM_001321855.2:c.2049C>T|NP_001308784.1:p.Ser683%3D|2427|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321856.2|protein_coding|15/25||NM_001321856.2:c.2049C>T|NP_001308785.1:p.Ser683%3D|2182|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_001321857.2|protein_coding|15/25||NM_001321857.2:c.2046C>T|NP_001308786.1:p.Ser682%3D|2340|2046|682|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|JAK1|3716|Transcript|NM_002227.4|protein_coding|15/25||NM_002227.4:c.2049C>T|NP_002218.2:p.Ser683%3D|2343|2049|683|S|agC/agT|rs2230587&COSV61087573||-1||EntrezGene||||||1:g.65311262G>A|0.1502|0.2029|0.1764|0.131|0.3165|0.1244|0.1141|0.1334|0.1575|0.3165|EAS&gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2752:2748:1348,1400:0,0:0,2748:0.9985:0,2:40.1:1:36.4:1:1:0:60:84.875:0.9989:0:1.1	0/1:223:104:53,51:57,62:119,104:0.4664:2,2:40.1:1:36.6:1:0.6882:1.13:60:103:0.4682:0:1.1
    152. 

  152. 1	65321179	65321179	C	A	intronic	JAK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	199	1	65321179	.	C	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1627;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.01182;SOR=0;LSEQ=GATACAGCCTGGCTCTGGCA;RSEQ=AGGGAGACGAACCTCGGGGC;CSQ=A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001320923.2|protein_coding||12/25|NM_001320923.2:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321852.2|protein_coding||11/24|NM_001321852.2:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321853.2|protein_coding||13/26|NM_001321853.2:c.1648+13G>T|||||||||-1||EntrezGene||YES||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321854.2|protein_coding||12/25|NM_001321854.2:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321855.2|protein_coding||12/25|NM_001321855.2:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321856.2|protein_coding||11/24|NM_001321856.2:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321857.2|protein_coding||11/24|NM_001321857.2:c.1645+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||,A|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_002227.4|protein_coding||11/24|NM_002227.4:c.1648+13G>T|||||||||-1||EntrezGene||||||1:g.65321179C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1627:0:0,0:941,685:1626,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:199:2:1,1:113,84:197,2:0.0101:2,2:33.5:1:37:0:1:1.34319:60:4:0.0101:0:1
    153. 

  153. 1	65321181	65321181	G	T	intronic	JAK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	201	1	65321181	.	G	T	37	v3;f0.01;pSTD;q22.5;SN1.5;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1675;VD=1;AF=0.0006;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.03186;SOR=0.05963;LSEQ=TACAGCCTGGCTCTGGCACA;RSEQ=GGAGACGAACCTCGGGGCTT;CSQ=T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001320923.2|protein_coding||12/25|NM_001320923.2:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321852.2|protein_coding||11/24|NM_001321852.2:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321853.2|protein_coding||13/26|NM_001321853.2:c.1648+11C>A|||||||||-1||EntrezGene||YES||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321854.2|protein_coding||12/25|NM_001321854.2:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321855.2|protein_coding||12/25|NM_001321855.2:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321856.2|protein_coding||11/24|NM_001321856.2:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_001321857.2|protein_coding||11/24|NM_001321857.2:c.1645+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||,T|intron_variant|MODIFIER|JAK1|3716|Transcript|NM_002227.4|protein_coding||11/24|NM_002227.4:c.1648+11C>A|||||||||-1||EntrezGene||||||1:g.65321181G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1675:1:0,1:959,715:1674,1:0.0006:2,0:52:0:11:0:0.42746:0:60:0:0:0:8	0/1:201:2:1,1:113,86:199,2:0.01:2,2:29:1:37:0:1:1.31214:60:4:0.01:0:1
    154. 

  154. 1	65323340	65323340	T	C	exonic	JAK1	.	nonsynonymous SNV	JAK1:NM_001321852:exon10:c.A1457G:p.E486G,JAK1:NM_001321856:exon10:c.A1457G:p.E486G,JAK1:NM_001321857:exon10:c.A1457G:p.E486G,JAK1:NM_002227:exon10:c.A1457G:p.E486G,JAK1:NM_001320923:exon11:c.A1457G:p.E486G,JAK1:NM_001321854:exon11:c.A1457G:p.E486G,JAK1:NM_001321855:exon11:c.A1457G:p.E486G,JAK1:NM_001321853:exon12:c.A1457G:p.E486G	.	.	.	.	.	.	.	.	.	.	.	0.313	0.139	T	0.421	0.336	B	0.107	0.296	B	.	.	.	0.996	0.429	D	1.385	0.346	L	2.05	0.207	T	-0.4	0.138	N	0.455	0.507	-0.969	0.375	T	0.011	0.041	T	0.007	0.196	T	2.750	0.391	21.1	0.994	0.603	0.908	0.520	D	c	-0.153	0.032	1.000	0.446	0.722	0.854	0	4.62	0.568	4.139	0.575	1.061	0.807	1.000	0.715	1.000	0.888	14.499	0.671	SH2 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	174	1	65323340	.	T	C	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2599;VD=2;AF=0.0008;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0216;SOR=0.06641;LSEQ=AGCCAGTGTCCTGACTGACC;RSEQ=CAGACTTCTCAAAGCAGGTG;CSQ=C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001320923.2|protein_coding|11/26||NM_001320923.2:c.1457A>G|NP_001307852.1:p.Glu486Gly|1674|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321852.2|protein_coding|10/25||NM_001321852.2:c.1457A>G|NP_001308781.1:p.Glu486Gly|1677|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321853.2|protein_coding|12/27||NM_001321853.2:c.1457A>G|NP_001308782.1:p.Glu486Gly|1936|1457|486|E/G|gAg/gGg|||-1||EntrezGene||YES||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321854.2|protein_coding|11/26||NM_001321854.2:c.1457A>G|NP_001308783.1:p.Glu486Gly|1852|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321855.2|protein_coding|11/26||NM_001321855.2:c.1457A>G|NP_001308784.1:p.Glu486Gly|1835|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321856.2|protein_coding|10/25||NM_001321856.2:c.1457A>G|NP_001308785.1:p.Glu486Gly|1590|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_001321857.2|protein_coding|10/25||NM_001321857.2:c.1457A>G|NP_001308786.1:p.Glu486Gly|1751|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|JAK1|3716|Transcript|NM_002227.4|protein_coding|10/25||NM_002227.4:c.1457A>G|NP_002218.2:p.Glu486Gly|1751|1457|486|E/G|gAg/gGg|||-1||EntrezGene||||||1:g.65323340T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2599:2:1,1:1483,1113:2596,2:0.0008:2,2:17:1:37:0:1:1.33227:60:4:0.0008:0:1	0/1:174:2:1,1:94,78:172,2:0.0115:2,2:31:1:37:0:1:1.20383:60:4:0.0116:0:1
    155. 

  155. 1	65330487	65330487	G	A	exonic	JAK1	.	stopgain	JAK1:NM_001321852:exon8:c.C1159T:p.Q387X,JAK1:NM_001321856:exon8:c.C1159T:p.Q387X,JAK1:NM_001321857:exon8:c.C1159T:p.Q387X,JAK1:NM_002227:exon8:c.C1159T:p.Q387X,JAK1:NM_001320923:exon9:c.C1159T:p.Q387X,JAK1:NM_001321854:exon9:c.C1159T:p.Q387X,JAK1:NM_001321855:exon9:c.C1159T:p.Q387X,JAK1:NM_001321853:exon10:c.C1159T:p.Q387X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.862	0.987	40	0.998	0.914	0.975	0.750	D	c	1.171	1.047	1.0	0.983	0.731	0.878	0	5.58	0.843	9.251	0.946	1.048	0.713	1.000	0.715	0.999	0.750	19.947	0.972	FERM domain|PH domain-like	.	.	ID=COSV100691769;OCCURENCE=1(kidney)	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU131777781	KIRP-US|1|278|0.00359712	0.25	37	70	1	65330487	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=189;VD=2;AF=0.0106;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.53174;SOR=inf;LSEQ=TACCATTTTCTTGTTGTCCT;RSEQ=CTTGTTAATGCTGACCACAG;CSQ=A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001320923.2|protein_coding|9/26||NM_001320923.2:c.1159C>T|NP_001307852.1:p.Gln387Ter|1376|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321852.2|protein_coding|8/25||NM_001321852.2:c.1159C>T|NP_001308781.1:p.Gln387Ter|1379|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321853.2|protein_coding|10/27||NM_001321853.2:c.1159C>T|NP_001308782.1:p.Gln387Ter|1638|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||YES||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321854.2|protein_coding|9/26||NM_001321854.2:c.1159C>T|NP_001308783.1:p.Gln387Ter|1554|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321855.2|protein_coding|9/26||NM_001321855.2:c.1159C>T|NP_001308784.1:p.Gln387Ter|1537|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321856.2|protein_coding|8/25||NM_001321856.2:c.1159C>T|NP_001308785.1:p.Gln387Ter|1292|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_001321857.2|protein_coding|8/25||NM_001321857.2:c.1159C>T|NP_001308786.1:p.Gln387Ter|1453|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1,A|stop_gained|HIGH|JAK1|3716|Transcript|NM_002227.4|protein_coding|8/25||NM_002227.4:c.1159C>T|NP_002218.2:p.Gln387Ter|1453|1159|387|Q/*|Cag/Tag|COSV100691769||-1||EntrezGene||||||1:g.65330487G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:189:2:1,1:88,99:187,2:0.0106:2,2:64:1:37:0:1:1.12:60:4:0.0106:0:1	0/0:70:0:0,0:38,32:70,0:0:2,0:39.1:1:36.5:1:1:0:60:69:1:0:0
    156. 

  156. 1	65330629	65330629	-	T	exonic	JAK1	.	frameshift insertion	JAK1:NM_001321852:exon8:c.1016dupA:p.N339Kfs*2,JAK1:NM_001321856:exon8:c.1016dupA:p.N339Kfs*2,JAK1:NM_001321857:exon8:c.1016dupA:p.N339Kfs*2,JAK1:NM_002227:exon8:c.1016dupA:p.N339Kfs*2,JAK1:NM_001320923:exon9:c.1016dupA:p.N339Kfs*2,JAK1:NM_001321854:exon9:c.1016dupA:p.N339Kfs*2,JAK1:NM_001321855:exon9:c.1016dupA:p.N339Kfs*2,JAK1:NM_001321853:exon10:c.1016dupA:p.N339Kfs*2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	25	1	65330629	.	A	AT	38	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=27;VD=2;AF=0.0741;SHIFT3=7;MSI=8;MSILEN=1;SSF=0.26471;SOR=inf;LSEQ=AGTTTTTTCCGCTTCAGTTT;RSEQ=TTTTTTTCCTTTTCAACAGA;CSQ=T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001320923.2|protein_coding|9/26||NM_001320923.2:c.1016dup|NP_001307852.1:p.Asn339LysfsTer2|1233-1234|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321852.2|protein_coding|8/25||NM_001321852.2:c.1016dup|NP_001308781.1:p.Asn339LysfsTer2|1236-1237|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321853.2|protein_coding|10/27||NM_001321853.2:c.1016dup|NP_001308782.1:p.Asn339LysfsTer2|1495-1496|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||YES||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321854.2|protein_coding|9/26||NM_001321854.2:c.1016dup|NP_001308783.1:p.Asn339LysfsTer2|1411-1412|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321855.2|protein_coding|9/26||NM_001321855.2:c.1016dup|NP_001308784.1:p.Asn339LysfsTer2|1394-1395|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321856.2|protein_coding|8/25||NM_001321856.2:c.1016dup|NP_001308785.1:p.Asn339LysfsTer2|1149-1150|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_001321857.2|protein_coding|8/25||NM_001321857.2:c.1016dup|NP_001308786.1:p.Asn339LysfsTer2|1310-1311|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||,T|frameshift_variant|HIGH|JAK1|3716|Transcript|NM_002227.4|protein_coding|8/25||NM_002227.4:c.1016dup|NP_002218.2:p.Asn339LysfsTer2|1310-1311|1016-1017|339|N/KX|aat/aaAt|||-1||EntrezGene||||||1:g.65330636dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:27:2:1,1:7,18:25,2:0.0741:2,2:36.9:1:38.5:0:0.51282:2.47:62.4:4:0.0769:0:0	0/0:25:0:0,0:7,18:25,0:0:2,0:32.9:1:34:1:1:0:60:11.5:1:0:0
    157. 

  157. 1	78413254	78413254	C	A	downstream	FUBP1	dist=833	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	155	1	78413254	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.88211;SOR=0;LSEQ=TGCACTTCAACAGACAATGG;RSEQ=AAGACAGACTGTATTTGCAT;CSQ=A|downstream_gene_variant|MODIFIER|NEXN|91624|Transcript|NM_001172309.2|protein_coding|||||||||||3674|1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|21/21||NM_001303433.2:c.*1197G>T||3263|||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|21/21||NM_001376055.1:c.*1197G>T||3260|||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||19/20|NM_001376056.1:c.1924-993G>T|||||||||-1||EntrezGene||YES||||1:g.78413254C>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|20/20||NM_001376057.1:c.*1197G>T||3197|||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_003902.5|protein_coding|20/20||NM_003902.5:c.*1197G>T||3200|||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|downstream_gene_variant|MODIFIER|NEXN|91624|Transcript|NM_144573.4|protein_coding|||||||||||3674|1||EntrezGene||YES||||1:g.78413254C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||19/20|NR_130152.2:n.1992-17G>T|||||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||19/22|NR_146539.2:n.1992-17G>T|||||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||19/22|NR_146540.2:n.1995-17G>T|||||||||-1||EntrezGene||||||1:g.78413254C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:5,5:10,0:0:2,0:44.4:1:37:0:1:0:60:20:1:0:0.1	0/1:155:2:1,1:62,91:153,2:0.0129:2,2:35.5:1:37:0:1:1.46:60:4:0.013:0:1
    158. 

  158. 1	78414310	78414310	-	A	UTR3	FUBP1	NM_003902:c.*140_*141insT;NM_001303433:c.*140_*141insT	.	.	.	0.1951	0.0804	0.2126	0.2453	0.2554	0.0563	0.2683	0.2542	rs762644775	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU9977545	BTCA-SG|4|71|0.056338	0.5	123	25	1	78414310	.	C	CA	123	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2;VD=1;AF=0.5;SHIFT3=18;MSI=19;MSILEN=1;SSF=0.65812;SOR=1.47706;LSEQ=ATAGATATTTTGTACATTTT;RSEQ=AAAAAAAAAAAAAAAAAAGG;CSQ=A|downstream_gene_variant|MODIFIER|NEXN|91624|Transcript|NM_001172309.2|protein_coding||||||||||rs60897865|4730|1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|21/21||NM_001303433.2:c.*140dup||2206-2207|||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|21/21||NM_001376055.1:c.*140dup||2203-2204|||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||19/20|NM_001376056.1:c.1923+529dup|||||||rs60897865||-1||EntrezGene||YES||||1:g.78414328dup||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|20/20||NM_001376057.1:c.*140dup||2140-2141|||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|3_prime_UTR_variant|MODIFIER|FUBP1|8880|Transcript|NM_003902.5|protein_coding|20/20||NM_003902.5:c.*140dup||2143-2144|||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|downstream_gene_variant|MODIFIER|NEXN|91624|Transcript|NM_144573.4|protein_coding||||||||||rs60897865|4730|1||EntrezGene||YES||||1:g.78414328dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||19/20|NR_130152.2:n.1991+529dup|||||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||19/22|NR_146539.2:n.1991+529dup|||||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||19/22|NR_146540.2:n.1994+529dup|||||||rs60897865||-1||EntrezGene||||||1:g.78414328dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:1,0:1,0:1,1:0.5:0,0:18.9:0:41.2:0:1:0:66.8:2:0.5:0:0	0/1:25:10:10,0:8,0:8,10:0.4:0,0:39.3:1:37.1:1:1:0:60.1:20:0.4348:0.04:2
    159. 

  159. 1	78420999	78420999	G	A	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon18:c.C1721T:p.P574L,FUBP1:NM_001303433:exon19:c.C1784T:p.P595L	.	.	.	.	.	.	.	.	.	.	.	0.017	0.512	D	0.77	0.419	P	0.3	0.393	B	0.020	0.271	N	1	0.810	D	1.545	0.392	L	1.33	0.356	T	-2.64	0.576	D	0.628	0.647	-1.097	0.044	T	0.071	0.288	T	0.012	0.301	T	5.647	0.769	26.6	0.995	0.668	0.978	0.774	D	c	0.520	0.614	1.000	0.747	0.707	0.730	0	5.8	0.921	8.002	0.879	1.048	0.713	1.000	0.715	1.000	0.888	20.071	0.977	.	.	.	ID=COSV53938755;OCCURENCE=1(skin),1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	76	1	78420999	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.4842;SOR=0;LSEQ=CAACCTGTCCAGCTGGGGCT;RSEQ=GATTCTGCTGATCTCCTTGT;CSQ=A|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|19/21||NM_001303433.2:c.1784C>T|NP_001290362.1:p.Pro595Leu|1852|1784|595|P/L|cCa/cTa|COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|19/21||NM_001376055.1:c.1781C>T|NP_001362984.1:p.Pro594Leu|1849|1781|594|P/L|cCa/cTa|COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|18/21||NM_001376056.1:c.1718C>T|NP_001362985.1:p.Pro573Leu|1786|1718|573|P/L|cCa/cTa|COSV53938755||-1||EntrezGene||YES||||1:g.78420999G>A|||||||||||||1|1,A|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|18/20||NM_001376057.1:c.1718C>T|NP_001362986.1:p.Pro573Leu|1786|1718|573|P/L|cCa/cTa|COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|18/20||NM_003902.5:c.1721C>T|NP_003893.2:p.Pro574Leu|1789|1721|574|P/L|cCa/cTa|COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|18/21||NR_130152.2:n.1786C>T||1786|||||COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|18/23||NR_146539.2:n.1786C>T||1786|||||COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|18/23||NR_146540.2:n.1789C>T||1789|||||COSV53938755||-1||EntrezGene||||||1:g.78420999G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:33:0:0,0:22,11:33,0:0:2,0:42:1:37:0:1:0:60:66:1:0:0.1	0/1:76:2:1,1:33,41:74,2:0.0263:2,2:31.5:1:37:0:1:1.24:60:4:0.0267:0:1
    160. 

  160. 1	78422287	78422287	C	T	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon17:c.G1675A:p.A559T,FUBP1:NM_001303433:exon18:c.G1738A:p.A580T	.	.	.	.	.	.	.	.	.	.	.	0.552	0.082	T	0.155	0.265	B	0.049	0.237	B	0.000	0.523	D	1	0.810	D	1.525	0.387	L	1.4	0.336	T	-0.71	0.202	N	0.408	0.490	-1.064	0.108	T	0.046	0.199	T	0.012	0.313	T	3.919	0.528	23.5	0.993	0.601	0.965	0.695	D	c	0.073	0.265	1.000	0.747	0.707	0.730	0	5.76	0.907	5.969	0.699	0.935	0.490	1.000	0.715	0.998	0.697	19.966	0.973	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	194	1	78422287	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=149;VD=2;AF=0.0134;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.18799;SOR=inf;LSEQ=AGTTTGAGTTGTAGTTGGTG;RSEQ=ACCTGCAGGGGCTGCTGGTG;CSQ=T|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|18/21||NM_001303433.2:c.1738G>A|NP_001290362.1:p.Ala580Thr|1806|1738|580|A/T|Gca/Aca|||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|18/21||NM_001376055.1:c.1735G>A|NP_001362984.1:p.Ala579Thr|1803|1735|579|A/T|Gca/Aca|||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|17/21||NM_001376056.1:c.1672G>A|NP_001362985.1:p.Ala558Thr|1740|1672|558|A/T|Gca/Aca|||-1||EntrezGene||YES||||1:g.78422287C>T||||||||||||||,T|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|17/20||NM_001376057.1:c.1672G>A|NP_001362986.1:p.Ala558Thr|1740|1672|558|A/T|Gca/Aca|||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|17/20||NM_003902.5:c.1675G>A|NP_003893.2:p.Ala559Thr|1743|1675|559|A/T|Gca/Aca|||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|17/21||NR_130152.2:n.1740G>A||1740|||||||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|17/23||NR_146539.2:n.1740G>A||1740|||||||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|17/23||NR_146540.2:n.1743G>A||1743|||||||-1||EntrezGene||||||1:g.78422287C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:149:2:2,0:95,52:147,2:0.0134:2,0:14:0:37:0:0.54254:0:60:4:0.0134:0:1	0/0:194:0:0,0:107,87:194,0:0:2,0:36.7:1:36.2:1:1:0:60:193:1:0:0.1
    161. 

  161. 1	78422385	78422385	G	T	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon17:c.C1577A:p.A526D,FUBP1:NM_001303433:exon18:c.C1640A:p.A547D	.	.	.	.	.	.	.	.	.	.	.	0.143	0.253	T	0.008	0.135	B	0.004	0.093	B	0.007	0.315	N	0.990	0.412	D	0	0.065	N	1.49	0.317	T	-0.36	0.138	N	0.388	0.502	-1.011	0.265	T	0.016	0.066	T	.	.	.	3.159	0.439	22.6	0.992	0.537	0.908	0.520	D	c	-0.230	0.028	1.000	0.437	0.707	0.730	0	5.63	0.861	5.445	0.661	1.048	0.713	1.000	0.715	0.866	0.362	14.180	0.650	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	143	1	78422385	.	G	T	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=246;VD=3;AF=0.0122;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.25177;SOR=inf;LSEQ=TTGGATCCGTTCCTGCCTTA;RSEQ=CTAAAATAAATGAAAGTTCA;CSQ=T|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|18/21||NM_001303433.2:c.1640C>A|NP_001290362.1:p.Ala547Asp|1708|1640|547|A/D|gCt/gAt|||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|18/21||NM_001376055.1:c.1637C>A|NP_001362984.1:p.Ala546Asp|1705|1637|546|A/D|gCt/gAt|||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|17/21||NM_001376056.1:c.1574C>A|NP_001362985.1:p.Ala525Asp|1642|1574|525|A/D|gCt/gAt|||-1||EntrezGene||YES||||1:g.78422385G>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|17/20||NM_001376057.1:c.1574C>A|NP_001362986.1:p.Ala525Asp|1642|1574|525|A/D|gCt/gAt|||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|17/20||NM_003902.5:c.1577C>A|NP_003893.2:p.Ala526Asp|1645|1577|526|A/D|gCt/gAt|||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|17/21||NR_130152.2:n.1642C>A||1642|||||||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|17/23||NR_146539.2:n.1642C>A||1642|||||||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|17/23||NR_146540.2:n.1645C>A||1645|||||||-1||EntrezGene||||||1:g.78422385G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:246:3:1,2:118,125:243,3:0.0122:2,2:22.7:1:28.3:1:1:1.88331:60:2:0.0084:0:1	0/0:143:0:0,0:55,88:143,0:0:2,0:32.2:1:35.5:1:1:0:60:70.5:1:0:0.1
    162. 

  162. 1	78422437	78422438	CA	-	intronic	FUBP1	.	.	.	0.022	3.292e-05	0	0.0013	0	0	0	0	0	rs753532747	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU63815688	BRCA-EU|1|569|0.00175747,PRAD-CA|1|306|0.00326797,BTCA-SG|1|71|0.0140845,GACA-JP|4|585|0.00683761	0.25	74	72	1	78422436	.	TCA	T	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=152;VD=4;AF=0.0263;SHIFT3=13;MSI=7;MSILEN=2;SSF=0.20931;SOR=inf;LSEQ=GTGAAGTCTGTAATTCTCTC;RSEQ=CACACACACACACCACCCCC;CSQ=-|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001303433.2|protein_coding||17/20|NM_001303433.2:c.1640-53_1640-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376055.1|protein_coding||17/20|NM_001376055.1:c.1637-53_1637-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||16/20|NM_001376056.1:c.1574-53_1574-52del|||||||rs369403301||-1||EntrezGene||YES||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376057.1|protein_coding||16/19|NM_001376057.1:c.1574-53_1574-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_003902.5|protein_coding||16/19|NM_003902.5:c.1577-53_1577-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||16/20|NR_130152.2:n.1642-53_1642-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||16/22|NR_146539.2:n.1642-53_1642-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||16/22|NR_146540.2:n.1645-53_1645-52del|||||||rs369403301||-1||EntrezGene||||||1:g.78422450_78422451del|0.004017|0.003019|0.004384|0.007089|0.004431|0.00544|0.002986|0.002452|0.006555|0.02203|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:152:4:1,3:53,95:148,4:0.0263:2,2:43.5:1:37:0:1:1.66849:60:8:0.0265:0:0	0/0:72:0:0,0:14,58:72,0:0:2,0:40.1:1:35.8:1:1:0:60:71:1:0:0.2
    163. 

  163. 1	78425859	78425859	C	T	intronic	FUBP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	96	1	78425859	.	C	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=3;AF=0.0698;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02818;SOR=inf;LSEQ=GATAACACACAAATAATAAG;RSEQ=ATCTTCTACCTGGATCAGGA;CSQ=T|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001303433.2|protein_coding||17/20|NM_001303433.2:c.1639+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376055.1|protein_coding||17/20|NM_001376055.1:c.1636+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||16/20|NM_001376056.1:c.1573+10G>A|||||||||-1||EntrezGene||YES||||1:g.78425859C>T||||||||||||||,T|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_001376057.1|protein_coding||16/19|NM_001376057.1:c.1573+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant|MODIFIER|FUBP1|8880|Transcript|NM_003902.5|protein_coding||16/19|NM_003902.5:c.1576+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||16/20|NR_130152.2:n.1641+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||16/22|NR_146539.2:n.1641+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||16/22|NR_146540.2:n.1644+10G>A|||||||||-1||EntrezGene||||||1:g.78425859C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:43:3:2,1:33,7:40,3:0.0698:2,2:24.3:1:37:0:0.46965:2.2997:60:6:0.0714:0:1.3	0/0:96:0:0,0:60,36:96,0:0:2,0:36.2:1:36:1:1:0:60:47:1:0:0
    164. 

  164. 1	78426184	78426184	-	A	intronic	FUBP1	.	.	.	0.011	3.368e-05	0	0	0	0	0	6.951e-05	0	rs545766306	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	76	1	78426184	.	C	CA	38	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=18;VD=2;AF=0.1111;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.035;SOR=inf;LSEQ=AAAGGATTTACTGGGCCCTA;RSEQ=AAAAAAAAGGATGACATAGA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding||15/20|NM_001303433.2:c.1408-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding||15/20|NM_001376055.1:c.1405-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||14/20|NM_001376056.1:c.1342-5dup|||||||rs545766306||-1||EntrezGene||YES||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding||14/19|NM_001376057.1:c.1342-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding||14/19|NM_003902.5:c.1345-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||14/20|NR_130152.2:n.1410-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||14/22|NR_146539.2:n.1410-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||14/22|NR_146540.2:n.1413-5dup|||||||rs545766306||-1||EntrezGene||||||1:g.78426192dup|0.0003901|0.0002627|0.0004295|0.0004985|0.0004387|0.0001548|0.0004723|0.0004281|0.000238|0.01143|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:18:2:1,1:3,13:16,2:0.1111:2,2:49.7:1:38.7:0:0.40523:3.89:62.8:4:0.1176:0:0	0/0:76:0:0,0:22,52:74,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    165. 

  165. 1	78429361	78429361	T	C	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon13:c.A1081G:p.R361G,FUBP1:NM_001303433:exon14:c.A1144G:p.R382G	.	.	.	.	.	.	.	.	.	.	.	0.136	0.270	T	0.999	0.764	D	0.978	0.725	D	0.000	0.843	D	1.000	0.588	D	1.87	0.498	L	0.95	0.433	T	-2.63	0.564	D	0.807	0.814	-1.030	0.203	T	0.101	0.375	T	0.030	0.523	D	3.949	0.532	23.6	0.997	0.774	0.945	0.612	D	c	0.020	0.090	0.999	0.372	0.707	0.730	0	3.15	0.351	2.405	0.440	0.088	0.194	1.000	0.715	1.000	0.888	12.440	0.548	K Homology domain, type 1	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	290	1	78429361	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.04629;SOR=inf;LSEQ=GTTGCCTTGACCTCTACCTC;RSEQ=TCCTCGACCACCAGGTCCAG;CSQ=C|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|14/21||NM_001303433.2:c.1144A>G|NP_001290362.1:p.Arg382Gly|1212|1144|382|R/G|Aga/Gga|rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|14/21||NM_001376055.1:c.1141A>G|NP_001362984.1:p.Arg381Gly|1209|1141|381|R/G|Aga/Gga|rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|13/21||NM_001376056.1:c.1078A>G|NP_001362985.1:p.Arg360Gly|1146|1078|360|R/G|Aga/Gga|rs1158364154||-1||EntrezGene||YES||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|13/20||NM_001376057.1:c.1078A>G|NP_001362986.1:p.Arg360Gly|1146|1078|360|R/G|Aga/Gga|rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|13/20||NM_003902.5:c.1081A>G|NP_003893.2:p.Arg361Gly|1149|1081|361|R/G|Aga/Gga|rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|13/21||NR_130152.2:n.1146A>G||1146|||||rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|13/23||NR_146539.2:n.1146A>G||1146|||||rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|13/23||NR_146540.2:n.1149A>G||1149|||||rs1158364154||-1||EntrezGene||||||1:g.78429361T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:38,40:78,2:0.025:2,2:40:0:37:0:1:1.05:60:4:0.0263:0:1.5	0/0:290:0:0,0:149,140:289,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    166. 

  166. 1	78429756	78429756	T	C	exonic	FUBP1	.	synonymous SNV	FUBP1:NM_003902:exon12:c.A1032G:p.R344R,FUBP1:NM_001303433:exon13:c.A1095G:p.R365R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	168	1	78429756	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.87076;SOR=0;LSEQ=TTCTATCAAACCTGAACACT;RSEQ=CGAAGAAGGTCTGTAATAAT;CSQ=C|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|13/21||NM_001303433.2:c.1095A>G|NP_001290362.1:p.Arg365%3D|1163|1095|365|R|cgA/cgG|||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|13/21||NM_001376055.1:c.1092A>G|NP_001362984.1:p.Arg364%3D|1160|1092|364|R|cgA/cgG|||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|12/21||NM_001376056.1:c.1029A>G|NP_001362985.1:p.Arg343%3D|1097|1029|343|R|cgA/cgG|||-1||EntrezGene||YES||||1:g.78429756T>C||||||||||||||,C|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|12/20||NM_001376057.1:c.1029A>G|NP_001362986.1:p.Arg343%3D|1097|1029|343|R|cgA/cgG|||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding|12/20||NM_003902.5:c.1032A>G|NP_003893.2:p.Arg344%3D|1100|1032|344|R|cgA/cgG|||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|12/21||NR_130152.2:n.1097A>G||1097|||||||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|12/23||NR_146539.2:n.1097A>G||1097|||||||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|12/23||NR_146540.2:n.1100A>G||1100|||||||-1||EntrezGene||||||1:g.78429756T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:6,6:12,0:0:2,0:30.3:1:36:1:1:0:60:24:1:0:0.1	0/1:168:2:1,1:105,61:166,2:0.0119:2,2:64.5:1:37:0:1:1.7154:60:4:0.012:0:1
    167. 

  167. 1	78430393	78430393	C	G	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon10:c.G775C:p.G259R,FUBP1:NM_001303433:exon11:c.G838C:p.G280R	.	.	.	.	.	.	.	.	.	.	.	0.081	0.334	T	0.989	0.609	D	0.791	0.559	P	0.000	0.843	D	1	0.810	D	2.07	0.570	M	0.92	0.445	T	-2.0	0.461	N	0.49	0.561	-1.071	0.092	T	0.116	0.409	T	0.013	0.322	T	3.908	0.526	23.5	0.999	0.988	0.994	0.954	D	c	0.461	0.527	1.000	0.747	0.707	0.730	0	4.77	0.603	6.163	0.715	0.852	0.362	1.000	0.715	1.000	0.888	14.935	0.705	K Homology domain, type 1	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	143	1	78430393	.	C	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=16;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.8083;SOR=0;LSEQ=CCGAACTTCTCTGAAACCGC;RSEQ=TTGATCACGAATTAACTCTA;CSQ=G|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|11/21||NM_001303433.2:c.838G>C|NP_001290362.1:p.Gly280Arg|906|838|280|G/R|Ggc/Cgc|||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|11/21||NM_001376055.1:c.835G>C|NP_001362984.1:p.Gly279Arg|903|835|279|G/R|Ggc/Cgc|||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|10/21||NM_001376056.1:c.772G>C|NP_001362985.1:p.Gly258Arg|840|772|258|G/R|Ggc/Cgc|||-1||EntrezGene||YES||||1:g.78430393C>G||||||||||||||,G|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|10/20||NM_001376057.1:c.772G>C|NP_001362986.1:p.Gly258Arg|840|772|258|G/R|Ggc/Cgc|||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|missense_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|10/20||NM_003902.5:c.775G>C|NP_003893.2:p.Gly259Arg|843|775|259|G/R|Ggc/Cgc|||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|10/21||NR_130152.2:n.840G>C||840|||||||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|10/23||NR_146539.2:n.840G>C||840|||||||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|10/23||NR_146540.2:n.843G>C||843|||||||-1||EntrezGene||||||1:g.78430393C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:16:0:0,0:9,7:16,0:0:2,0:40.4:1:37:0:1:0:60:32:1:0:0	0/1:143:2:1,1:69,72:141,2:0.014:2,2:20.5:1:37:0:1:1.04:60:4:0.0144:0:1
    168. 

  168. 1	78432639	78432639	A	G	exonic	FUBP1	.	nonsynonymous SNV	FUBP1:NM_003902:exon6:c.T344C:p.I115T,FUBP1:NM_001303433:exon7:c.T407C:p.I136T	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.988	0.764	D	0.000	0.843	D	1	0.810	D	4.435	0.988	H	0.96	0.429	T	-4.43	0.775	D	0.97	0.981	0.123	0.846	D	0.374	0.733	T	.	.	.	6.027	0.829	27.9	0.998	0.919	0.988	0.874	D	c	1.051	0.944	1.000	0.747	0.707	0.730	0	5.46	0.799	9.325	0.960	1.199	0.960	1.000	0.715	1.000	0.888	15.817	0.783	K Homology domain|K Homology domain, type 1	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	48	1	78432639	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCACCTCCTCTGCCAATT;RSEQ=CTAGTTAGAAAAAAAAAAAT;CSQ=G|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|7/21||NM_001303433.2:c.407T>C|NP_001290362.1:p.Ile136Thr|475|407|136|I/T|aTa/aCa|||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|7/21||NM_001376055.1:c.404T>C|NP_001362984.1:p.Ile135Thr|472|404|135|I/T|aTa/aCa|||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|6/21||NM_001376056.1:c.341T>C|NP_001362985.1:p.Ile114Thr|409|341|114|I/T|aTa/aCa|||-1||EntrezGene||YES||||1:g.78432639A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|6/20||NM_001376057.1:c.341T>C|NP_001362986.1:p.Ile114Thr|409|341|114|I/T|aTa/aCa|||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|FUBP1|8880|Transcript|NM_003902.5|protein_coding|6/20||NM_003902.5:c.344T>C|NP_003893.2:p.Ile115Thr|412|344|115|I/T|aTa/aCa|||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|6/21||NR_130152.2:n.409T>C||409|||||||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|6/23||NR_146539.2:n.409T>C||409|||||||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|6/23||NR_146540.2:n.412T>C||412|||||||-1||EntrezGene||||||1:g.78432639A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:48:2:1,1:15,31:46,2:0.0417:2,2:17:1:37:0:1:2.03:60:4:0.0435:0:2
    169. 

  169. 1	78432647	78432647	-	A	intronic	FUBP1	.	.	.	0.0078	0.0005	0	0	0	0.0075	0	0	0.0011	rs200233459	rs200233459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	79	42	1	78432647	.	G	GA	79	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=Insertion;DP=0;VD=0;AF=0;SHIFT3=11;MSI=12;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTGCCAATTACTAGTTA;RSEQ=AAAAAAAAAAATTTTTTTTT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding||6/20|NM_001303433.2:c.407-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding||6/20|NM_001376055.1:c.404-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||5/20|NM_001376056.1:c.341-9dup|||||||rs71590706||-1||EntrezGene||YES||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding||5/19|NM_001376057.1:c.341-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding||5/19|NM_003902.5:c.344-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||5/20|NR_130152.2:n.409-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||5/22|NR_146539.2:n.409-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||5/22|NR_146540.2:n.412-9dup|||||||rs71590706||-1||EntrezGene||||||1:g.78432658dup|0.002141|0.0009556|0.002346|0.002736|0.006223|0.001574|0.001598|0.00249|0.002457|0.007765|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:42:4:1,3:13,24:37,4:0.0952:2,2:32:1:39.5:0:1:1.6072:64:8:0.1081:0:0.3
    170. 

  170. 1	78432740	78432740	A	G	exonic	FUBP1	.	synonymous SNV	FUBP1:NM_003902:exon5:c.T336C:p.V112V,FUBP1:NM_001303433:exon6:c.T399C:p.V133V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	33	1	78432740	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGTTACTTACTGAATCC;RSEQ=ACCATTCCATCTGGAACTTT;CSQ=G|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|6/21||NM_001303433.2:c.399T>C|NP_001290362.1:p.Val133%3D|467|399|133|V|gtT/gtC|||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|6/21||NM_001376055.1:c.396T>C|NP_001362984.1:p.Val132%3D|464|396|132|V|gtT/gtC|||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|5/21||NM_001376056.1:c.333T>C|NP_001362985.1:p.Val111%3D|401|333|111|V|gtT/gtC|||-1||EntrezGene||YES||||1:g.78432740A>G||||||||||||||,G|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|5/20||NM_001376057.1:c.333T>C|NP_001362986.1:p.Val111%3D|401|333|111|V|gtT/gtC|||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding|5/20||NM_003902.5:c.336T>C|NP_003893.2:p.Val112%3D|404|336|112|V|gtT/gtC|||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|5/21||NR_130152.2:n.401T>C||401|||||||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|5/23||NR_146539.2:n.401T>C||401|||||||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|5/23||NR_146540.2:n.404T>C||404|||||||-1||EntrezGene||||||1:g.78432740A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:33:2:1,1:16,15:31,2:0.0606:2,2:65:1:37:0:1:1.06462:60:4:0.0625:0:1
    171. 

  171. 1	78435701	78435701	-	A	splicing	FUBP1	NM_003902:exon2:c.121-2->T;NM_001303433:exon2:c.121-2->T	.	.	0.41	0.0016	0.0016	0.0044	0	0.0006	0.0153	0.0006	0.0062	rs752631352	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	79	81	1	78435701	.	T	TA	79	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2;VD=0;AF=0;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.90538;SOR=0;LSEQ=CTCCAATTTTTGCTGCAATC;RSEQ=AAAAAAAAAAAAGAAAAATA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding||1/20|NM_001303433.2:c.121-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding||1/20|NM_001376055.1:c.121-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding||1/20|NM_001376056.1:c.121-3dup|||||||rs202224025||-1||EntrezGene||YES||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding||1/19|NM_001376057.1:c.121-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding||1/19|NM_003902.5:c.121-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_130152.2|misc_RNA||1/20|NR_130152.2:n.189-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146539.2|misc_RNA||1/22|NR_146539.2:n.189-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FUBP1|8880|Transcript|NR_146540.2|misc_RNA||1/22|NR_146540.2:n.189-3dup|||||||rs202224025||-1||EntrezGene||||||1:g.78435713dup|0.0279|0.02928|0.04634|0.03199|0.0368|0.01168|0.0244|0.03657|0.02515|0.04634|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:0,1:1,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:81:4:1,3:32,40:72,4:0.0494:2,2:27.1:1:39.7:0:0.62838:2.37494:64.4:8:0.0548:0:0.3
    172. 

  172. 1	78444626	78444629	GCCG	CCCC	exonic	FUBP1	.	nonframeshift substitution	FUBP1:NM_001303433:exon1:c.60_63delinsGGGG:p.G20G,FUBP1:NM_003902:exon1:c.60_63delinsGGGG:p.G20G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	29	88	1	78444626	.	GCCG	CCCC	29	v3;f0.01;pSTD;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Complex;DP=792;VD=1;AF=0.0013;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02775;SOR=0.05476;LSEQ=TTAACTCCTCCACCACCACC;RSEQ=CCACCACCGCCACCAGCTGA;CSQ=CCCC|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001303433.2|protein_coding|1/21||NM_001303433.2:c.60_63delinsGGGG|NP_001290362.1:p.GlyGly20%3D|128-131|60-63|20-21|GG|ggCGGC/ggGGGG|||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|upstream_gene_variant|MODIFIER|DNAJB4|11080|Transcript|NM_001317099.2|protein_coding|||||||||||1239|1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|upstream_gene_variant|MODIFIER|DNAJB4|11080|Transcript|NM_001317100.2|protein_coding|||||||||||230|1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|upstream_gene_variant|MODIFIER|DNAJB4|11080|Transcript|NM_001317101.2|protein_coding|||||||||||230|1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|upstream_gene_variant|MODIFIER|DNAJB4|11080|Transcript|NM_001317102.2|protein_coding|||||||||||230|1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376055.1|protein_coding|1/21||NM_001376055.1:c.60_63delinsGGGG|NP_001362984.1:p.GlyGly20%3D|128-131|60-63|20-21|GG|ggCGGC/ggGGGG|||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376056.1|protein_coding|1/21||NM_001376056.1:c.60_63delinsGGGG|NP_001362985.1:p.GlyGly20%3D|128-131|60-63|20-21|GG|ggCGGC/ggGGGG|||-1||EntrezGene||YES||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_001376057.1|protein_coding|1/20||NM_001376057.1:c.60_63delinsGGGG|NP_001362986.1:p.GlyGly20%3D|128-131|60-63|20-21|GG|ggCGGC/ggGGGG|||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|synonymous_variant|LOW|FUBP1|8880|Transcript|NM_003902.5|protein_coding|1/20||NM_003902.5:c.60_63delinsGGGG|NP_003893.2:p.GlyGly20%3D|128-131|60-63|20-21|GG|ggCGGC/ggGGGG|||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_130152.2|misc_RNA|1/21||NR_130152.2:n.128_131delinsGGGG||128-131|||||||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146539.2|misc_RNA|1/23||NR_146539.2:n.128_131delinsGGGG||128-131|||||||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||,CCCC|non_coding_transcript_exon_variant|MODIFIER|FUBP1|8880|Transcript|NR_146540.2|misc_RNA|1/23||NR_146540.2:n.128_131delinsGGGG||128-131|||||||-1||EntrezGene||||||1:g.78444626_78444629delinsCCCC||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:792:1:1,0:287,468:755,1:0.0013:2,0:36:0:24.5:0:0.38095:0:60:2:0.0017:0:6	0/1:88:2:2,0:28,54:82,2:0.0227:2,0:28:1:29.3:1:0.12478:0:60:4:0.0317:0.0114:1
    173. 

  173. 1	85733374	85733374	C	T	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon3:c.G605A:p.G202E,BCL10:NM_003921:exon3:c.G638A:p.G213E	0.15	0.0467	0.0142	0.0979	0.0166	0.1467	0.0450	0.0527	0.05	rs3768235	rs3768235	0.372	0.115	T	0.0	0.026	B	0.0	0.013	B	0.795	0.067	N	1.000	0.195	P	-1.01	0.011	N	.	.	.	-1.17	0.299	N	0.035	0.020	-0.973	0.366	T	0.011	0.042	T	.	.	.	1.357	0.227	12.56	0.991	0.516	0.251	0.224	N	c	-0.880	-0.740	1.000	0.409	0.722	0.854	0	-0.914	0.099	0.257	0.180	0.892	0.403	0.706	0.284	0.994	0.587	5.265	0.148	.	.	.	ID=COSV65353501;OCCURENCE=1(breast),1(liver),1(large_intestine),1(stomach),3(haematopoietic_and_lymphoid_tissue),1(lung)	389438	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU580721	LAML-KR|3|205|0.0146341,COCA-CN|1|321|0.00311526,BRCA-KR|1|50|0.02	0.5	242	208	1	85733374	.	C	T	242	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=31;AF=0.4921;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.54003;SOR=0.9876;LSEQ=CACTAGAGTTTGCACAAGTT;RSEQ=CTTCTTCTTCTAACTGTAGA;CSQ=T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.605G>A|NP_001307644.1:p.Gly202Glu|885|605|202|G/E|gGa/gAa|rs3768235&COSV65353501||-1||EntrezGene||||||1:g.85733374C>T|0.06508|0.01022|0.0799|0.02544|0.152|0.04615|0.05432|0.05858|0.09305|0.1538|EAS|benign|0&1|1&1,T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.638G>A|NP_003912.1:p.Gly213Glu|918|638|213|G/E|gGa/gAa|rs3768235&COSV65353501||-1||EntrezGene||YES||||1:g.85733374C>T|0.06508|0.01022|0.0799|0.02544|0.152|0.04615|0.05432|0.05858|0.09305|0.1538|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:63:31:20,11:22,10:32,31:0.4921:2,2:36.4:1:36.6:1:0.79281:1.20633:60:62:0.5082:0:1.1	0/1:208:103:63,40:58,46:104,103:0.4952:2,2:40.5:1:36.2:1:0.48154:1.25:60:102:0.5025:0:1.1
    174. 

  174. 1	85733386	85733386	A	G	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon3:c.T593C:p.L198S,BCL10:NM_003921:exon3:c.T626C:p.L209S	.	.	.	.	.	.	.	.	.	.	.	0.96	0.021	T	0.002	0.090	B	0.001	0.040	B	0.875	0.072	N	0.992	0.239	N	-0.805	0.016	N	.	.	.	0.46	0.031	N	0.093	0.104	-0.897	0.483	T	0.006	0.022	T	0.004	0.088	T	1.628	0.257	14.00	0.988	0.453	0.548	0.294	D	c	-0.576	-0.299	1.000	0.451	0.722	0.854	0	3.35	0.373	2.566	0.454	1.140	0.893	0.967	0.338	0.992	0.562	1.286	0.019	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	224	1	85733386	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=73;VD=2;AF=0.0274;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.05979;SOR=inf;LSEQ=CACAAGTTCCTTCTTCTTCT;RSEQ=ACTGTAGATCTGGTGGCAAA;CSQ=G|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.593T>C|NP_001307644.1:p.Leu198Ser|873|593|198|L/S|tTa/tCa|COSV65354131||-1||EntrezGene||||||1:g.85733386A>G|||||||||||||1|1,G|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.626T>C|NP_003912.1:p.Leu209Ser|906|626|209|L/S|tTa/tCa|COSV65354131||-1||EntrezGene||YES||||1:g.85733386A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:73:2:1,1:49,22:71,2:0.0274:2,2:20:1:37:0:0.53387:2.20047:60:4:0.0282:0:1.5	0/0:224:0:0,0:131,93:224,0:0:2,0:38.3:1:36.2:1:1:0:60:73.667:1:0:0.6
    175. 

  175. 1	85733490	85733490	C	T	exonic	BCL10	.	synonymous SNV	BCL10:NM_001320715:exon3:c.G489A:p.L163L,BCL10:NM_003921:exon3:c.G522A:p.L174L	0.0001	.	.	.	.	.	.	.	.	rs774139089	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	298	1	85733490	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=149;VD=2;AF=0.0134;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.11061;SOR=inf;LSEQ=CTGCCTACTTCTAGAACAGG;RSEQ=AAATTCAGAGAAGAATTAGT;CSQ=T|synonymous_variant|LOW|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.489G>A|NP_001307644.1:p.Leu163%3D|769|489|163|L|ttG/ttA|rs774139089||-1||EntrezGene||||||1:g.85733490C>T|7.954e-06|0|0|0|5.437e-05|0|8.792e-06|0|0|5.437e-05|gnomAD_EAS|||,T|synonymous_variant|LOW|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.522G>A|NP_003912.1:p.Leu174%3D|802|522|174|L|ttG/ttA|rs774139089||-1||EntrezGene||YES||||1:g.85733490C>T|7.954e-06|0|0|0|5.437e-05|0|8.792e-06|0|0|5.437e-05|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:149:2:1,1:80,67:147,2:0.0134:2,2:16.5:1:37:0:1:1.1926:60:4:0.0135:0:1	0/0:298:0:0,0:152,145:297,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    176. 

  176. 1	85733527	85733527	G	A	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon3:c.C452T:p.T151M,BCL10:NM_003921:exon3:c.C485T:p.T162M	0.0021	6.457e-05	0	0	0	0.0006	0	0	0.0010	rs200837308	rs200837308	0.008	0.586	D	1.0	0.899	D	0.993	0.797	D	0.000	0.559	D	0.999	0.455	D	1.905	0.510	L	.	.	.	-2.3	0.511	N	0.694	0.699	-0.433	0.710	T	0.336	0.703	T	0.014	0.335	T	5.434	0.737	26.1	0.999	0.934	0.966	0.697	D	c	0.611	0.579	1.000	0.747	0.722	0.854	0	5.98	0.971	5.788	0.685	0.998	0.613	1.000	0.715	0.637	0.296	18.633	0.913	.	.	.	ID=COSV65353478;OCCURENCE=3(stomach)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU121082585	GACA-JP|1|585|0.0017094	0.25	236	327	1	85733527	.	G	A	236	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=179;VD=90;AF=0.5028;SHIFT3=0;MSI=2;MSILEN=3;SSF=0;SOR=inf;LSEQ=TAGTAGAAAAAAAGGGCGTC;RSEQ=TGCTGGATTCTCCTTCTGGA;CSQ=A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.452C>T|NP_001307644.1:p.Thr151Met|732|452|151|T/M|aCg/aTg|rs200837308&COSV65353478||-1||EntrezGene||||||1:g.85733527G>A|0.0002346|0|0|0|0.002175|0|0.0001055|0.0001629|0.000196|0.002175|gnomAD_EAS||0&1|0&1,A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.485C>T|NP_003912.1:p.Thr162Met|765|485|162|T/M|aCg/aTg|rs200837308&COSV65353478||-1||EntrezGene||YES||||1:g.85733527G>A|0.0002346|0|0|0|0.002175|0|0.0001055|0.0001629|0.000196|0.002175|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:179:90:44,46:49,40:89,90:0.5028:2,2:36.8:1:36.4:1:0.45571:1.27889:60:89:0.5:0:1.1	0/0:327:0:0,0:165,162:327,0:0:2,0:39:1:36.4:1:1:0:60:162.5:1:0:0.1
    177. 

  177. 1	85733608	85733608	C	A	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon3:c.G371T:p.R124I,BCL10:NM_003921:exon3:c.G404T:p.R135I	.	.	.	.	.	.	.	.	.	.	.	0.033	0.443	D	0.7	0.399	P	0.483	0.453	P	0.000	0.629	D	1	0.810	D	1.175	0.300	L	.	.	.	-3.25	0.652	D	0.747	0.744	-0.666	0.620	T	0.229	0.595	T	0.008	0.202	T	5.693	0.777	26.8	0.983	0.394	0.986	0.841	D	c	0.481	0.563	1.000	0.747	0.722	0.854	0	5.98	0.971	4.351	0.589	0.892	0.403	1.000	0.715	0.999	0.750	20.452	0.991	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	265	1	85733608	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.11558;SOR=inf;LSEQ=TACTCTCATCTGAATTTGAT;RSEQ=TGGAGAGGTTGTTCGTGGCT;CSQ=A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.371G>T|NP_001307644.1:p.Arg124Ile|651|371|124|R/I|aGa/aTa|||-1||EntrezGene||||||1:g.85733608C>A||||||||||||||,A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.404G>T|NP_003912.1:p.Arg135Ile|684|404|135|R/I|aGa/aTa|||-1||EntrezGene||YES||||1:g.85733608C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:54,81:135,2:0.0146:2,2:43.5:1:37:0:1:1.5:60:4:0.0146:0:1	0/0:265:0:0,0:107,158:265,0:0:2,0:25:1:11:0:1:0:60:0:0:0:4
    178. 

  178. 1	85733626	85733626	G	T	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon3:c.C353A:p.A118D,BCL10:NM_003921:exon3:c.C386A:p.A129D	.	.	.	.	.	.	.	.	.	.	.	0.05	0.395	D	0.421	0.336	B	0.203	0.353	B	0.003	0.361	N	0.900	0.361	D	1.735	0.450	L	.	.	.	-1.86	0.435	N	0.626	0.651	-0.992	0.321	T	0.098	0.367	T	0.002	0.048	T	4.821	0.647	24.8	0.997	0.785	0.949	0.626	D	c	0.236	0.387	1.000	0.747	0.722	0.854	0	5.98	0.971	4.370	0.590	0.998	0.613	1.000	0.715	0.999	0.750	12.247	0.537	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	225	1	85733626	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=116;VD=2;AF=0.0172;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.11506;SOR=inf;LSEQ=ATCTGGAGAGGTTGTTCGTG;RSEQ=CTCCATCTGGAAAAGGTTCA;CSQ=T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|3/3||NM_001320715.2:c.353C>A|NP_001307644.1:p.Ala118Asp|633|353|118|A/D|gCc/gAc|||-1||EntrezGene||||||1:g.85733626G>T||||||||||||||,T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.386C>A|NP_003912.1:p.Ala129Asp|666|386|129|A/D|gCc/gAc|||-1||EntrezGene||YES||||1:g.85733626G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:116:2:1,1:43,71:114,2:0.0172:2,2:43:0:37:0:1:1.64:60:4:0.0177:0:1	0/0:225:0:0,0:84,141:225,0:0:2,0:37.3:1:36.5:1:1:0:60:74:1:0:0.1
    179. 

  179. 1	85733637	85733637	A	-	exonic	BCL10	.	frameshift deletion	BCL10:NM_003921:exon3:c.375delT:p.P126Qfs*22	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	201	1	85733636	.	GA	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=95;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.46038;SOR=0;LSEQ=GTTGTTCGTGGCTCCATCTG;RSEQ=AAAGGTTCACAACTGCTACA;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|BCL10|8915|Transcript|NM_001320715.2|protein_coding||2/2|NM_001320715.2:c.347-5del|||||||||-1||EntrezGene||||||1:g.85733640del||||||||||||||,-|frameshift_variant|HIGH|BCL10|8915|Transcript|NM_003921.5|protein_coding|3/3||NM_003921.5:c.375del|NP_003912.1:p.Pro126GlnfsTer22|655|375|125|F/X|ttT/tt|||-1||EntrezGene||YES||||1:g.85733640del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:95:0:0,0:35,60:95,0:0:2,0:35.6:1:36.5:1:1:0:60:94:1:0:0.3	0/1:201:2:1,1:75,124:199,2:0.01:2,2:45.5:1:37:0:1:1.65:60:4:0.01:0:0
    180. 

  180. 1	85736343	85736343	C	T	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon2:c.G304A:p.E102K,BCL10:NM_003921:exon2:c.G304A:p.E102K	.	.	.	.	.	.	.	.	.	.	.	0.067	0.359	T	0.818	0.437	P	0.559	0.477	P	0.000	0.629	D	0.996	0.432	D	1.67	0.430	L	0.91	0.449	T	-1.75	0.414	N	0.519	0.561	-1.101	0.039	T	0.096	0.362	T	0.008	0.204	T	5.511	0.749	26.3	0.999	0.988	0.969	0.715	D	c	0.516	0.594	1.000	0.747	0.722	0.854	0	5.99	0.973	4.596	0.605	0.852	0.362	1.000	0.715	1.000	0.888	15.590	0.762	Death-like domain	.	.	ID=COSV105298992;OCCURENCE=1(urinary_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	82	1	85736343	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=2;AF=0.1176;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02804;SOR=inf;LSEQ=ATTTCTAAGTTTCAGCACTT;RSEQ=ATCTGTAATCTTCTGTATCA;CSQ=T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|2/3||NM_001320715.2:c.304G>A|NP_001307644.1:p.Glu102Lys|584|304|102|E/K|Gaa/Aaa|||-1||EntrezGene||||||1:g.85736343C>T||||||||||||||,T|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|2/3||NM_003921.5:c.304G>A|NP_003912.1:p.Glu102Lys|584|304|102|E/K|Gaa/Aaa|||-1||EntrezGene||YES||||1:g.85736343C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:17:2:1,1:8,7:15,2:0.1176:2,2:27.5:1:37:0:1:1.13389:60:4:0.1176:0:1	0/0:82:0:0,0:57,25:82,0:0:2,0:36.7:1:35.9:1:1:0:60:26.333:1:0:0.1
    181. 

  181. 1	85736352	85736352	T	C	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon2:c.A295G:p.I99V,BCL10:NM_003921:exon2:c.A295G:p.I99V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.992	0.629	D	0.992	0.790	D	0.000	0.843	D	1.000	0.537	D	2.045	0.562	M	0.87	0.464	T	-0.85	0.232	N	0.437	0.501	-0.774	0.567	T	0.185	0.535	T	0.008	0.220	T	4.812	0.646	24.8	0.998	0.889	0.976	0.758	D	c	0.702	0.708	1.000	0.747	0.722	0.854	0	5.99	0.973	4.602	0.606	0.964	0.580	1.000	0.715	1.000	0.888	16.494	0.840	CARD domain|Death-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	91	1	85736352	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.63577;SOR=0;LSEQ=TTTCAGCACTTCATCTGTAA;RSEQ=CTTCTGTATCAGGAAGTTCT;CSQ=C|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|2/3||NM_001320715.2:c.295A>G|NP_001307644.1:p.Ile99Val|575|295|99|I/V|Att/Gtt|||-1||EntrezGene||||||1:g.85736352T>C||||||||||||||,C|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|2/3||NM_003921.5:c.295A>G|NP_003912.1:p.Ile99Val|575|295|99|I/V|Att/Gtt|||-1||EntrezGene||YES||||1:g.85736352T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:13,10:23,0:0:2,0:27.9:1:36.5:1:1:0:60:46:1:0:0.1	0/1:91:2:1,1:57,32:89,2:0.022:2,2:43.5:1:37:0:1:1.76928:60:4:0.0222:0:1
    182. 

  182. 1	85736510	85736510	-	T	exonic	BCL10	.	frameshift insertion	BCL10:NM_001320715:exon2:c.136dupA:p.I46Nfs*4,BCL10:NM_003921:exon2:c.136dupA:p.I46Nfs*4	.	.	.	.	.	.	.	.	.	rs387906351	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	21298	T-cell_acute_lymphoblastic_leukemia|Carcinoma_of_colon	Human_Phenotype_Ontology:HP:0006727,MONDO:MONDO:0004963,MedGen:C1961099,SNOMED_CT:277575008|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000	no_assertion_criteria_provided	Pathogenic	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU130116504	READ-US|1|143|0.00699301	0.25	38	100	1	85736510	.	A	AT	38	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=10;VD=0;AF=0;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.82569;SOR=0;LSEQ=CAGTGTCTTCTCTACTGAGT;RSEQ=TTTTTTTTGCACGTAGATGA;CSQ=T|frameshift_variant|HIGH|BCL10|8915|Transcript|NM_001320715.2|protein_coding|2/3||NM_001320715.2:c.136dup|NP_001307644.1:p.Ile46AsnfsTer4|416-417|136-137|46|I/NX|ata/aAta|rs387906351||-1||EntrezGene||||||1:g.85736518dup||||||||||||pathogenic||1,T|frameshift_variant|HIGH|BCL10|8915|Transcript|NM_003921.5|protein_coding|2/3||NM_003921.5:c.136dup|NP_003912.1:p.Ile46AsnfsTer4|416-417|136-137|46|I/NX|ata/aAta|rs387906351||-1||EntrezGene||YES||||1:g.85736518dup||||||||||||pathogenic||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:3,7:10,0:0:2,0:42.7:1:35.8:1:1:0:60:20:1:0:0	0/1:100:2:1,1:40,55:95,2:0.02:2,2:53.9:1:38.7:0:1:1.37:62.8:4:0.0211:0:0
    183. 

  183. 1	85741968	85741968	G	C	intronic	BCL10	.	.	.	0.17	0.0628	0.0172	0.0933	0.0563	0.1388	0.0725	0.0771	0.0663	rs12562182	rs12562182	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65353769;OCCURENCE=2(liver),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU10026866	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235	0.25	204	12	1	85741968	.	G	C	204	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=58;AF=0.3694;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00519;SOR=inf;LSEQ=CGCCCGCCCTGGGCACAGCT;RSEQ=CGTTACTCACGTCCTTCTTC;CSQ=C|intron_variant|MODIFIER|BCL10|8915|Transcript|NM_001320715.2|protein_coding||1/2|NM_001320715.2:c.57+11C>G|||||||rs12562182&COSV65353769||-1||EntrezGene||||||1:g.85741968G>C|0.0933|0.0159|0.1115|0.04523|0.1213|0.07633|0.08408|0.08851|0.1593|0.1677|SAS||0&1|0&1,C|intron_variant|MODIFIER|BCL10|8915|Transcript|NM_003921.5|protein_coding||1/2|NM_003921.5:c.57+11C>G|||||||rs12562182&COSV65353769||-1||EntrezGene||YES||||1:g.85741968G>C|0.0933|0.0159|0.1115|0.04523|0.1213|0.07633|0.08408|0.08851|0.1593|0.1677|SAS||0&1|0&1,C|upstream_gene_variant|MODIFIER|LOC646626|646626|Transcript|NR_045484.1|lncRNA||||||||||rs12562182&COSV65353769|73|1||EntrezGene||YES||||1:g.85741968G>C|0.0933|0.0159|0.1115|0.04523|0.1213|0.07633|0.08408|0.08851|0.1593|0.1677|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:157:58:19,39:42,56:98,58:0.3694:2,2:38.5:1:34.9:1:0.23762:1.53523:60:28:0.3784:0:2	0/0:12:0:0,0:5,7:12,0:0:2,0:41.6:1:31.7:1:1:0:60:5:1:0:1.9
    184. 

  184. 1	85742023	85742023	C	A	exonic	BCL10	.	nonsynonymous SNV	BCL10:NM_001320715:exon1:c.G13T:p.A5S,BCL10:NM_003921:exon1:c.G13T:p.A5S	0.12	0.0198	0.0032	0.0191	0.1026	0.1165	0.0049	0.0206	0.0224	rs12037217	rs12037217	0.025	0.473	D	0.0	0.026	B	0.001	0.040	B	0.229	0.159	N	0.971	0.256	N	0.69	0.170	N	.	.	.	-0.44	0.146	N	0.024	0.007	-1.010	0.268	T	0.023	0.098	T	.	.	.	3.053	0.427	22.4	0.995	0.684	0.275	0.231	N	c	-0.418	-0.231	1.000	0.747	0.442	0.072	0	3.19	0.356	1.770	0.379	0.935	0.490	0.983	0.354	0.943	0.417	10.137	0.417	.	.	.	ID=COSV65354093;OCCURENCE=1(lung)	448386	Immunodeficiency_37	MONDO:MONDO:0014491,MedGen:C4015195,OMIM:616098	criteria_provided,_single_submitter	Benign	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	MU22824378	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235	0.25	110	24	1	85742023	.	C	A	110	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=250;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCTCGGTGAGGGACGGTG;RSEQ=GGTGGGCTCCATGGTGGAGG;CSQ=A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_001320715.2|protein_coding|1/3||NM_001320715.2:c.13G>T|NP_001307644.1:p.Ala5Ser|293|13|5|A/S|Gca/Tca|rs12037217&CM062459&COSV65354093||-1||EntrezGene||||||1:g.85742023C>A|0.03004|0.004127|0.01915|0.08776|0.12|0.004535|0.02497|0.03492|0.01868|0.12|gnomAD_EAS|benign|0&0&1|1&1&1,A|missense_variant|MODERATE|BCL10|8915|Transcript|NM_003921.5|protein_coding|1/3||NM_003921.5:c.13G>T|NP_003912.1:p.Ala5Ser|293|13|5|A/S|Gca/Tca|rs12037217&CM062459&COSV65354093||-1||EntrezGene||YES||||1:g.85742023C>A|0.03004|0.004127|0.01915|0.08776|0.12|0.004535|0.02497|0.03492|0.01868|0.12|gnomAD_EAS|benign|0&0&1|1&1&1,A|upstream_gene_variant|MODIFIER|LOC646626|646626|Transcript|NR_045484.1|lncRNA||||||||||rs12037217&CM062459&COSV65354093|18|1||EntrezGene||YES||||1:g.85742023C>A|0.03004|0.004127|0.01915|0.08776|0.12|0.004535|0.02497|0.03492|0.01868|0.12|gnomAD_EAS|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:250:0:0,0:104,146:250,0:0:2,0:36.9:1:35.9:1:1:0:60:30.25:1:0:0.8	0/1:24:10:3,7:9,5:14,10:0.4167:2,2:36.1:1:33.2:1:0.21376:3.93763:60:9:0.4091:0:1.3
    185. 

  185. 1	97547922	97547922	A	G	exonic	DPYD	.	synonymous SNV	DPYD:NM_000110:exon22:c.T2871C:p.G957G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	193	1	97547922	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=29;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.75529;SOR=0;LSEQ=TTACAGGTCATGTAGCATTT;RSEQ=CCACAGTTGATACACATTTC;CSQ=G|synonymous_variant|LOW|DPYD|1806|Transcript|NM_000110.4|protein_coding|22/23||NM_000110.4:c.2871T>C|NP_000101.2:p.Gly957%3D|2983|2871|957|G|ggT/ggC|||-1||EntrezGene||YES||||1:g.97547922A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:29:0:0,0:15,14:29,0:0:2,0:36.9:1:36.6:1:1:0:60:58:1:0:0.2	0/1:193:2:1,1:101,90:191,2:0.0104:2,2:46.5:1:37:0:1:1.12155:60:4:0.0105:0:1
    186. 

  186. 1	97700372	97700372	A	G	ncRNA_intronic	DPYD-AS1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	196	1	97700372	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=113;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.40159;SOR=0;LSEQ=ACATTGCATTTGTGAGATGG;RSEQ=GATTTTTAAAAGGGACAGAC;CSQ=G|intron_variant|MODIFIER|DPYD|1806|Transcript|NM_000110.4|protein_coding||19/22|NM_000110.4:c.2442+36T>C|||||||rs1462769316||-1||EntrezGene||YES||||1:g.97700372A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|DPYD-AS1|100873932|Transcript|NR_046590.1|lncRNA||1/4|NR_046590.1:n.65-30598A>G|||||||rs1462769316||1||EntrezGene||YES||||1:g.97700372A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:113:0:0,0:75,38:113,0:0:2,0:35.4:1:36.7:1:1:0:60:112:1:0:0.1	0/1:196:2:1,1:130,64:194,2:0.0102:2,2:39.5:1:37:0:1:2.02336:60:4:0.0104:0:1.5
    187. 

  187. 1	97770870	97770870	G	A	exonic	DPYD	.	synonymous SNV	DPYD:NM_000110:exon18:c.C2244T:p.G748G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	44	285	1	97770870	.	G	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=290;VD=3;AF=0.0103;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.12763;SOR=inf;LSEQ=CCCACTGCTGGCCAAGGTGT;RSEQ=CCATCAGATTTTAATCCCAT;CSQ=A|synonymous_variant|LOW|DPYD|1806|Transcript|NM_000110.4|protein_coding|18/23||NM_000110.4:c.2244C>T|NP_000101.2:p.Gly748%3D|2356|2244|748|G|ggC/ggT|||-1||EntrezGene||YES||||1:g.97770870G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|DPYD-AS1|100873932|Transcript|NR_046590.1|lncRNA||2/4|NR_046590.1:n.129-875G>A|||||||||1||EntrezGene||YES||||1:g.97770870G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:290:3:1,2:133,154:287,3:0.0103:2,2:45:1:28.3:1:1:1.72415:60:2:0.0069:0:1	0/0:285:0:0,0:138,147:285,0:0:2,0:38.6:1:36.4:1:1:0:60:70.25:1:0:0.1
    188. 

  188. 1	97770950	97770950	C	T	ncRNA_intronic	DPYD-AS1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	191	1	97770950	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=118;VD=2;AF=0.0169;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.14506;SOR=inf;LSEQ=ACCACCTATGCAAGACACAT;RSEQ=AACATTTTCATGCAGCTCTT;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|DPYD|1806|Transcript|NM_000110.4|protein_coding||17/22|NM_000110.4:c.2180-16G>A|||||||||-1||EntrezGene||YES||||1:g.97770950C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DPYD-AS1|100873932|Transcript|NR_046590.1|lncRNA||2/4|NR_046590.1:n.129-795C>T|||||||||1||EntrezGene||YES||||1:g.97770950C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:118:2:1,1:37,79:116,2:0.0169:2,2:29.5:1:37:0:0.54223:2.12:60:4:0.0172:0:1	0/0:191:0:0,0:69,122:191,0:0:2,0:37.6:1:36.9:1:1:0:60:382:1:0:0.1
    189. 

  189. 1	97770956	97770956	T	C	ncRNA_intronic	DPYD-AS1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	182	1	97770956	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.39579;SOR=0;LSEQ=TATGCAAGACACATCAACAT;RSEQ=TTCATGCAGCTCTTATAAGA;CSQ=C|intron_variant|MODIFIER|DPYD|1806|Transcript|NM_000110.4|protein_coding||17/22|NM_000110.4:c.2180-22A>G|||||||||-1||EntrezGene||YES||||1:g.97770956T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|DPYD-AS1|100873932|Transcript|NR_046590.1|lncRNA||2/4|NR_046590.1:n.129-789T>C|||||||||1||EntrezGene||YES||||1:g.97770956T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:107:0:0,0:33,74:107,0:0:2,0:28.8:1:36.4:1:1:0:60:214:1:0:0.1	0/1:182:2:1,1:63,116:179,2:0.011:2,2:45:1:31:1:1:1.83:60:4:0.0112:0:1
    190. 

  190. 1	97915679	97915679	C	A	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon14:c.G1841T:p.S614I	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.105	0.974	H	-1.97	0.852	D	-5.85	0.885	D	0.511	0.965	0.627	0.923	D	0.749	0.915	D	0.166	0.845	D	6.351	0.877	29.4	0.996	0.740	0.981	0.798	D	c	0.829	0.793	1.000	0.747	0.638	0.428	0	5.31	0.750	7.568	0.814	0.892	0.403	1.000	0.715	0.995	0.604	18.986	0.927	Aldolase-type TIM barrel|Dihydroorotate dehydrogenase domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	344	1	97915679	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=49;VD=2;AF=0.0408;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01527;SOR=inf;LSEQ=AATATGCAGCCGTTTTCTCA;RSEQ=TGATGAGCTCAATATTCAGA;CSQ=A|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|14/23||NM_000110.4:c.1841G>T|NP_000101.2:p.Ser614Ile|1953|1841|614|S/I|aGt/aTt|||-1||EntrezGene||YES||||1:g.97915679C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:49:2:1,1:25,22:47,2:0.0408:2,2:48:1:37:0:1:1.13339:60:4:0.0417:0:1	0/0:344:0:0,0:184,160:344,0:0:2,0:38.5:1:35.4:1:1:0:60:25.462:1:0:0.2
    191. 

  191. 1	97981355	97981355	C	T	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon13:c.G1667A:p.S556N	.	.	.	.	.	.	.	.	.	.	.	0.029	0.457	D	0.386	0.327	B	0.283	0.387	B	0.000	0.843	N	1.000	0.588	D	1.13	0.290	L	-0.67	0.725	T	-2.09	0.476	N	0.084	0.084	-0.738	0.586	T	0.164	0.501	T	0.039	0.588	D	3.941	0.531	23.5	0.994	0.627	0.962	0.678	D	c	0.048	0.143	0.738	0.231	0.638	0.428	0	4.29	0.502	5.713	0.678	0.892	0.403	1.000	0.715	0.984	0.507	14.030	0.640	Aldolase-type TIM barrel|Dihydroorotate dehydrogenase domain	.	.	ID=COSV64592046;OCCURENCE=2(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	291	1	97981355	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=2;AF=0.0227;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.05344;SOR=inf;LSEQ=CTCTTCGAATCATTGATGTG;RSEQ=TGGTGGCTGGAGTTGCGCTA;CSQ=T|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|13/23||NM_000110.4:c.1667G>A|NP_000101.2:p.Ser556Asn|1779|1667|556|S/N|aGc/aAc|rs1354053040&COSV64592046||-1||EntrezGene||YES||||1:g.97981355C>T|7.98e-06|0|0|0|0|0|1.767e-05|0|0|1.767e-05|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:88:2:1,1:51,35:86,2:0.0227:2,2:28:1:37:0:1:1.45075:60:4:0.023:0:1	0/0:291:0:0,0:162,129:291,0:0:2,0:37.6:1:35.9:1:1:0:60:35.375:1:0:0.2
    192. 

  192. 1	98039394	98039394	C	T	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon11:c.G1261A:p.E421K	.	.	.	.	.	.	.	.	.	.	.	0.453	0.089	T	0.003	0.102	B	0.006	0.112	B	0.000	0.843	D	1	0.810	D	2.445	0.712	M	-2.8	0.911	D	-2.49	0.542	N	0.607	0.756	0.024	0.827	D	0.622	0.867	D	0.075	0.724	D	2.879	0.407	21.8	0.997	0.790	0.976	0.759	D	c	0.160	0.294	1.000	0.747	0.638	0.428	0	5.81	0.924	7.469	0.798	0.931	0.441	1.000	0.715	0.405	0.255	17.852	0.886	FAD/NAD(P)-binding domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	170	1	98039394	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=6;SSF=0.5551;SOR=0;LSEQ=GACCATCTGATCTTCATCTT;RSEQ=ATTCCATTTTCCAGTTTCAT;CSQ=T|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|11/23||NM_000110.4:c.1261G>A|NP_000101.2:p.Glu421Lys|1373|1261|421|E/K|Gaa/Aaa|||-1||EntrezGene||YES||||1:g.98039394C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:58:0:0,0:30,28:58,0:0:2,0:37.4:1:36.8:1:1:0:60:116:1:0:0.1	0/1:170:2:1,1:100,68:168,2:0.0118:2,2:32:1:37:0:1:1.46714:60:4:0.0118:0:1
    193. 

  193. 1	98039401	98039401	T	-	exonic	DPYD	.	frameshift deletion	DPYD:NM_000110:exon11:c.1254delA:p.K418Nfs*12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	178	1	98039400	.	AT	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=59;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.56329;SOR=0;LSEQ=CTGATCTTCATCTTCATTCC;RSEQ=TTTCCAGTTTCATCTTGCTC;CSQ=-|frameshift_variant|HIGH|DPYD|1806|Transcript|NM_000110.4|protein_coding|11/23||NM_000110.4:c.1254del|NP_000101.2:p.Lys418AsnfsTer12|1366|1254|418|K/X|aaA/aa|||-1||EntrezGene||YES||||1:g.98039404del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:59:0:0,0:30,29:59,0:0:2,0:37:1:35.7:1:1:0:60:58:1:0:0.1	0/1:178:2:1,1:99,77:176,2:0.0112:2,2:32.5:1:37:0:1:1.28387:60:4:0.0114:0:0
    194. 

  194. 1	98039554	98039554	C	A	intronic	DPYD	.	.	.	0.0001	3.231e-05	0	0	0	0	0	6.672e-05	0	rs368600943	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	110	1	98039554	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.88344;SOR=0;LSEQ=AAAACAGAACAGAGAAGAAA;RSEQ=TTGAAAATGTTTCTTATTCC;CSQ=A|intron_variant|MODIFIER|DPYD|1806|Transcript|NM_000110.4|protein_coding||10/22|NM_000110.4:c.1129-28G>T|||||||rs368600943||-1||EntrezGene||YES||||1:g.98039554C>A|3.264e-05|6.363e-05|0|0|0|0|4.549e-05|0.0003353|0|0.0003353|gnomAD_OTH|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:2,5:7,0:0:2,0:24.4:1:37:0:1:0:60:14:1:0:0.4	0/1:110:2:1,1:28,80:108,2:0.0182:2,2:33:1:37:0:0.45955:2.82:60:4:0.0182:0:1
    195. 

  195. 1	98058931	98058931	C	T	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon10:c.G971A:p.C324Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.917	0.635	D	0.000	0.843	D	1	0.810	D	1.73	0.448	L	-2.48	0.891	D	-9.11	0.982	D	0.507	0.936	0.353	0.884	D	0.756	0.917	D	0.098	0.770	D	6.478	0.893	30	0.998	0.858	0.984	0.818	D	c	0.815	0.833	1.000	0.747	0.638	0.428	0	6.17	0.997	7.557	0.811	0.935	0.490	1.000	0.715	0.997	0.653	19.060	0.930	FAD/NAD(P)-binding domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	297	1	98058931	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=177;VD=2;AF=0.0113;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13895;SOR=inf;LSEQ=TCGATGGCAATGGAGAGTGA;RSEQ=AGGCGCACATTCCTGAATGA;CSQ=T|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|10/23||NM_000110.4:c.971G>A|NP_000101.2:p.Cys324Tyr|1083|971|324|C/Y|tGt/tAt|||-1||EntrezGene||YES||||1:g.98058931C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:177:2:1,1:80,95:175,2:0.0113:2,2:38:0:37:0:1:1.19:60:4:0.0113:0:1	0/0:297:0:0,0:117,180:297,0:0:2,0:33.6:1:36.8:1:1:0:60:594:1:0:0.1
    196. 

  196. 1	98348873	98348873	C	T	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon2:c.G97A:p.A33T,DPYD:NM_001160301:exon2:c.G97A:p.A33T	.	.	.	.	.	.	.	.	.	.	.	0.561	0.083	T	0.001	0.067	B	0.002	0.063	B	0.002	0.382	N	1.000	0.231	N	0.55	0.145	N	-1.68	0.829	D	0.36	0.057	N	0.132	0.152	-1.002	0.292	T	0.115	0.408	T	0.012	0.301	T	2.033	0.305	16.42	0.973	0.329	0.183	0.200	N	c	-0.556	-0.347	0.009	0.118	0.693	0.558	0	3.56	0.397	0.840	0.271	0.935	0.490	0.485	0.266	0.979	0.486	10.606	0.444	Alpha-helical ferredoxin	.	.	ID=COSV60076086;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	1	98348873	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.73402;SOR=0;LSEQ=TTTCTTGTCTAATTTCTTGG;RSEQ=CGAAGTGGAACGCAGAGTTG;CSQ=T|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|2/23||NM_000110.4:c.97G>A|NP_000101.2:p.Ala33Thr|209|97|33|A/T|Gcc/Acc|COSV60076086||-1||EntrezGene||YES||||1:g.98348873C>T|||||||||||||1|1,T|missense_variant|MODERATE|DPYD|1806|Transcript|NM_001160301.1|protein_coding|2/6||NM_001160301.1:c.97G>A|NP_001153773.1:p.Ala33Thr|234|97|33|A/T|Gcc/Acc|COSV60076086||-1||EntrezGene||||||1:g.98348873C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:26:0:0,0:13,13:26,0:0:2,0:33.7:1:36.1:1:1:0:60:52:1:0:0.4	0/1:156:2:1,1:72,82:154,2:0.0128:2,2:33.5:1:37:0:1:1.14:60:4:0.0132:0:2
    197. 

  197. 1	98348885	98348885	G	A	exonic	DPYD	.	nonsynonymous SNV	DPYD:NM_000110:exon2:c.C85T:p.R29C,DPYD:NM_001160301:exon2:c.C85T:p.R29C	0.93	0.7199	0.5991	0.7769	0.8642	0.9284	0.7140	0.7626	0.7352	rs1801265	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV60076627;OCCURENCE=1(skin)	106000	Dihydropyrimidine_dehydrogenase_deficiency|not_provided	MONDO:MONDO:0010130,MedGen:C1959620,OMIM:274270,Orphanet:ORPHA1675|MedGen:CN517202	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	MU4134499	SKCA-BR|1|100|0.01,COCA-CN|5|321|0.0155763	0.75	263	155	1	98348885	.	G	A	263	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=6;AF=0.2222;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00212;LSEQ=TTTCTTGGCCGAAGTGGAAC;RSEQ=CAGAGTTGCATGAGTTTGTG;CSQ=A|missense_variant|MODERATE|DPYD|1806|Transcript|NM_000110.4|protein_coding|2/23||NM_000110.4:c.85C>T|NP_000101.2:p.Arg29Cys|197|85|29|R/C|Cgt/Tgt|rs1801265&CM970421&COSV60076627||-1||EntrezGene||YES||||1:g.98348885G>A|0.7718|0.5869|0.7887|0.8847|0.928|0.7068|0.7774|0.7744|0.745|0.928|gnomAD_EAS|not_provided&benign|0&0&1|1&1&1,A|missense_variant|MODERATE|DPYD|1806|Transcript|NM_001160301.1|protein_coding|2/6||NM_001160301.1:c.85C>T|NP_001153773.1:p.Arg29Cys|222|85|29|R/C|Cgt/Tgt|rs1801265&CM970421&COSV60076627||-1||EntrezGene||||||1:g.98348885G>A|0.7718|0.5869|0.7887|0.8847|0.928|0.7068|0.7774|0.7744|0.745|0.928|gnomAD_EAS|not_provided&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:27:6:3,3:10,9:19,6:0.2222:2,2:35:1:37:0:1:1.10643:60:12:0.2308:0:1.2	1/1:155:154:69,85:0,0:0,154:0.9935:0,2:39.7:1:36.3:1:1:0:60:50.333:0.9934:0:1.1
    198. 

  198. 1	98348901	98348901	T	C	exonic	DPYD	.	synonymous SNV	DPYD:NM_000110:exon2:c.A69G:p.Q23Q,DPYD:NM_001160301:exon2:c.A69G:p.Q23Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	148	1	98348901	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.70636;SOR=0;LSEQ=GAACGCAGAGTTGCATGAGT;RSEQ=TGTGTTCGAGGATTTAAAGC;CSQ=C|synonymous_variant|LOW|DPYD|1806|Transcript|NM_000110.4|protein_coding|2/23||NM_000110.4:c.69A>G|NP_000101.2:p.Gln23%3D|181|69|23|Q|caA/caG|||-1||EntrezGene||YES||||1:g.98348901T>C||||||||||||||,C|synonymous_variant|LOW|DPYD|1806|Transcript|NM_001160301.1|protein_coding|2/6||NM_001160301.1:c.69A>G|NP_001153773.1:p.Gln23%3D|206|69|23|Q|caA/caG|||-1||EntrezGene||||||1:g.98348901T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:28:0:0,0:15,13:28,0:0:2,0:36.9:1:35.3:1:1:0:60:56:1:0:0.3	0/1:148:2:1,1:61,85:146,2:0.0135:2,2:51.5:1:31:1:1:1.39:60:4:0.0137:0:2
    199. 

  199. 1	115251167	115251167	C	A	exonic	NRAS	.	nonsynonymous SNV	NRAS:NM_002524:exon5:c.G559T:p.V187L	.	.	.	.	.	.	.	.	.	.	.	0.319	0.136	T	0.0	0.026	B	0.001	0.040	B	0.527	0.117	U	0.997	0.229	N	1.11	0.288	L	-0.26	0.672	T	-0.52	0.162	N	0.067	0.054	-1.079	0.076	T	0.054	0.230	T	0.005	0.138	T	2.633	0.378	20.4	0.981	0.376	0.890	0.489	D	c	-0.375	-0.175	0.997	0.351	0.707	0.730	0	4.84	0.620	-0.139	0.103	0.935	0.490	0.120	0.230	1.000	0.888	2.212	0.037	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	256	1	115251167	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=115;VD=3;AF=0.0261;SHIFT3=0;MSI=3;MSILEN=2;SSF=0.02925;SOR=inf;LSEQ=CTCACCTTGTTACATCACCA;RSEQ=ACATGGCAATCCCATACAAC;CSQ=A|missense_variant|MODERATE|NRAS|4893|Transcript|NM_002524.5|protein_coding|5/7||NM_002524.5:c.559G>T|NP_002515.1:p.Val187Leu|690|559|187|V/L|Gtg/Ttg|||-1||EntrezGene||YES||||1:g.115251167C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:115:3:1,2:61,51:112,3:0.0261:2,2:61.3:1:28.3:1:0.59408:2.37448:60:2:0.018:0:1.3	0/0:256:0:0,0:138,118:256,0:0:2,0:40.4:1:36.8:1:1:0:60:512:1:0:0
    200. 

  200. 1	115251172	115251172	G	A	exonic	NRAS	.	nonsynonymous SNV	NRAS:NM_002524:exon5:c.C554T:p.P185L	.	.	.	.	.	.	.	.	.	.	.	0.08	0.335	T	0.0	0.026	B	0.001	0.040	B	0.009	0.308	U	0.683	0.332	D	0.625	0.159	N	-0.21	0.663	T	-0.64	0.187	N	0.284	0.343	-1.037	0.182	T	0.097	0.365	T	0.007	0.200	T	3.121	0.435	22.6	0.979	0.359	0.987	0.854	D	c	-0.093	0.142	1.000	0.747	0.707	0.730	0	5.76	0.907	3.982	0.564	1.048	0.713	0.995	0.385	0.996	0.625	20.328	0.987	.	.	.	ID=COSV65757313;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	268	1	115251172	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=117;VD=2;AF=0.0171;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0918;SOR=inf;LSEQ=CTTGTTACATCACCACACAT;RSEQ=GCAATCCCATACAACCCTGA;CSQ=A|missense_variant|MODERATE|NRAS|4893|Transcript|NM_002524.5|protein_coding|5/7||NM_002524.5:c.554C>T|NP_002515.1:p.Pro185Leu|685|554|185|P/L|cCa/cTa|COSV65757313||-1||EntrezGene||YES||||1:g.115251172G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:117:2:1,1:63,52:115,2:0.0171:2,2:38:1:37:0:1:1.20954:60:4:0.0175:0:1.5	0/0:268:0:0,0:142,126:268,0:0:2,0:38.9:1:36:1:1:0:60:43.667:1:0:0
    201. 

  201. 1	115251228	115251228	G	A	exonic	NRAS	.	synonymous SNV	NRAS:NM_002524:exon5:c.C498T:p.Y166Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	74	236	1	115251228	.	G	A	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=4;AF=0.0374;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00911;SOR=inf;LSEQ=CTGTTGAGTTTTTTCATTCG;RSEQ=TACTGGCGTATTTCTCTTAC;CSQ=A|synonymous_variant|LOW|NRAS|4893|Transcript|NM_002524.5|protein_coding|5/7||NM_002524.5:c.498C>T|NP_002515.1:p.Tyr166%3D|629|498|166|Y|taC/taT|||-1||EntrezGene||YES||||1:g.115251228G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:4:2,2:46,57:103,4:0.0374:2,2:44:1:37:0:1:1.24:60:8:0.0385:0:1	0/0:236:0:0,0:107,129:236,0:0:2,0:39.9:1:36.4:1:1:0:60:77.667:1:0:0
    202. 

  202. 1	115251234	115251234	G	A	exonic	NRAS	.	synonymous SNV	NRAS:NM_002524:exon5:c.C492T:p.R164R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	225	1	115251234	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=100;VD=2;AF=0.02;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09402;SOR=inf;LSEQ=AGTTTTTTCATTCGGTACTG;RSEQ=CGTATTTCTCTTACCAGTGT;CSQ=A|synonymous_variant|LOW|NRAS|4893|Transcript|NM_002524.5|protein_coding|5/7||NM_002524.5:c.492C>T|NP_002515.1:p.Arg164%3D|623|492|164|R|cgC/cgT|||-1||EntrezGene||YES||||1:g.115251234G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:100:2:1,1:43,55:98,2:0.02:2,2:48:0:37:0:1:1.28:60:4:0.0206:0:1	0/0:225:0:0,0:101,124:225,0:0:2,0:40.3:1:36.5:1:1:0:60:224:1:0:0
    203. 

  203. 1	115256444	115256444	T	C	exonic	NRAS	.	synonymous SNV	NRAS:NM_002524:exon3:c.A267G:p.S89S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	160	1	115256444	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.45102;SOR=0;LSEQ=TAGAGGTTAATATCCGCAAA;RSEQ=GACTTGCTATTATTGATGGC;CSQ=C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001007553.3|protein_coding|||||||||||3093|-1||EntrezGene||||||1:g.115256444T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001130523.3|protein_coding|||||||||||3093|-1||EntrezGene||||||1:g.115256444T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242891.2|protein_coding|||||||||||3093|-1||EntrezGene||YES||||1:g.115256444T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242892.2|protein_coding|||||||||||3093|-1||EntrezGene||||||1:g.115256444T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242893.2|protein_coding|||||||||||3093|-1||EntrezGene||||||1:g.115256444T>C||||||||||||||,C|synonymous_variant|LOW|NRAS|4893|Transcript|NM_002524.5|protein_coding|3/7||NM_002524.5:c.267A>G|NP_002515.1:p.Ser89%3D|398|267|89|S|tcA/tcG|||-1||EntrezGene||YES||||1:g.115256444T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_007158.6|protein_coding|||||||||||3093|-1||EntrezGene||||||1:g.115256444T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:78:0:0,0:47,31:78,0:0:2,0:32.3:1:35.8:1:1:0:60:25:1:0:0.1	0/1:160:2:1,1:85,73:158,2:0.0125:2,2:13:0:37:0:1:1.16327:60:4:0.0127:0:1
    204. 

  204. 1	115256503	115256503	G	T	exonic	NRAS	.	nonsynonymous SNV	NRAS:NM_002524:exon3:c.C208A:p.Q70K	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.583	0.370	P	0.415	0.431	B	0.000	0.537	U	1	0.810	D	1.605	0.410	L	-0.42	0.695	T	-3.84	0.722	D	0.832	0.820	-0.584	0.655	T	0.225	0.590	T	0.033	0.549	D	5.043	0.679	25.2	0.995	0.705	0.994	0.952	D	c	0.516	0.603	1.000	0.747	0.722	0.854	0	5.08	0.682	9.899	0.986	1.048	0.713	1.000	0.715	1.000	0.888	18.663	0.914	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	179	1	115256503	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.18718;SOR=inf;LSEQ=TTCGCCTGTCCTCATGTATT;RSEQ=GTCTCTCATGGCACTGTACT;CSQ=T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001007553.3|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||||||1:g.115256503G>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001130523.3|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||||||1:g.115256503G>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242891.2|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||YES||||1:g.115256503G>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242892.2|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||||||1:g.115256503G>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242893.2|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||||||1:g.115256503G>T|||||||||||||1|1,T|missense_variant|MODERATE|NRAS|4893|Transcript|NM_002524.5|protein_coding|3/7||NM_002524.5:c.208C>A|NP_002515.1:p.Gln70Lys|339|208|70|Q/K|Caa/Aaa|COSV54744612||-1||EntrezGene||YES||||1:g.115256503G>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_007158.6|protein_coding||||||||||COSV54744612|3034|-1||EntrezGene||||||1:g.115256503G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:66,69:135,2:0.0146:2,2:10:0:37:0:1:1.05:60:4:0.0147:0:1	0/0:179:0:0,0:79,100:179,0:0:2,0:40.7:1:36:1:1:0:60:88.5:1:0:0.1
    205. 

  205. 1	115256514	115256514	G	A	exonic	NRAS	.	nonsynonymous SNV	NRAS:NM_002524:exon3:c.C197T:p.A66V	.	.	.	.	.	.	.	.	.	.	.	0.017	0.512	D	0.042	0.201	B	0.028	0.201	B	0.000	0.559	U	1	0.810	D	2.815	0.823	M	-1.12	0.776	T	-3.8	0.717	D	0.786	0.777	-0.360	0.733	T	0.361	0.723	T	0.026	0.494	D	4.927	0.662	25.0	0.998	0.901	0.993	0.940	D	c	0.347	0.478	1.000	0.747	0.722	0.854	0	5.08	0.682	9.899	0.986	1.048	0.713	1.000	0.715	1.000	0.888	18.663	0.914	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	174	1	115256514	.	G	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=133;VD=2;AF=0.015;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.18688;SOR=inf;LSEQ=TCATGTATTGGTCTCTCATG;RSEQ=CACTGTACTCTTCTTGTCCA;CSQ=A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001007553.3|protein_coding|||||||||||3023|-1||EntrezGene||||||1:g.115256514G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001130523.3|protein_coding|||||||||||3023|-1||EntrezGene||||||1:g.115256514G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242891.2|protein_coding|||||||||||3023|-1||EntrezGene||YES||||1:g.115256514G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242892.2|protein_coding|||||||||||3023|-1||EntrezGene||||||1:g.115256514G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242893.2|protein_coding|||||||||||3023|-1||EntrezGene||||||1:g.115256514G>A||||||||||||||,A|missense_variant|MODERATE|NRAS|4893|Transcript|NM_002524.5|protein_coding|3/7||NM_002524.5:c.197C>T|NP_002515.1:p.Ala66Val|328|197|66|A/V|gCc/gTc|||-1||EntrezGene||YES||||1:g.115256514G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_007158.6|protein_coding|||||||||||3023|-1||EntrezGene||||||1:g.115256514G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:133:2:1,1:66,65:131,2:0.015:2,2:37.5:1:31:1:1:1.01527:60:4:0.0154:0:2	0/0:174:0:0,0:79,95:174,0:0:2,0:40.1:1:36.2:1:1:0:60:86:1:0:0.1
    206. 

  206. 1	115256535	115256535	G	A	exonic	NRAS	.	nonsynonymous SNV	NRAS:NM_002524:exon3:c.C176T:p.A59V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.978	0.725	D	0.000	0.559	U	1	0.810	D	3.385	0.917	M	-2.43	0.887	D	-3.71	0.706	D	0.871	0.859	1.022	0.976	D	0.876	0.959	D	0.468	0.946	D	4.583	0.614	24.4	0.999	0.976	0.991	0.912	D	c	0.976	0.850	1.000	0.747	0.722	0.854	0	4.14	0.477	9.865	0.984	1.048	0.713	1.000	0.715	1.000	0.888	14.776	0.692	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	146	1	115256535	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=125;VD=2;AF=0.016;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.21184;SOR=inf;LSEQ=CACTGTACTCTTCTTGTCCA;RSEQ=CTGTATCCAGTATGTCCAAC;CSQ=A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001007553.3|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||||||1:g.115256535G>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001130523.3|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||||||1:g.115256535G>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242891.2|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||YES||||1:g.115256535G>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242892.2|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||||||1:g.115256535G>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_001242893.2|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||||||1:g.115256535G>A|||||||||||||1&1|1&1,A|missense_variant|MODERATE|NRAS|4893|Transcript|NM_002524.5|protein_coding|3/7||NM_002524.5:c.176C>T|NP_002515.1:p.Ala59Val|307|176|59|A/V|gCt/gTt|COSV54738004&COSV54746465||-1||EntrezGene||YES||||1:g.115256535G>A|||||||||||||1&1|1&1,A|downstream_gene_variant|MODIFIER|CSDE1|7812|Transcript|NM_007158.6|protein_coding||||||||||COSV54738004&COSV54746465|3002|-1||EntrezGene||||||1:g.115256535G>A|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:125:2:1,1:61,62:123,2:0.016:2,2:61:1:37:0:1:1.02:60:4:0.0161:0:1	0/0:146:0:0,0:67,79:146,0:0:2,0:41.5:1:36.5:1:1:0:60:292:1:0:0.1
    207. 

  207. 1	118165691	118165691	C	T	exonic	FAM46C	.	synonymous SNV	FAM46C:NM_017709:exon2:c.C201T:p.H67H	0.36	0.2835	0.2237	0.2470	0.2384	0.0927	0.3663	0.3202	0.3190	rs1630312	rs1630312	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65616400;OCCURENCE=1(liver),1(large_intestine),1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU152136	COCA-CN|3|321|0.00934579	0.25	281	447	1	118165691	.	C	T	281	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4397;VD=4;AF=0.0009;SHIFT3=0;MSI=2;MSILEN=3;SSF=0;SOR=0.00105;LSEQ=GAGGCAGGCATCAAAGTGCA;RSEQ=GACGTCCGGCTGAATGGCTC;CSQ=T|synonymous_variant|LOW|FAM46C|54855|Transcript|NM_017709.4|protein_coding|2/2||NM_017709.4:c.201C>T|NP_060179.2:p.His67%3D|334|201|67|H|caC/caT|rs1630312&COSV65616400&COSV65616610||1||EntrezGene||YES||||1:g.118165691C>T|0.2602|0.2191|0.2035|0.2105|0.09324|0.3565|0.3114|0.2586|0.2047|0.3565|gnomAD_FIN||0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4397:4:3,1:2300,2092:4392,4:0.0009:2,2:39:1:37:0:0.62654:2.73:60:8:0.0009:0:1	0/1:447:210:116,94:122,115:237,210:0.4698:2,2:36.7:1:36.5:1:0.44824:1.16:60:209:0.4697:0:1.1
    208. 

  208. 1	120056475	120056475	A	T	exonic	HSD3B1	.	nonsynonymous SNV	HSD3B1:NM_000862:exon4:c.A329T:p.E110V,HSD3B1:NM_001328615:exon4:c.A329T:p.E110V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.98	0.574	D	0.925	0.643	D	0.000	0.629	D	1.000	0.484	D	3.89	0.961	H	-2.7	0.905	D	-6.12	0.900	D	0.578	0.608	0.867	0.952	D	0.842	0.947	D	0.069	0.706	D	5.687	0.776	26.8	0.991	0.527	0.962	0.678	D	c	0.607	0.456	0.001	0.083	0.487	0.133	0	3.7	0.414	5.551	0.668	0.833	0.339	1.000	0.715	0.561	0.281	10.610	0.444	3-beta hydroxysteroid dehydrogenase/isomerase|NAD(P)-binding domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	167	1	120056475	.	A	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=900;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02437;SOR=0;LSEQ=AGGTACCCAGCTCCTGTTAG;RSEQ=GGCCTGTGTCCAAGCTAGTG;CSQ=T|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_000862.3|protein_coding|4/4||NM_000862.3:c.329A>T|NP_000853.1:p.Glu110Val|467|329|110|E/V|gAg/gTg|||1||EntrezGene||YES||||1:g.120056475A>T||||||||||||||,T|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_001328615.1|protein_coding|4/4||NM_001328615.1:c.329A>T|NP_001315544.1:p.Glu110Val|424|329|110|E/V|gAg/gTg|||1||EntrezGene||||||1:g.120056475A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:900:0:0,0:579,319:898,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:167:2:1,1:118,47:165,2:0.012:2,2:41:1:37:0:0.49347:2.49486:60:4:0.012:0:1
    209. 

  209. 1	120057158	120057158	C	T	exonic	HSD3B1	.	synonymous SNV	HSD3B1:NM_000862:exon4:c.C1012T:p.L338L,HSD3B1:NM_001328615:exon4:c.C1012T:p.L338L	0.67	0.3701	0.0963	0.5431	0.3841	0.6566	0.5444	0.4424	0.4602	rs6203	rs6203	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52489861;OCCURENCE=1(liver),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU89685	LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.75	395	278	1	120057158	.	C	T	395	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1987;VD=1977;AF=0.995;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=230.128;LSEQ=ATAAGAAGGCTCAGCGAGAT;RSEQ=TGGCGTATAAGCCACTCTAC;CSQ=T|synonymous_variant|LOW|HSD3B1|3283|Transcript|NM_000862.3|protein_coding|4/4||NM_000862.3:c.1012C>T|NP_000853.1:p.Leu338%3D|1150|1012|338|L|Ctg/Ttg|rs6203&CM021275&COSV52489861||1||EntrezGene||YES||||1:g.120057158C>T|0.4515|0.08108|0.5694|0.356|0.6719|0.5392|0.4361|0.4467|0.4101|0.6719|gnomAD_EAS||0&0&1|0&1&1,T|synonymous_variant|LOW|HSD3B1|3283|Transcript|NM_001328615.1|protein_coding|4/4||NM_001328615.1:c.1012C>T|NP_001315544.1:p.Leu338%3D|1107|1012|338|L|Ctg/Ttg|rs6203&CM021275&COSV52489861||1||EntrezGene||||||1:g.120057158C>T|0.4515|0.08108|0.5694|0.356|0.6719|0.5392|0.4361|0.4467|0.4101|0.6719|gnomAD_EAS||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1987:1977:1003,974:0,0:0,1977:0.995:0,2:37.3:1:36.1:1:1:0:58:64.9:0.9969:0:1.6	0/1:278:128:68,60:74,75:149,128:0.4604:2,2:33.8:1:36.3:1:0.62988:1.15:57.2:63:0.4684:0:1.6
    210. 

  210. 1	120057162	120057162	C	T	exonic	HSD3B1	.	nonsynonymous SNV	HSD3B1:NM_000862:exon4:c.C1016T:p.A339V,HSD3B1:NM_001328615:exon4:c.C1016T:p.A339V	0.	.	.	.	.	.	.	.	.	rs761719743	.	0.022	0.486	D	0.135	0.561	B	0.019	0.467	B	0.000	0.843	D	0.910	0.275	N	0	0.065	N	-2.35	0.881	D	-2.42	0.531	N	0.218	0.277	-0.373	0.729	T	0.461	0.791	T	0.078	0.730	D	3.428	0.470	23.0	0.982	0.382	0.861	0.450	D	c	-0.135	-0.190	0.002	0.094	0.487	0.133	0	2.32	0.278	7.400	0.790	-0.330	0.074	1.000	0.715	0.177	0.212	10.019	0.410	NAD(P)-binding domain	.	.	ID=COSV99347821;OCCURENCE=1(liver),1(large_intestine),1(central_nervous_system)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU128959529	UCEC-US|1|531|0.00188324,COAD-US|1|402|0.00248756,LIHC-US|1|364|0.00274725,LGG-US|1|508|0.0019685	0.25	58	278	1	120057162	.	C	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1989;VD=3;AF=0.0015;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.02748;SOR=0.1387;LSEQ=GAAGGCTCAGCGAGATCTGG;RSEQ=GTATAAGCCACTCTACAGCT;CSQ=T|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_000862.3|protein_coding|4/4||NM_000862.3:c.1016C>T|NP_000853.1:p.Ala339Val|1154|1016|339|A/V|gCg/gTg|rs761719743&COSV99347821||1||EntrezGene||YES||||1:g.120057162C>T|1.195e-05|0|2.894e-05|0|0|0|1.764e-05|0|0|2.894e-05|gnomAD_AMR||0&1|0&1,T|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_001328615.1|protein_coding|4/4||NM_001328615.1:c.1016C>T|NP_001315544.1:p.Ala339Val|1111|1016|339|A/V|gCg/gTg|rs761719743&COSV99347821||1||EntrezGene||||||1:g.120057162C>T|1.195e-05|0|2.894e-05|0|0|0|1.764e-05|0|0|2.894e-05|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1989:3:2,1:993,992:1985,3:0.0015:2,2:24.3:1:33:1:1:2:51.3:6:0.0016:0:2.7	0/1:278:3:2,1:139,136:275,3:0.0108:2,2:61.7:1:37:0:1:1.95:60:6:0.0109:0:1.7
    211. 

  211. 1	120057246	120057246	C	A	exonic	HSD3B1	.	nonsynonymous SNV	HSD3B1:NM_000862:exon4:c.C1100A:p.T367N,HSD3B1:NM_001328615:exon4:c.C1100A:p.T367N	0.94	0.7697	0.8843	0.8141	0.6887	0.9312	0.7460	0.6915	0.7485	rs1047303	rs1047303	0.303	0.143	T	0.01	0.172	B	0.022	0.193	B	0.233	0.035	N	1	0.090	P	2.52	0.738	M	-0.58	0.714	T	-1.11	0.287	N	0.023	0.010	-1.061	0.114	T	0.151	0.479	T	.	.	.	-1.422	0.019	0.003	0.264	0.013	0.023	0.066	N	c	-1.379	-1.470	0.000	0.029	0.487	0.133	0	-0.043	0.131	-0.311	0.081	-2.891	0.002	0.000	0.063	0.000	0.016	4.839	0.128	.	.	.	ID=COSV52489946;OCCURENCE=1(liver),1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU89705	COCA-CN|5|321|0.0155763	1	379	235	1	120057246	.	C	A	379	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1398;VD=1395;AF=0.9979;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.62723;SOR=0;LSEQ=TGTGGACCGGCACAAGGAGA;RSEQ=CCTGAAGTCCAAGACTCAGT;CSQ=A|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_000862.3|protein_coding|4/4||NM_000862.3:c.1100C>A|NP_000853.1:p.Thr367Asn|1238|1100|367|T/N|aCc/aAc|rs1047303&COSV52489946||1||EntrezGene||YES||||1:g.120057246C>A|0.7548|0.8923|0.8502|0.666|0.9374|0.7415|0.6736|0.7184|0.8104|0.9374|gnomAD_EAS|drug_response|0&1|1&1,A|missense_variant|MODERATE|HSD3B1|3283|Transcript|NM_001328615.1|protein_coding|4/4||NM_001328615.1:c.1100C>A|NP_001315544.1:p.Thr367Asn|1195|1100|367|T/N|aCc/aAc|rs1047303&COSV52489946||1||EntrezGene||||||1:g.120057246C>A|0.7548|0.8923|0.8502|0.666|0.9374|0.7415|0.6736|0.7184|0.8104|0.9374|gnomAD_EAS|drug_response|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1398:1395:549,846:1,1:2,1395:0.9979:2,2:35.3:1:36.3:1:1:1.54045:56:106.308:0.9978:0:1.7	1/1:235:235:86,149:0,0:0,235:1:0,2:36.4:1:36.4:1:1:0:56:77.333:1:0:1.3
    212. 

  212. 1	120462830	120462830	G	-	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	100	1	120462829	.	AG	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=402;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.03936;SOR=0;LSEQ=GCAGACACAGCCCAGTGAAG;RSEQ=GGGAAGAGGCCCGGTGCTGA;CSQ=-|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||30/33|NM_024408.4:c.5479+22del|||||||||-1||EntrezGene||YES||||1:g.120462833del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:402:0:0,0:316,86:402,0:0:2,0:37:1:36.5:1:1:0:60:66:1:0:0.1	0/1:100:2:1,1:74,24:98,2:0.02:2,2:35.5:1:37:0:0.43939:3.04131:60:4:0.02:0:0
    213. 

  213. 1	120464332	120464332	T	C	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	92	1	120464332	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=117;VD=2;AF=0.0171;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.3122;SOR=inf;LSEQ=GTGGTTCTACCATGGCCACC;RSEQ=CACCTTTACTTTCTTTGGCT;CSQ=C|splice_donor_region_variant&intron_variant|LOW|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||29/33|NM_024408.4:c.5310+4A>G|||||||||-1||EntrezGene||YES||||1:g.120464332T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:117:2:1,1:60,55:115,2:0.0171:2,2:23:1:37:0:1:1.09009:60:4:0.0171:0:1	0/0:92:0:0,0:52,40:92,0:0:2,0:42:1:36.6:1:1:0:60:184:1:0:0
    214. 

  214. 1	120465556	120465556	C	T	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	60	1	120465556	.	C	T	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=4;AF=0.0234;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.29753;SOR=inf;LSEQ=GATGCTGCCTTAAGACATAT;RSEQ=TCAGGAATTAGAATACTGTC;CSQ=T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||26/33|NM_024408.4:c.4860-155G>A|||||||||-1||EntrezGene||YES||||1:g.120465556C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:4:1,3:14,153:167,4:0.0234:2,2:27:1:37:0:0.30972:3.6:60:8:0.0234:0:1	0/0:60:0:0,0:4,56:60,0:0:2,0:28.4:1:36:1:1:0:60:59:1:0:0.2
    215. 

  215. 1	120467951	120467951	G	A	exonic	NOTCH2	.	synonymous SNV	NOTCH2:NM_024408:exon25:c.C4488T:p.C1496C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56694853;OCCURENCE=1(skin)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	58	271	1	120467951	.	G	A	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3827;VD=2;AF=0.0005;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00259;SOR=0.04681;LSEQ=CATGTCTTGCTGTTCCCCTG;RSEQ=CATTCAAAGTTGTCAAACAG;CSQ=A|synonymous_variant|LOW|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|25/34||NM_024408.4:c.4488C>T|NP_077719.2:p.Cys1496%3D|4744|4488|1496|C|tgC/tgT|COSV56694853||-1||EntrezGene||YES||||1:g.120467951G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3827:2:1,1:2062,1757:3819,2:0.0005:2,2:27:1:37:0:1:1.17354:60:4:0.0005:0:1	0/1:271:3:2,1:166,102:268,3:0.0111:2,2:20.3:1:37:0:1:1.23:60:6:0.0112:0:1
    216. 

  216. 1	120468425	120468425	G	A	exonic	NOTCH2	.	synonymous SNV	NOTCH2:NM_024408:exon25:c.C4014T:p.S1338S	0.16	0.0125	0.0100	0.0119	0.0066	0.1403	0.0049	0.0022	0.0112	rs17024525	rs17024525	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56691791;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),3(prostate),1(lung),1(biliary_tract)	249379	Hajdu-Cheney_syndrome|not_specified	MONDO:MONDO:0007057,MedGen:C0917715,OMIM:102500,Orphanet:ORPHA955,SNOMED_CT:63122002|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	1	MU19403740	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	218	123	1	120468425	.	G	A	218	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1016;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGCTCTGGCACCTTGCCCC;RSEQ=GAAAATCCCTGTGGAAATCA;CSQ=A|synonymous_variant|LOW|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|25/34||NM_024408.4:c.4014C>T|NP_077719.2:p.Ser1338%3D|4270|4014|1338|S|tcC/tcT|rs17024525&COSV56691791||-1||EntrezGene||YES||||1:g.120468425G>A|0.01768|0.0121|0.01951|0.002897|0.1586|0.004624|0.002653|0.01164|0.0035|0.1586|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1016:0:0,0:292,724:1016,0:0:2,0:33.2:1:36.4:1:1:0:60:100.6:1:0:0.1	1/0:123:63:11,52:18,41:59,63:0.5122:2,2:35.7:1:36.6:1:0.13555:2.06291:60:126:0.525:0:1.1
    217. 

  217. 1	120477982	120477982	G	A	UTR3	NOTCH2	NM_001200001:c.*60C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	162	1	120477982	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.81859;SOR=0;LSEQ=GATGTAGAACTAAATGCTTG;RSEQ=AATGAAGCTAGTCTTCCTAT;CSQ=A|3_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|22/22||NM_001200001.2:c.*60C>T||4024|||||||-1||EntrezGene||||||1:g.120477982G>A||||||||||||||,A|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||22/33|NM_024408.4:c.3655+113C>T|||||||||-1||EntrezGene||YES||||1:g.120477982G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:17:0:0,0:16,1:17,0:0:1,0:23.5:1:35.6:1:1:0:60:34:1:0:0.1	0/1:162:2:1,1:124,36:160,2:0.0123:2,2:19:1:37:0:0.40572:3.41116:60:4:0.0125:0:1
    218. 

  218. 1	120483161	120483161	G	C	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	83	1	120483161	.	G	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=143;VD=2;AF=0.014;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.39933;SOR=inf;LSEQ=CTAGGGGAGCTGAGTGAATG;RSEQ=GAAGGAAGTCAATTACCTGA;CSQ=C|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||19/21|NM_001200001.2:c.3183+17C>G|||||||||-1||EntrezGene||||||1:g.120483161G>C||||||||||||||,C|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||19/33|NM_024408.4:c.3183+17C>G|||||||||-1||EntrezGene||YES||||1:g.120483161G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:143:2:1,1:116,25:141,2:0.014:2,2:26:0:37:0:0.33163:4.56949:60:4:0.014:0:1	0/0:83:0:0,0:71,12:83,0:0:2,0:33.8:1:35.9:1:1:0:60:40.5:1:0:0.3
    219. 

  219. 1	120496314	120496314	G	A	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	224	1	120496314	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=165;VD=2;AF=0.0121;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.17929;SOR=inf;LSEQ=TCACAGAGACACTTATATCT;RSEQ=AAAGAAGACAAAACTTTTTA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||13/21|NM_001200001.2:c.2220-3C>T|||||||||-1||EntrezGene||||||1:g.120496314G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||13/33|NM_024408.4:c.2220-3C>T|||||||||-1||EntrezGene||YES||||1:g.120496314G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:165:2:1,1:53,110:163,2:0.0121:2,2:44:0:37:0:0.54878:2.07:60:4:0.0123:0:1	0/0:224:0:0,0:87,137:224,0:0:2,0:36.6:1:36.1:1:1:0:60:73.667:1:0:0.1
    220. 

  220. 1	120506329	120506329	A	G	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon11:c.T1783C:p.C595R,NOTCH2:NM_024408:exon11:c.T1783C:p.C595R	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.981	0.689	D	0.932	0.693	D	0.001	0.412	U	1	0.810	D	4.37	0.986	H	-12.4	1.000	D	-10.26	0.989	D	0.981	0.984	1.451	1.000	D	1.000	1.000	D	0.404	0.935	D	6.152	0.848	28.5	0.998	0.843	0.967	0.704	D	c	1.067	0.979	1.000	0.747	0.744	0.983	0	5.73	0.897	9.325	0.960	1.199	0.960	1.000	0.715	0.999	0.750	15.493	0.752	EGF-like calcium-binding domain|EGF-like domain|EGF-like, conserved site|Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	389	1	120506329	.	A	G	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1392;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00225;SOR=0;LSEQ=GCCCATGTACCCGGGATTGC;RSEQ=GATGCAGGTGTAGGAATCAA;CSQ=G|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|11/22||NM_001200001.2:c.1783T>C|NP_001186930.1:p.Cys595Arg|2039|1783|595|C/R|Tgc/Cgc|||-1||EntrezGene||||||1:g.120506329A>G||||||||||||||,G|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|11/34||NM_024408.4:c.1783T>C|NP_077719.2:p.Cys595Arg|2039|1783|595|C/R|Tgc/Cgc|||-1||EntrezGene||YES||||1:g.120506329A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1392:0:0,0:618,774:1392,0:0:2,0:38:1:36.5:1:1:0:60:98.429:1:0:0.1	0/1:389:4:2,2:173,212:385,4:0.0103:2,2:27.5:1:37:0:1:1.22:60:8:0.0103:0:1
    221. 

  221. 1	120508090	120508090	C	A	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon10:c.G1667T:p.C556F,NOTCH2:NM_024408:exon10:c.G1667T:p.C556F	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.899	D	0.999	0.916	D	0.001	0.412	U	1	0.810	D	4.625	0.993	H	-12.4	1.000	D	-9.24	0.983	D	0.947	0.943	1.592	1.000	D	1.000	1.000	D	0.140	0.823	D	6.940	0.934	33	0.991	0.533	0.992	0.931	D	c	1.005	0.859	1.000	0.747	0.737	0.974	0	4.91	0.638	7.505	0.804	0.935	0.490	1.000	0.715	0.996	0.625	17.281	0.870	EGF-like calcium-binding domain|EGF-like calcium-binding, conserved site|EGF-like domain|EGF-like, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	38	269	1	120508090	.	C	A	38	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1309;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00491;SOR=0;LSEQ=TCTTACCTGTGGCACACTGG;RSEQ=ATTCATAGCCATTCGGGTGA;CSQ=A|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|10/22||NM_001200001.2:c.1667G>T|NP_001186930.1:p.Cys556Phe|1923|1667|556|C/F|tGc/tTc|||-1||EntrezGene||||||1:g.120508090C>A||||||||||||||,A|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|10/34||NM_024408.4:c.1667G>T|NP_077719.2:p.Cys556Phe|1923|1667|556|C/F|tGc/tTc|||-1||EntrezGene||YES||||1:g.120508090C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1309:0:0,0:640,669:1309,0:0:2,0:35.3:1:36.2:1:1:0:60:80.812:1:0:0.1	0/1:269:3:1,2:161,105:266,3:0.0112:2,2:35.7:1:24.3:1:0.56504:3.05372:60:2:0.0076:0:1
    222. 

  222. 1	120509098	120509098	G	A	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon9:c.C1468T:p.H490Y,NOTCH2:NM_024408:exon9:c.C1468T:p.H490Y	.	.	.	.	.	.	.	.	.	.	.	0.667	0.046	T	0.998	0.764	D	0.996	0.832	D	0.002	0.387	U	1.000	0.588	D	0.915	0.234	L	-2.87	0.915	D	-0.6	0.178	N	0.206	0.354	0.080	0.838	D	0.581	0.849	D	0.115	0.795	D	2.867	0.405	21.7	0.839	0.145	0.956	0.652	D	c	-0.057	0.058	1.000	0.747	0.706	0.609	0	4.83	0.617	3.589	0.535	0.142	0.226	1.000	0.715	0.999	0.750	13.807	0.626	EGF-like calcium-binding domain|EGF-like domain|EGF-like, conserved site|Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	174	1	120509098	.	G	A	58	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=735;VD=3;AF=0.0041;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.24498;SOR=0.35299;LSEQ=ATTTATTTCTAATTCACAAT;RSEQ=CACACCTTTGAAACCTAAAC;CSQ=A|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|9/22||NM_001200001.2:c.1468C>T|NP_001186930.1:p.His490Tyr|1724|1468|490|H/Y|Cat/Tat|||-1||EntrezGene||||||1:g.120509098G>A||||||||||||||,A|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|9/34||NM_024408.4:c.1468C>T|NP_077719.2:p.His490Tyr|1724|1468|490|H/Y|Cat/Tat|||-1||EntrezGene||YES||||1:g.120509098G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:735:3:1,2:289,442:731,3:0.0041:2,2:22:1:37:0:1:1.30723:60:6:0.0041:0:1	0/1:174:2:1,1:65,107:172,2:0.0115:2,2:26:1:37:0:1:1.64:60:4:0.0116:0:1
    223. 

  223. 1	120529540	120529540	C	T	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	193	1	120529540	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.17161;SOR=inf;LSEQ=AACAGTCTGCCTCTGGTTAC;RSEQ=AATCCATATCCCATTCTGGT;CSQ=T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||5/21|NM_001200001.2:c.874+43G>A|||||||||-1||EntrezGene||||||1:g.120529540C>T||||||||||||||,T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||5/33|NM_024408.4:c.874+43G>A|||||||||-1||EntrezGene||YES||||1:g.120529540C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:94,41:135,2:0.0146:2,2:37:0:37:0:0.52072:2.27727:60:4:0.0146:0:1	0/0:193:0:0,0:137,56:193,0:0:2,0:34:1:36.3:1:1:0:60:192:1:0:0
    224. 

  224. 1	120529757	120529757	A	T	intronic	NOTCH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	95	1	120529757	.	A	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.24351;SOR=0;LSEQ=AATCTCATACAGAAGAAACG;RSEQ=CCTGCTCTGTTCCCACAGAA;CSQ=T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||4/21|NM_001200001.2:c.752-52T>A|||||||||-1||EntrezGene||||||1:g.120529757A>T||||||||||||||,T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||4/33|NM_024408.4:c.752-52T>A|||||||||-1||EntrezGene||YES||||1:g.120529757A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:97:0:0,0:26,71:97,0:0:2,0:36.2:1:35.8:1:1:0:60:31.333:1:0:0.7	0/1:95:2:1,1:23,70:93,2:0.0211:2,2:43:1:37:0:0.44345:3:60:4:0.0215:0:1
    225. 

  225. 1	120548174	120548174	G	A	exonic	NOTCH2	.	stopgain	NOTCH2:NM_001200001:exon3:c.C193T:p.R65X,NOTCH2:NM_024408:exon3:c.C193T:p.R65X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.141	0.183	U	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.369	0.967	36	0.998	0.852	0.877	0.471	D	c	0.883	0.748	0.010	0.120	0.706	0.609	0	5.4	0.779	1.296	0.328	0.892	0.403	0.903	0.313	1.000	0.888	11.958	0.521	EGF-like calcium-binding domain|EGF-like domain;EGF-like domain	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	189	478	1	120548174	.	G	A	189	Q0	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1490;VD=37;AF=0.0248;SHIFT3=1;MSI=1;MSILEN=1;SSF=3e-05;SOR=inf;LSEQ=GTTCTTCTCACAGGGGTCTC;RSEQ=ATGTTGACAATATTCCCCCA;CSQ=A|stop_gained|HIGH|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|3/22||NM_001200001.2:c.193C>T|NP_001186930.1:p.Arg65Ter|449|193|65|R/*|Cga/Tga|rs1280158106||-1||EntrezGene||||||1:g.120548174G>A||||||||||||||,A|stop_gained|HIGH|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|3/34||NM_024408.4:c.193C>T|NP_077719.2:p.Arg65Ter|449|193|65|R/*|Cga/Tga|rs1280158106||-1||EntrezGene||YES||||1:g.120548174G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1490:37:18,19:567,885:1452,37:0.0248:2,2:41.9:1:36.4:1:0.23849:1.48:1.4:74:0.0252:0:1.8	0/0:478:0:0,0:193,284:477,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    226. 

  226. 1	120572547	120572547	T	C	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon2:c.A137G:p.N46S,NOTCH2:NM_024408:exon2:c.A137G:p.N46S	0.5	0.3958	0.2468	0.4290	0.4357	0.4569	0.4509	0.4535	0.4356	rs61788900	rs141882865	0.129	0.268	T	0.01	0.402	B	0.005	0.516	B	0.002	0.366	U	0.001	0.452	P	0.885	0.217	L	-0.03	0.631	T	-1.39	0.344	N	0.132	0.152	-0.943	0.421	T	0.124	0.429	T	.	.	.	2.196	0.325	17.48	0.993	0.591	0.793	0.390	D	c	-0.046	0.099	0.960	0.284	0.706	0.609	0	5.05	0.674	4.045	0.568	0.899	0.412	1.000	0.715	1.000	0.888	11.233	0.480	EGF-like domain	.	.	ID=COSV56680759;OCCURENCE=4(penis),2(large_intestine),1(biliary_tract),4(haematopoietic_and_lymphoid_tissue),1(kidney),1(pancreas),4(thyroid),17(upper_aerodigestive_tract)	789836	Hajdu-Cheney_syndrome	MONDO:MONDO:0007057,MedGen:C0917715,OMIM:102500,Orphanet:ORPHA955,SNOMED_CT:63122002	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU617194	LAML-KR|2|205|0.0097561,COCA-CN|2|321|0.00623053,THCA-CN|1|50|0.02	0.5	199	390	1	120572547	.	T	C	199	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=96;VD=8;AF=0.0833;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.2627;SOR=0.71535;LSEQ=ACTTGCAGTATCCTGTGCCA;RSEQ=TGTGGTAGGTAACACACATT;CSQ=C|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|2/22||NM_001200001.2:c.137A>G|NP_001186930.1:p.Asn46Ser|393|137|46|N/S|aAt/aGt|rs61788900&COSV56680759||-1||EntrezGene||||||1:g.120572547T>C|0.4401|0.2243|0.4124|0.4611|0.4556|0.4595|0.4632|0.4561|0.4595|0.4632|gnomAD_NFE|benign|0&1|1&1,C|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|2/34||NM_024408.4:c.137A>G|NP_077719.2:p.Asn46Ser|393|137|46|N/S|aAt/aGt|rs61788900&COSV56680759||-1||EntrezGene||YES||||1:g.120572547T>C|0.4401|0.2243|0.4124|0.4611|0.4556|0.4595|0.4632|0.4561|0.4595|0.4632|gnomAD_NFE|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:96:8:4,4:47,41:88,8:0.0833:2,2:15:1:34:1:1:1.14471:1.9:16:0.086:0:2.4	0/1:390:44:25,19:190,155:345,44:0.1128:2,2:40.5:1:36.5:1:0.87313:1.07:4.3:88:0.1186:0:2.1
    227. 

  227. 1	120572572	120572572	C	T	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon2:c.G112A:p.E38K,NOTCH2:NM_024408:exon2:c.G112A:p.E38K	0.49	0.3980	0.2513	0.4313	0.4424	0.4578	0.4521	0.4551	0.4362	rs61788901	rs146242578	0.058	0.377	T	0.044	0.203	B	0.036	0.216	B	0.003	0.353	U	0.433	0.322	P	0.02	0.080	N	0.13	0.610	T	-0.38	0.134	N	0.317	0.378	-1.097	0.044	T	0.049	0.210	T	.	.	.	2.535	0.366	19.69	0.994	0.619	0.426	0.267	N	c	-0.573	-0.420	0.035	0.142	0.706	0.609	0	2.14	0.264	0.426	0.209	0.795	0.322	0.999	0.424	0.988	0.529	7.030	0.240	EGF-like domain	.	.	ID=COSV56680772;OCCURENCE=4(large_intestine),1(central_nervous_system),1(biliary_tract),2(haematopoietic_and_lymphoid_tissue),1(thyroid),18(upper_aerodigestive_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU4547029	LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|4|321|0.0124611	0.5	203	413	1	120572572	.	C	T	203	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=108;VD=8;AF=0.0741;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.18858;SOR=0.65473;LSEQ=GTAGGTAACACACATTCCTT;RSEQ=ATTTACACAGGGTTCATAGC;CSQ=T|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|2/22||NM_001200001.2:c.112G>A|NP_001186930.1:p.Glu38Lys|368|112|38|E/K|Gaa/Aaa|rs61788901&COSV56680772||-1||EntrezGene||||||1:g.120572572C>T|0.4427|0.2282|0.4201|0.4658|0.4561|0.4602|0.4646|0.4585|0.4636|0.4658|gnomAD_ASJ||0&1|0&1,T|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|2/34||NM_024408.4:c.112G>A|NP_077719.2:p.Glu38Lys|368|112|38|E/K|Gaa/Aaa|rs61788901&COSV56680772||-1||EntrezGene||YES||||1:g.120572572C>T|0.4427|0.2282|0.4201|0.4658|0.4561|0.4602|0.4646|0.4585|0.4636|0.4658|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:108:8:5,3:49,51:100,8:0.0741:2,2:32.1:1:37:0:0.71589:1.73:5.2:16:0.0748:0:2.4	0/1:413:45:22,23:186,182:368,45:0.109:2,2:35.7:1:37:0:0.87538:1.06823:6.1:90:0.1108:0:2.1
    228. 

  228. 1	120572612	120572612	T	C	splicing	NOTCH2	NM_024408:exon2:c.74-2A>G;NM_001200001:exon2:c.74-2A>G	.	.	.	.	.	.	.	.	.	.	.	.	rs3872062	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.501	0.603	24.3	0.987	0.443	0.789	0.387	D	c	0.972	0.805	0.960	0.284	0.078	0.016	0	5.05	0.674	4.045	0.568	0.899	0.412	1.000	0.715	0.911	0.388	11.233	0.480	.	.	.	ID=COSV56703932;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU28781434	LAML-KR|1|205|0.00487805	0.25	154	362	1	120572612	.	T	C	154	Q0	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=99;VD=20;AF=0.202;SHIFT3=0;MSI=5;MSILEN=1;SSF=0;SOR=inf;LSEQ=CCATCTCGACACTGCAATGC;RSEQ=AAAAATAAAAACAAATGCAC;CSQ=C|splice_acceptor_variant|HIGH|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||1/21|NM_001200001.2:c.74-2A>G|||||||rs1553210735&COSV56703932||-1||EntrezGene||||||1:g.120572612T>C|||||||||||||0&1|0&1,C|splice_acceptor_variant|HIGH|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||1/33|NM_024408.4:c.74-2A>G|||||||rs1553210735&COSV56703932||-1||EntrezGene||YES||||1:g.120572612T>C|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:99:20:9,11:36,42:78,20:0.202:2,2:40.8:1:35.8:1:1:1.04714:0:40:0.202:0:1	0/0:362:0:0,0:147,215:362,0:0:2,0:37.5:1:36.7:1:1:0:3.3:180:1:0:0.2
    229. 

  229. 1	120611876	120611876	C	T	intronic	NOTCH2	.	.	.	0.49	0.3961	0.2494	0.4381	0.4301	0.4497	0.4583	0.4525	0.4387	rs11801062	rs11801062	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56686095;OCCURENCE=1(oesophagus),11(meninges),2(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU17520224	COCA-CN|7|321|0.0218069,PEME-CA|1|112|0.00892857,ESCA-CN|1|332|0.00301205	0.5	152	24	1	120611876	.	C	T	152	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=22;AF=0.275;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.51693;SOR=1.13657;LSEQ=CTTCCCACACAGAGAAGGAC;RSEQ=GAGGGGGAGAAGGGTCGCCC;CSQ=T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding||1/21|NM_001200001.2:c.73+72G>A|||||||rs11801062&COSV56686095||-1||EntrezGene||||||1:g.120611876C>T|0.4447|0.2639|0.4321|0.457|0.4557|0.4558|0.4613|0.4595|0.456|0.4613|gnomAD_NFE||0&1|0&1,T|intron_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding||1/33|NM_024408.4:c.73+72G>A|||||||rs11801062&COSV56686095||-1||EntrezGene||YES||||1:g.120611876C>T|0.4447|0.2639|0.4321|0.457|0.4557|0.4558|0.4613|0.4595|0.456|0.4613|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:22:14,8:37,21:58,22:0.275:2,2:33.6:1:34.1:1:1:1.00672:47.3:10:0.2597:0:2.6	0/1:24:6:5,1:13,5:18,6:0.25:2,2:20.5:1:37:0:1:1.88:47:12:0.25:0:2.5
    230. 

  230. 1	120611960	120611960	C	T	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon1:c.G61A:p.A21T,NOTCH2:NM_024408:exon1:c.G61A:p.A21T	0.42	0.0644	0.1695	0.0369	0.0505	0.0059	0.0054	0.0408	0.0340	rs2603926	rs139076095	0.642	0.050	T	0.0	0.184	B	0.0	0.112	B	.	.	.	1.000	0.182	N	0.625	0.159	N	0.38	0.576	T	0.05	0.064	N	0.136	0.157	-0.954	0.402	T	0.018	0.077	T	.	.	.	3.041	0.426	22.4	0.951	0.256	0.256	0.225	N	c	-0.860	-0.710	1.000	0.500	0.733	0.969	0	2.14	0.264	0.960	0.286	0.683	0.296	0.998	0.411	0.912	0.389	6.561	0.215	.	.	.	ID=COSV56681399;OCCURENCE=4(breast),1(peritoneum),2(liver),2(large_intestine),2(central_nervous_system),3(biliary_tract),3(stomach),6(haematopoietic_and_lymphoid_tissue),1(kidney),13(urinary_tract),4(skin),1(prostate),2(lung),1(thyroid),37(upper_aerodigestive_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU869951	MELA-AU|1|183|0.00546448,SKCA-BR|2|100|0.02,LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,GACA-CN|1|123|0.00813008,COCA-CN|2|321|0.00623053,LINC-JP|2|394|0.00507614,BTCA-JP|2|239|0.0083682,BLCA-CN|9|103|0.0873786,WT-US|1|102|0.00980392,ALL-US|4|150|0.0266667	0.5	167	45	1	120611960	.	C	T	167	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=23;AF=0.1797;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01785;SOR=4.67903;LSEQ=ATACTCACCATGCGCGGGGG;RSEQ=CGCGCAGCACAGCCAGAGCG;CSQ=T|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.61G>A|NP_001186930.1:p.Ala21Thr|317|61|21|A/T|Gcc/Acc|rs2603926&COSV56681399||-1||EntrezGene||||||1:g.120611960C>T|0.1154|0.1924|0.06149|0.09213|0.05008|0.1418|0.1505|0.07215|0.09302|0.1924|gnomAD_AFR||0&1|0&1,T|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.61G>A|NP_077719.2:p.Ala21Thr|317|61|21|A/T|Gcc/Acc|rs2603926&COSV56681399||-1||EntrezGene||YES||||1:g.120611960C>T|0.1154|0.1924|0.06149|0.09213|0.05008|0.1418|0.1505|0.07215|0.09302|0.1924|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:128:23:17,6:50,55:105,23:0.1797:2,2:38.3:1:37:0:0.03647:3.09:12.2:46:0.1825:0:1.5	0/1:45:2:1,1:21,22:43,2:0.0444:2,2:25.5:1:37:0:1:1.05:3.5:4:0.0455:0:1
    231. 

  231. 1	120611964	120611964	G	C	exonic	NOTCH2	.	nonsynonymous SNV	NOTCH2:NM_001200001:exon1:c.C57G:p.C19W,NOTCH2:NM_024408:exon1:c.C57G:p.C19W	0.47	0.3877	0.2278	0.4293	0.4312	0.4526	0.4558	0.4469	0.4300	rs11810554	rs11810554	0.185	0.215	T	0.001	0.090	B	0.0	0.013	B	.	.	.	0.970	0.257	N	1.04	0.263	L	0.4	0.573	T	-0.77	0.214	N	0.257	0.313	-1.048	0.151	T	0.036	0.155	T	.	.	.	2.208	0.327	17.56	0.782	0.118	0.331	0.245	N	c	-0.571	-0.463	1.000	0.500	0.733	0.969	0	2.04	0.257	0.647	0.243	0.760	0.310	0.998	0.411	0.868	0.363	6.759	0.226	.	.	.	ID=COSV56680365;OCCURENCE=1(oesophagus),18(meninges),1(large_intestine),18(central_nervous_system),1(biliary_tract),5(haematopoietic_and_lymphoid_tissue),4(soft_tissue),2(urinary_tract),23(prostate),1(thyroid),56(upper_aerodigestive_tract)	789838	Hajdu-Cheney_syndrome	MONDO:MONDO:0007057,MedGen:C0917715,OMIM:102500,Orphanet:ORPHA955,SNOMED_CT:63122002	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU815514	LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763,ESCA-CN|1|332|0.00301205,BLCA-CN|1|103|0.00970874	0.5	177	45	1	120611964	.	G	C	177	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=127;VD=32;AF=0.252;SHIFT3=3;MSI=2;MSILEN=2;SSF=0.38197;SOR=0.83009;LSEQ=TCACCATGCGCGGGGGCCGC;RSEQ=CAGCACAGCCAGAGCGCCAG;CSQ=C|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.57C>G|NP_001186930.1:p.Cys19Trp|313|57|19|C/W|tgC/tgG|rs11810554&COSV56680365||-1||EntrezGene||||||1:g.120611964G>C|0.4434|0.2583|0.4276|0.4559|0.4668|0.4584|0.4595|0.4588|0.4561|0.4668|gnomAD_EAS|benign|0&1|1&1,C|missense_variant|MODERATE|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.57C>G|NP_077719.2:p.Cys19Trp|313|57|19|C/W|tgC/tgG|rs11810554&COSV56680365||-1||EntrezGene||YES||||1:g.120611964G>C|0.4434|0.2583|0.4276|0.4559|0.4668|0.4584|0.4595|0.4588|0.4561|0.4668|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:127:32:14,18:50,45:95,32:0.252:2,2:34.6:1:35.4:1:0.41923:1.42454:52.7:15:0.2459:0:2.5	0/1:45:13:7,6:15,17:32,13:0.2889:2,2:47:1:37:0:0.74945:1.31:53.6:26:0.2955:0:2.3
    232. 

  232. 1	120612003	120612004	GG	-	exonic	NOTCH2	.	frameshift deletion	NOTCH2:NM_001200001:exon1:c.17_18del:p.P6Rfs*27,NOTCH2:NM_024408:exon1:c.17_18del:p.P6Rfs*27	0.44	0.0832	0.1426	0.0356	0.0893	0.0528	0.0095	0.0877	0.0616	rs372504208	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	215181	not_specified	MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU632957	COCA-CN|2|321|0.00623053,PBCA-DE|3|499|0.00601202,OV-AU|1|93|0.0107527,LINC-JP|1|394|0.00253807,GACA-JP|6|585|0.0102564,ESCA-CN|1|332|0.00301205,THCA-SA|3|243|0.0123457	0.5	117	38	1	120612002	.	CGG	C	117	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=129;VD=9;AF=0.0698;SHIFT3=2;MSI=4;MSILEN=1;SSF=0.29005;SOR=2.76235;LSEQ=CAGCAGCGCCCACAGCAGAG;RSEQ=GGCGCAGGGCGGGCATCTTC;CSQ=-|frameshift_variant|HIGH|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.17_18del|NP_001186930.1:p.Pro6ArgfsTer27|273-274|17-18|6|P/X|cCC/c|rs372504208||-1||EntrezGene||||||1:g.120612005_120612006del|0.1715|0.2029|0.1158|0.128|0.11|0.2505|0.203|0.1144|0.1594|0.2505|gnomAD_FIN|uncertain_significance&benign||1,-|frameshift_variant|HIGH|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.17_18del|NP_077719.2:p.Pro6ArgfsTer27|273-274|17-18|6|P/X|cCC/c|rs372504208||-1||EntrezGene||YES||||1:g.120612005_120612006del|0.1715|0.2029|0.1158|0.128|0.11|0.2505|0.203|0.1144|0.1594|0.2505|gnomAD_FIN|uncertain_significance&benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:129:9:5,4:53,67:120,9:0.0698:2,2:37.7:1:37:0:0.73044:1.57:25.9:18:0.0698:0:1.3	0/1:38:1:0,1:14,23:37,1:0.0263:2,0:56:0:37:0:1:0:7:2:0.0278:0:1
    233. 

  233. 1	120612006	120612006	G	A	exonic	NOTCH2	.	synonymous SNV	NOTCH2:NM_001200001:exon1:c.C15T:p.R5R,NOTCH2:NM_024408:exon1:c.C15T:p.R5R	0.48	0.3802	0.2426	0.4346	0.4070	0.4369	0.4496	0.4286	0.4243	rs4021006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56680371;OCCURENCE=2(breast),1(liver),18(meninges),3(large_intestine),3(central_nervous_system),2(ovary),2(haematopoietic_and_lymphoid_tissue),1(skin),2(thyroid),1(upper_aerodigestive_tract),1(eye)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU657255	SKCA-BR|2|100|0.02,LICA-CN|3|402|0.00746269,COCA-CN|7|321|0.0218069	0.5	162	35	1	120612006	.	G	A	162	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=125;VD=24;AF=0.192;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.26713;SOR=0.68819;LSEQ=AGCGCCCACAGCAGAGCGGG;RSEQ=CGCAGGGCGGGCATCTTCTC;CSQ=A|synonymous_variant|LOW|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.15C>T|NP_001186930.1:p.Arg5%3D|271|15|5|R|cgC/cgT|rs4021006&COSV56680229&COSV56680371||-1||EntrezGene||||||1:g.120612006G>A|0.4509|0.297|0.4472|0.451|0.4622|0.4663|0.4601|0.4592|0.4676|0.4744|SAS||0&1&1|1&1&1,A|synonymous_variant|LOW|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.15C>T|NP_077719.2:p.Arg5%3D|271|15|5|R|cgC/cgT|rs4021006&COSV56680229&COSV56680371||-1||EntrezGene||YES||||1:g.120612006G>A|0.4509|0.297|0.4472|0.451|0.4622|0.4663|0.4601|0.4592|0.4676|0.4744|SAS||0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:125:24:8,16:48,53:101,24:0.192:2,2:37:1:35.5:1:0.25683:1.8029:52.8:48:0.192:0:2.1	0/1:35:9:3,6:10,16:26,9:0.2571:2,2:29.3:1:35.7:1:1:1.24217:56.6:18:0.2571:0:2.3
    234. 

  234. 1	120612034	120612034	T	G	UTR5	NOTCH2	NM_024408:c.-14A>C;NM_001200001:c.-14A>C	.	.	0.3	0.0415	0.0623	0.0043	0.0735	0.0098	0.0052	0.0465	0.0354	rs201668322	rs201668322	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56680857;OCCURENCE=2(bone),2(stomach),1(haematopoietic_and_lymphoid_tissue),1(skin),2(prostate),3(meninges),13(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU28577910	MELA-AU|3|183|0.0163934,SKCA-BR|3|100|0.03,LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526,PBCA-DE|2|499|0.00400802,GACA-JP|2|585|0.0034188	0.25	103	30	1	120612034	.	T	G	103	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=99;VD=7;AF=0.0707;SHIFT3=0;MSI=3;MSILEN=3;SSF=0.14895;SOR=inf;LSEQ=CGGGCATCTTCTCGGTCGCC;RSEQ=CCTCCTCCGCCGCCGCCGCC;CSQ=G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-14A>C||243|||||rs201668322&COSV56680857||-1||EntrezGene||||||1:g.120612034T>G|0.05931|0.07485|0.02886|0.03039|0.03095|0.08866|0.08808|0.03642|0.03411|0.08866|gnomAD_FIN||0&1|0&1,G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-14A>C||243|||||rs201668322&COSV56680857||-1||EntrezGene||YES||||1:g.120612034T>G|0.05931|0.07485|0.02886|0.03039|0.03095|0.08866|0.08808|0.03642|0.03411|0.08866|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:99:7:3,4:35,57:92,7:0.0707:2,2:24:1:37:0:1:1.22:27.6:14:0.0707:0:1.4	0/0:30:0:0,0:10,20:30,0:0:2,0:30.6:1:36.6:1:1:0:57.6:60:1:0:0.4
    235. 

  235. 1	120612038	120612046	CCTCCGCCG	-	UTR5	NOTCH2	NM_024408:c.-18_-26delCGGCGGAGG;NM_001200001:c.-18_-26delCGGCGGAGG	.	.	0.062	0.0719	0.1955	0.0389	0.0215	0.0054	0.0217	0.0429	0.0367	rs59571254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	157	25	1	120612037	.	TCCTCCGCCG	T	157	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=96;VD=20;AF=0.2083;SHIFT3=2;MSI=6;MSILEN=3;SSF=0.00612;SOR=inf;LSEQ=GCATCTTCTCGGTCGCCTCC;RSEQ=CCGCCGCCGCCGCCTGGGCA;CSQ=-|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-26_-18del||231-239|||||rs59571254||-1||EntrezGene||||||1:g.120612040_120612048del|0.005702|0.02865|0.001471|0.003723|0.0007941|0.003828|0.008554|0.006196|0.000983|0.04903|AA|||,-|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-26_-18del||231-239|||||rs59571254||-1||EntrezGene||YES||||1:g.120612040_120612048del|0.005702|0.02865|0.001471|0.003723|0.0007941|0.003828|0.008554|0.006196|0.000983|0.04903|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:96:20:11,9:25,51:76,20:0.2083:2,2:36.7:1:36.4:1:0.11767:2.47:18.9:40:0.2083:0.0417:0.9	0/0:25:0:0,0:7,18:25,0:0:2,0:33.8:1:36.5:1:1:0:57.1:50:1:0:0.4
    236. 

  236. 1	120612040	120612040	-	CCTCCGCCG	UTR5	NOTCH2	NM_024408:c.-21_-20insCGGCGGAGG;NM_001200001:c.-21_-20insCGGCGGAGG	.	.	0.083	.	.	.	.	.	.	.	.	rs782658834	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	141	25	1	120612040	.	T	TCCTCCGCCG	141	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=92;VD=15;AF=0.163;SHIFT3=2;MSI=8;MSILEN=3;SSF=0.24204;SOR=2.22739;LSEQ=TCTTCTCGGTCGCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCGCC;CSQ=CCTCCGCCG|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-21_-20insCGGCGGAGG||236-237|||||rs782658834||-1||EntrezGene||||||1:g.120612042_120612043insTCCGCCGCC||||||||||0.02216|EA|||,CCTCCGCCG|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-21_-20insCGGCGGAGG||236-237|||||rs782658834||-1||EntrezGene||YES||||1:g.120612042_120612043insTCCGCCGCC||||||||||0.02216|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:92:15:4,11:20,38:58,15:0.163:2,2:54:1:36.3:1:0.75982:1.44033:45.3:30:0.2055:0:1.4	0/1:25:2:0,2:6,13:19,2:0.08:2,0:31.5:1:37:1:1:0:59:4:0.0909:0.04:2.5
    237. 

  237. 1	120612043	120612043	G	T	UTR5	NOTCH2	NM_024408:c.-23C>A;NM_001200001:c.-23C>A	.	.	0.35	0.0544	0.1759	0.0751	0.0076	0.0794	0.0131	0.0065	0.0232	rs57122008	rs57122008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56683169;OCCURENCE=4(liver),1(oesophagus),1(meninges),2(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(skin),1(prostate)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15544411	LICA-CN|4|402|0.00995025,LAML-KR|2|205|0.0097561,COCA-CN|2|321|0.00623053	0.25	159	23	1	120612043	.	G	T	159	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=92;VD=20;AF=0.2174;SHIFT3=0;MSI=6;MSILEN=3;SSF=0.00717;SOR=inf;LSEQ=TCTCGGTCGCCTCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCTGG;CSQ=T|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-23C>A||234|||||rs57122008&COSV56683169||-1||EntrezGene||||||1:g.120612043G>T|0.09186|0.2554|0.1146|0.03703|0.1747|0.05894|0.06717|0.06322|0.05486|0.2554|gnomAD_AFR||0&1|0&1,T|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-23C>A||234|||||rs57122008&COSV56683169||-1||EntrezGene||YES||||1:g.120612043G>T|0.09186|0.2554|0.1146|0.03703|0.1747|0.05894|0.06717|0.06322|0.05486|0.2554|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:92:20:7,13:19,36:55,20:0.2174:2,2:33.4:1:37:0:1:1.02:60:40:0.2703:0:1.3	0/0:23:0:0,0:7,15:22,0:0:2,0:34.8:1:34.6:1:1:0:56.6:10:1:0:0.2
    238. 

  238. 1	120612154	120612154	C	G	UTR5	NOTCH2	NM_024408:c.-134G>C;NM_001200001:c.-134G>C	.	.	0.054	0.3439	0.3210	0.2982	0.4375	0.3602	0.2012	0.3904	0.3113	rs56375229	rs56375229	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56687009;OCCURENCE=3(large_intestine),2(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29481054	SKCA-BR|3|100|0.03,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579,ORCA-IN|2|178|0.011236	0.5	68	7	1	120612154	.	C	G	68	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=4;AF=0.1081;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06779;SOR=0.17177;LSEQ=GCTCAGGCCCTGGCGCTACG;RSEQ=TCCGAAGCCCAGGCGCAAAT;CSQ=G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-134G>C||123|||||rs56375229&COSV56687009||-1||EntrezGene||||||1:g.120612154C>G|||||||||||||0&1|0&1,G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-134G>C||123|||||rs56375229&COSV56687009||-1||EntrezGene||YES||||1:g.120612154C>G|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:4:2,2:11,22:33,4:0.1081:2,2:32.2:1:34:1:0.6016:1.96:44.5:8:0.1081:0:3	0/1:7:3:1,2:0,4:4,3:0.4286:0,2:44.7:1:37:0:0.42857:0:56.7:6:0.4286:0:2
    239. 

  239. 1	120612163	120612163	C	A	UTR5	NOTCH2	NM_024408:c.-143G>T;NM_001200001:c.-143G>T	.	.	0.065	0.3622	0.3589	0.3079	0.4590	0.3754	0.2145	0.3999	0.3230	rs55899574	rs55899574	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56685107;OCCURENCE=4(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29481063	SKCA-BR|1|100|0.01,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	74	7	1	120612163	.	C	A	74	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=4;AF=0.1143;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.07689;SOR=0.18269;LSEQ=CTGGCGCTACGCTCCGAAGC;RSEQ=CAGGCGCAAATGCCTCGACT;CSQ=A|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-143G>T||114|||||rs55899574&COSV56685107||-1||EntrezGene||||||1:g.120612163C>A|||||||||||||0&1|0&1,A|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-143G>T||114|||||rs55899574&COSV56685107||-1||EntrezGene||YES||||1:g.120612163C>A|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:35:4:2,2:11,20:31,4:0.1143:2,2:41.2:1:37:0:0.61765:1.79:44.5:8:0.1143:0:3	0/1:7:3:1,2:0,4:4,3:0.4286:0,2:41.7:1:37:0:0.42857:0:56.7:6:0.4286:0:2
    240. 

  240. 1	120612168	120612168	C	T	UTR5	NOTCH2	NM_024408:c.-148G>A;NM_001200001:c.-148G>A	.	.	0.043	0.3351	0.1414	0.3791	0.4087	0.4243	0.4282	0.4099	0.3871	rs11801102	rs11801102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56685951;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),2(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU721577	LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,ORCA-IN|1|178|0.00561798	0.5	37	7	1	120612168	.	C	T	37	v3	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=34;VD=2;AF=0.0588;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12843;SOR=0.16737;LSEQ=GCTACGCTCCGAAGCCCAGG;RSEQ=GCAAATGCCTCGACTCCCCG;CSQ=T|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-148G>A||109|||||rs11801102&COSV56685951||-1||EntrezGene||||||1:g.120612168C>T|||||||||||||0&1|0&1,T|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-148G>A||109|||||rs11801102&COSV56685951||-1||EntrezGene||YES||||1:g.120612168C>T|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:2:1,1:12,20:32,2:0.0588:2,2:45:1:37:0:1:1.64:50:4:0.0588:0:2	0/1:7:2:0,2:1,4:5,2:0.2857:2,0:38:1:37:0:1:0:57:4:0.2857:0:1
    241. 

  241. 1	120612194	120612194	C	G	UTR5	NOTCH2	NM_024408:c.-174G>C;NM_001200001:c.-174G>C	.	.	.	0.1009	0.1947	0.0721	0.0842	0.0141	0.0364	0.0868	0.0777	rs79247096	rs79247096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56682290;OCCURENCE=2(bone),4(breast),1(haematopoietic_and_lymphoid_tissue),3(pancreas),1(lung),2(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11338600	MELA-AU|1|183|0.00546448,PACA-CA|2|268|0.00746269,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,PBCA-DE|1|499|0.00200401,PRAD-CN|1|65|0.0153846,BRCA-KR|4|50|0.08	0.25	151	2	1	120612194	.	C	G	151	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=17;AF=0.5667;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.21169;SOR=inf;LSEQ=TGCCTCGACTCCCCGCGCCC;RSEQ=GAGTCCGCCGCTCCTCGGCC;CSQ=G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_001200001.2|protein_coding|1/22||NM_001200001.2:c.-174G>C||83|||||rs79247096&COSV56682290||-1||EntrezGene||||||1:g.120612194C>G|||||||||||||0&1|0&1,G|5_prime_UTR_variant|MODIFIER|NOTCH2|4853|Transcript|NM_024408.4|protein_coding|1/34||NM_024408.4:c.-174G>C||83|||||rs79247096&COSV56682290||-1||EntrezGene||YES||||1:g.120612194C>G|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:30:17:6,11:6,7:13,17:0.5667:2,2:39.3:1:37:0:0.71062:1.54757:33.9:34:0.5667:0:1.3	0/0:2:0:0,0:0,2:2,0:0:0,0:40:1:24:1:1:0:56.5:1:1:0:1.5
    242. 

  242. 1	149785105	149785105	G	-	exonic	HIST2H3D	.	frameshift deletion	HIST2H3D:NM_001123375:exon1:c.132delC:p.G45Afs*18	.	3.243e-05	0	0	0	0	0	6.692e-05	0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	0	1	149785104	.	CG	C	37	v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=Deletion;DP=35;VD=2;AF=0.0571;SHIFT3=2;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGCAGAGCCACGGTGC;RSEQ=GGCCGGTAGCGGTGCGGCTT;CSQ=-|upstream_gene_variant|MODIFIER|HIST2H2BF|440689|Transcript|NM_001024599.5|protein_coding||||||||||rs1553754952&COSV58944282|1180|-1||EntrezGene||||||1:g.149785107del|||||||||||||0&1|0&1,-|frameshift_variant|HIGH|HIST2H3D|653604|Transcript|NM_001123375.3|protein_coding|1/1||NM_001123375.3:c.132del|NP_001116847.1:p.Gly45AlafsTer18|144|132|44|P/X|ccC/cc|rs1553754952&COSV58944282||-1||EntrezGene||YES||||1:g.149785107del|||||||||||||0&1|0&1,-|upstream_gene_variant|MODIFIER|HIST2H2BF|440689|Transcript|NM_001161334.2|protein_coding||||||||||rs1553754952&COSV58944282|1180|-1||EntrezGene||YES||||1:g.149785107del|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:35:2:2,0:21,12:33,2:0.0571:2,0:50.5:1:37:0:0.53613:0:10:4:0.0571:0:0	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    243. 

  243. 1	149785143	149785143	C	T	exonic	HIST2H3D	.	nonsynonymous SNV	HIST2H3D:NM_001123375:exon1:c.G94A:p.A32T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.537	U	1.000	0.548	D	.	.	.	0.95	0.433	T	-2.9	0.608	D	0.5	0.545	-0.961	0.390	T	0.134	0.448	T	0.018	0.404	T	3.010	0.422	22.3	0.981	0.380	0.218	0.213	N	c	-0.023	-0.034	1.000	0.747	0.455	0.088	0	4.1	0.470	0.604	0.237	0.798	0.323	0.118	0.229	0.997	0.653	15.414	0.746	Histone H2A/H2B/H3|Histone-fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	1	1	149785143	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=2;AF=0.0357;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.96491;SOR=inf;LSEQ=CTTCTTCACCCCGCCCGTGG;RSEQ=CGGCGCGCTCTTGCGGGCCG;CSQ=T|upstream_gene_variant|MODIFIER|HIST2H2BF|440689|Transcript|NM_001024599.5|protein_coding||||||||||rs782094182|1218|-1||EntrezGene||||||1:g.149785143C>T|1.727e-05|0|0.0001237|0|0|0|0|0|0|0.0001237|gnomAD_AMR|||,T|missense_variant|MODERATE|HIST2H3D|653604|Transcript|NM_001123375.3|protein_coding|1/1||NM_001123375.3:c.94G>A|NP_001116847.1:p.Ala32Thr|106|94|32|A/T|Gcc/Acc|rs782094182||-1||EntrezGene||YES||||1:g.149785143C>T|1.727e-05|0|0.0001237|0|0|0|0|0|0|0.0001237|gnomAD_AMR|||,T|upstream_gene_variant|MODIFIER|HIST2H2BF|440689|Transcript|NM_001161334.2|protein_coding||||||||||rs782094182|1218|-1||EntrezGene||YES||||1:g.149785143C>T|1.727e-05|0|0.0001237|0|0|0|0|0|0|0.0001237|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:56:2:1,1:26,28:54,2:0.0357:2,2:50:1:37:0:1:1.08:33:4:0.0357:0:1	0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:25:0:1:0:48:2:1:0:0
    244. 

  244. 1	150549801	150549803	TGG	-	UTR3	MCL1	NM_021960:c.*50_*48delCCA;NM_001197320:c.*50_*48delCCA;NM_182763:c.*39_*37delCCA	.	.	0.0056	.	.	.	.	.	.	.	.	rs755159122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	85	94	1	150549800	.	TTGG	T	85	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=390;VD=5;AF=0.0128;SHIFT3=13;MSI=5;MSILEN=3;SSF=0.338;SOR=inf;LSEQ=TCCAACTGCATAAACTGGTT;RSEQ=TGGTGGTGGTGGTTGGTTAA;CSQ=-|3_prime_UTR_variant|MODIFIER|MCL1|4170|Transcript|NM_001197320.2|protein_coding|4/4||NM_001197320.2:c.*48_*50del||722-724|||||rs34100999||-1||EntrezGene||||||1:g.150549814_150549816del|0.0001165|6.339e-05|0.0002617|0.0004605|5.701e-05|4.815e-05|4.723e-05|0.0001786|0.0002221|0.005626|AA|||,-|3_prime_UTR_variant|MODIFIER|MCL1|4170|Transcript|NM_021960.5|protein_coding|3/3||NM_021960.5:c.*48_*50del||1181-1183|||||rs34100999||-1||EntrezGene||YES||||1:g.150549814_150549816del|0.0001165|6.339e-05|0.0002617|0.0004605|5.701e-05|4.815e-05|4.723e-05|0.0001786|0.0002221|0.005626|AA|||,-|3_prime_UTR_variant|MODIFIER|MCL1|4170|Transcript|NM_182763.3|protein_coding|2/2||NM_182763.3:c.*37_*39del||933-935|||||rs34100999||-1||EntrezGene||||||1:g.150549814_150549816del|0.0001165|6.339e-05|0.0002617|0.0004605|5.701e-05|4.815e-05|4.723e-05|0.0001786|0.0002221|0.005626|AA|||,-|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA||||||||||rs34100999|2773|-1||EntrezGene||YES||||1:g.150549814_150549816del|0.0001165|6.339e-05|0.0002617|0.0004605|5.701e-05|4.815e-05|4.723e-05|0.0001786|0.0002221|0.005626|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:390:5:3,2:226,159:385,5:0.0128:2,2:44.2:1:37:0:1:1.06:60:10:0.0129:0:0	0/0:94:0:0,0:73,21:94,0:0:2,0:33:1:36.1:1:1:0:60:46:1:0:0.1
    245. 

  245. 1	150549988	150549988	G	A	intronic	MCL1	.	.	.	.	.	.	.	.	.	.	.	.	rs1025392749	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	121	1	150549988	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=141;VD=2;AF=0.0142;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.28867;SOR=inf;LSEQ=CTAGAAAACAAAAAAGAAAA;RSEQ=CACATTTTCAAGTATGGGTT;CSQ=A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_001197320.2|protein_coding||3/3|NM_001197320.2:c.478-21C>T|||||||rs1025392749||-1||EntrezGene||||||1:g.150549988G>A|8.678e-06|0|0|0|0|0|1.88e-05|0|0|1.88e-05|gnomAD_NFE|||,A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_021960.5|protein_coding||2/2|NM_021960.5:c.937-21C>T|||||||rs1025392749||-1||EntrezGene||YES||||1:g.150549988G>A|8.678e-06|0|0|0|0|0|1.88e-05|0|0|1.88e-05|gnomAD_NFE|||,A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_182763.3|protein_coding||1/1|NM_182763.3:c.689-21C>T|||||||rs1025392749||-1||EntrezGene||||||1:g.150549988G>A|8.678e-06|0|0|0|0|0|1.88e-05|0|0|1.88e-05|gnomAD_NFE|||,A|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA||||||||||rs1025392749|2960|-1||EntrezGene||YES||||1:g.150549988G>A|8.678e-06|0|0|0|0|0|1.88e-05|0|0|1.88e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:141:2:1,1:42,97:139,2:0.0142:2,2:54.5:1:37:0:0.51844:2.29:60:4:0.0144:0:1	0/0:121:0:0,0:41,80:121,0:0:2,0:35:1:35.1:1:1:0:60:23.2:1:0:0.1
    246. 

  246. 1	150550019	150550019	-	A	intronic	MCL1	.	.	.	1.	0.9999	1	1	1	0.9994	1	0.9999	1	rs11428742	rs11428742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	229	85	1	150550019	.	T	TA	229	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=52;VD=48;AF=0.9231;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.14696;SOR=0.2919;LSEQ=AGTATGGGTTTCTGCTCTCT;RSEQ=ACAACACTACTATCCAGAGA;CSQ=A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_001197320.2|protein_coding||3/3|NM_001197320.2:c.478-53dup|||||||rs11428742||-1||EntrezGene||||||1:g.150550020dup|0.9999|0.9999|1|1|0.9999|1|0.9999|1|0.9999|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|||,A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_021960.5|protein_coding||2/2|NM_021960.5:c.937-53dup|||||||rs11428742||-1||EntrezGene||YES||||1:g.150550020dup|0.9999|0.9999|1|1|0.9999|1|0.9999|1|0.9999|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|||,A|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_182763.3|protein_coding||1/1|NM_182763.3:c.689-53dup|||||||rs11428742||-1||EntrezGene||||||1:g.150550020dup|0.9999|0.9999|1|1|0.9999|1|0.9999|1|0.9999|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|||,A|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA||||||||||rs11428742|2991|-1||EntrezGene||YES||||1:g.150550020dup|0.9999|0.9999|1|1|0.9999|1|0.9999|1|0.9999|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:52:48:9,39:1,3:4,48:0.9231:2,2:21.4:1:36.3:1:1:1.43327:60:47:0.94:0.3846:0.1	1/1:85:83:20,63:0,2:2,83:0.9765:0,2:34.3:1:36:1:1:0:60:82:0.9762:0.1529:0.1
    247. 

  247. 1	150551483	150551483	T	C	exonic	MCL1	.	nonsynonymous SNV	MCL1:NM_021960:exon1:c.A524G:p.Y175C,MCL1:NM_182763:exon1:c.A524G:p.Y175C	.	.	.	.	.	.	.	.	.	.	.	0.079	0.564	T	0.997	0.689	D	0.912	0.630	D	0.061	0.222	N	0.924	0.367	D	1.04	0.263	L	3.58	0.046	T	-2.1	0.754	N	0.697	0.712	-0.997	0.309	T	0.014	0.054	T	0.006	0.164	T	4.885	0.656	24.9	0.984	0.407	0.153	0.186	N	c	0.123	0.128	1.000	0.747	0.628	0.401	0	3.85	0.434	0.560	0.230	1.061	0.807	0.978	0.348	0.939	0.413	9.392	0.373	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	109	1	150551483	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1145;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00749;SOR=0;LSEQ=TAATCTCCAGCGACTGCCGG;RSEQ=ACAACTCGTCCTCCTCCTCC;CSQ=C|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_001197320.2|protein_coding||1/3|NM_001197320.2:c.109-44A>G|||||||||-1||EntrezGene||||||1:g.150551483T>C||||||||||||||,C|missense_variant|MODERATE|MCL1|4170|Transcript|NM_021960.5|protein_coding|1/3||NM_021960.5:c.524A>G|NP_068779.1:p.Tyr175Cys|604|524|175|Y/C|tAc/tGc|||-1||EntrezGene||YES||||1:g.150551483T>C||||||||||||||,C|missense_variant|MODERATE|MCL1|4170|Transcript|NM_182763.3|protein_coding|1/2||NM_182763.3:c.524A>G|NP_877495.1:p.Tyr175Cys|604|524|175|Y/C|tAc/tGc|||-1||EntrezGene||||||1:g.150551483T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA|||||||||||4455|-1||EntrezGene||YES||||1:g.150551483T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1145:0:0,0:515,629:1144,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:109:2:1,1:46,61:107,2:0.0183:2,2:30:0:37:0:1:1.32:60:4:0.0185:0:1
    248. 

  248. 1	150551492	150551494	TCC	-	exonic	MCL1	.	nonframeshift deletion	MCL1:NM_021960:exon1:c.513_515del:p.E171del,MCL1:NM_182763:exon1:c.513_515del:p.E171del	0.016	.	.	.	.	.	.	.	.	rs759789515	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	136	106	1	150551491	.	GTCC	G	136	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1127;VD=13;AF=0.0115;SHIFT3=11;MSI=4;MSILEN=3;SSF=0.30895;SOR=inf;LSEQ=AGCGACTGCCGGTACAACTC;RSEQ=TCCTCCTCCTCTGCTGGCGG;CSQ=-|intron_variant|MODIFIER|MCL1|4170|Transcript|NM_001197320.2|protein_coding||1/3|NM_001197320.2:c.109-55_109-53del|||||||rs759789515||-1||EntrezGene||||||1:g.150551503_150551505del|8.782e-05|0|0.0005497|0|0|4.668e-05|8.833e-06|0|3.267e-05|0.01643|AA|||,-|inframe_deletion|MODERATE|MCL1|4170|Transcript|NM_021960.5|protein_coding|1/3||NM_021960.5:c.513_515del|NP_068779.1:p.Glu171del|593-595|513-515|171-172|ED/D|gaGGAc/gac|rs759789515||-1||EntrezGene||YES||||1:g.150551503_150551505del|8.782e-05|0|0.0005497|0|0|4.668e-05|8.833e-06|0|3.267e-05|0.01643|AA|||,-|inframe_deletion|MODERATE|MCL1|4170|Transcript|NM_182763.3|protein_coding|1/2||NM_182763.3:c.513_515del|NP_877495.1:p.Glu171del|593-595|513-515|171-172|ED/D|gaGGAc/gac|rs759789515||-1||EntrezGene||||||1:g.150551503_150551505del|8.782e-05|0|0.0005497|0|0|4.668e-05|8.833e-06|0|3.267e-05|0.01643|AA|||,-|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA||||||||||rs759789515|4464|-1||EntrezGene||YES||||1:g.150551503_150551505del|8.782e-05|0|0.0005497|0|0|4.668e-05|8.833e-06|0|3.267e-05|0.01643|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1127:13:7,6:495,618:1113,13:0.0115:2,2:32.4:1:37:1:0.57991:1.46:60:26:0.0117:0.0018:0	0/0:106:0:0,0:45,61:106,0:0:2,0:40.4:1:36.3:1:1:0:60:52:1:0:0.1
    249. 

  249. 1	150551945	150551945	A	C	exonic	MCL1	.	nonsynonymous SNV	MCL1:NM_001197320:exon1:c.T62G:p.L21W,MCL1:NM_021960:exon1:c.T62G:p.L21W,MCL1:NM_182763:exon1:c.T62G:p.L21W	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.999	0.764	D	0.923	0.641	D	0.956	0.082	N	1	0.090	N	0.975	0.246	L	2.43	0.358	T	-0.56	0.425	N	0.479	0.546	-1.030	0.205	T	0.070	0.284	T	0.023	0.458	T	3.387	0.465	23.0	0.946	0.245	0.074	0.133	N	c	-0.171	-0.315	1.0	0.983	0.442	0.072	0	3.66	0.409	0.686	0.249	1.108	0.878	0.000	0.063	0.033	0.150	7.343	0.257	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.5	42	52	1	150551945	.	A	C	42	q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=383;VD=7;AF=0.0183;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.2933;SOR=0.46649;LSEQ=CGCCGCCGCTGCCGGCCCCC;RSEQ=AGCCGGCCCCCCCACAGTAG;CSQ=C|missense_variant|MODERATE|MCL1|4170|Transcript|NM_001197320.2|protein_coding|1/4||NM_001197320.2:c.62T>G|NP_001184249.1:p.Leu21Trp|142|62|21|L/W|tTg/tGg|||-1||EntrezGene||||||1:g.150551945A>C||||||||||||||,C|missense_variant|MODERATE|MCL1|4170|Transcript|NM_021960.5|protein_coding|1/3||NM_021960.5:c.62T>G|NP_068779.1:p.Leu21Trp|142|62|21|L/W|tTg/tGg|||-1||EntrezGene||YES||||1:g.150551945A>C||||||||||||||,C|missense_variant|MODERATE|MCL1|4170|Transcript|NM_182763.3|protein_coding|1/2||NM_182763.3:c.62T>G|NP_877495.1:p.Leu21Trp|142|62|21|L/W|tTg/tGg|||-1||EntrezGene||||||1:g.150551945A>C||||||||||||||,C|upstream_gene_variant|MODIFIER|ADAMTSL4-AS1|574406|Transcript|NR_104133.1|lncRNA|||||||||||4917|-1||EntrezGene||YES||||1:g.150551945A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:383:7:7,0:204,171:375,7:0.0183:2,0:53.9:1:15:1:0.01835:0:60:0.4:0.0065:0:4.3	0/1:52:2:2,0:27,23:50,2:0.0385:2,0:14.5:1:31:1:0.49698:0:60:4:0.0435:0:1
    250. 

  250. 1	155874280	155874280	G	A	exonic	RIT1	.	nonsynonymous SNV	RIT1:NM_001256820:exon4:c.C143T:p.A48V,RIT1:NM_001256821:exon5:c.C302T:p.A101V,RIT1:NM_006912:exon5:c.C251T:p.A84V	.	.	.	.	.	.	.	.	.	rs869025196	.	0.0	0.912	D	1.0	0.899	D	0.981	0.736	D	0.000	0.843	D	1	0.810	D	2.445	0.712	M	-1.12	0.776	T	-3.69	0.712	D	0.805	0.807	0.087	0.839	D	0.543	0.832	D	0.248	0.890	D	6.862	0.929	33	0.999	0.992	0.986	0.848	D	c	0.789	0.801	1.000	0.747	0.707	0.730	0	5.76	0.907	8.087	0.893	0.998	0.613	1.000	0.715	0.999	0.750	19.572	0.954	P-loop containing nucleoside triphosphate hydrolase|Small GTP-binding protein domain	.	.	.	181506	Noonan_syndrome|not_provided	MONDO:MONDO:0018997,MeSH:D009634,MedGen:C0028326,OMIM:PS163950,Orphanet:ORPHA648,SNOMED_CT:205824006|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Likely_pathogenic	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	0	1	155874280	.	G	A	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=2;AF=0.5;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATATACTGGTCCCGCATG;RSEQ=CTGTAAACTCTGCCTAGAGG;CSQ=A|missense_variant|MODERATE|RIT1|6016|Transcript|NM_001256820.2|protein_coding|4/5||NM_001256820.2:c.143C>T|NP_001243749.1:p.Ala48Val|252|143|48|A/V|gCc/gTc|rs869025196&CM169032||-1||EntrezGene||||||1:g.155874280G>A||||||||||||likely_pathogenic||1&1,A|missense_variant|MODERATE|RIT1|6016|Transcript|NM_001256821.2|protein_coding|5/6||NM_001256821.2:c.302C>T|NP_001243750.1:p.Ala101Val|335|302|101|A/V|gCc/gTc|rs869025196&CM169032||-1||EntrezGene||YES||||1:g.155874280G>A||||||||||||likely_pathogenic||1&1,A|missense_variant|MODERATE|RIT1|6016|Transcript|NM_006912.6|protein_coding|5/6||NM_006912.6:c.251C>T|NP_008843.1:p.Ala84Val|401|251|84|A/V|gCc/gTc|rs869025196&CM169032||-1||EntrezGene||||||1:g.155874280G>A||||||||||||likely_pathogenic||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:1,1:1,1:2,2:0.5:2,2:58:1:37:0:1:1:60:4:0.5:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    251. 

  251. 1	156785617	156785617	G	A	UTR5	NTRK1	NM_001007792:c.-5G>A	.	.	0.82	0.6243	0.5074	0.6926	0.6887	0.8288	0.6437	0.6591	0.6449	rs1800601	rs1800601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63884607;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(large_intestine)	364541	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU718802	LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763	1	375	120	1	156785617	.	G	A	375	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1339;VD=1337;AF=0.9985;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.22715;SOR=5.60426;LSEQ=AGGGAGTGAGTGGGCAACTC;RSEQ=GCGCATGAAGGAGGTACTCC;CSQ=A|5_prime_UTR_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|1/17||NM_001007792.1:c.-5G>A||76|||||rs1800601&COSV63884607||1||EntrezGene||||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1,A|intron_variant|MODIFIER|SH2D2A|9047|Transcript|NM_001161441.2|protein_coding||2/8|NM_001161441.2:c.123+181C>T|||||||rs1800601&COSV63884607||-1||EntrezGene||YES||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1,A|intron_variant|MODIFIER|SH2D2A|9047|Transcript|NM_001161442.2|protein_coding||2/8|NM_001161442.2:c.69+181C>T|||||||rs1800601&COSV63884607||-1||EntrezGene||||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1,A|intron_variant|MODIFIER|SH2D2A|9047|Transcript|NM_001161443.2|protein_coding||1/7|NM_001161443.2:c.39+181C>T|||||||rs1800601&COSV63884607||-1||EntrezGene||||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1,A|intron_variant|MODIFIER|SH2D2A|9047|Transcript|NM_001161444.2|protein_coding||2/7|NM_001161444.2:c.123+181C>T|||||||rs1800601&COSV63884607||-1||EntrezGene||||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1,A|intron_variant|MODIFIER|SH2D2A|9047|Transcript|NM_003975.4|protein_coding||2/8|NM_003975.4:c.123+181C>T|||||||rs1800601&COSV63884607||-1||EntrezGene||||||1:g.156785617G>A|0.674|0.4989|0.6951|0.6983|0.8177|0.649|0.6775|0.6685|0.6549|0.8177|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1339:1337:606,731:0,1:1,1337:0.9985:0,2:37.9:1:36.2:1:1:0:60:57.13:0.9985:0:1.1	1/1:120:119:45,74:0,0:0,119:0.9917:0,2:39:1:35.8:1:1:0:60:38.667:0.9915:0:1.1
    252. 

  252. 1	156834182	156834182	G	T	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon2:c.G249T:p.E83D,NTRK1:NM_002529:exon2:c.G249T:p.E83D,NTRK1:NM_001007792:exon3:c.G159T:p.E53D	.	.	.	.	.	.	.	.	.	.	.	0.288	0.155	T	0.0	0.026	B	0.0	0.013	B	0.431	0.127	N	1	0.090	N	0.98	0.250	L	-2.65	0.902	D	-0.01	0.076	N	0.119	0.149	-0.841	0.526	T	0.230	0.595	T	0.029	0.515	D	0.811	0.171	9.529	0.988	0.466	0.097	0.152	N	c	-0.924	-0.884	0.998	0.370	0.765	0.991	0	0.336	0.151	-0.109	0.107	0.031	0.150	0.000	0.063	0.204	0.218	4.358	0.105	Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	162	1	156834182	.	G	T	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1591;VD=1;AF=0.0006;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02392;SOR=0.05051;LSEQ=CAGCATCTGCAGCATCTGGA;RSEQ=CTCCGTGATCTGAGGGGCCT;CSQ=T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|3/17||NM_001007792.1:c.159G>T|NP_001007793.1:p.Glu53Asp|239|159|53|E/D|gaG/gaT|||1||EntrezGene||||||1:g.156834182G>T||||||||||||||,T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|2/16||NM_001012331.2:c.249G>T|NP_001012331.1:p.Glu83Asp|319|249|83|E/D|gaG/gaT|||1||EntrezGene||||||1:g.156834182G>T||||||||||||||,T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|2/17||NM_002529.4:c.249G>T|NP_002520.2:p.Glu83Asp|319|249|83|E/D|gaG/gaT|||1||EntrezGene||YES||||1:g.156834182G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1591:1:1,0:823,767:1590,1:0.0006:2,0:54:0:11:0:1:0:60:0:0:0:4	0/1:162:2:1,1:80,80:160,2:0.0123:2,2:42.5:1:37:0:1:1:60:4:0.0124:0:1
    253. 

  253. 1	156836733	156836733	T	C	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon4:c.T391C:p.S131P,NTRK1:NM_002529:exon4:c.T391C:p.S131P,NTRK1:NM_001007792:exon5:c.T301C:p.S101P	.	.	.	.	.	.	.	.	.	.	.	0.013	0.546	D	0.061	0.670	B	0.147	0.658	B	0.026	0.259	N	1.000	0.588	D	0.53	0.137	N	0.33	0.583	T	-2.64	0.571	D	0.68	0.867	-0.791	0.557	T	0.102	0.377	T	0.037	0.574	D	5.571	0.758	26.4	0.999	0.949	0.942	0.602	D	c	0.136	0.247	1.000	0.747	0.616	0.391	0	4.51	0.544	5.191	0.647	1.061	0.807	1.000	0.715	0.995	0.604	10.139	0.417	Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	161	1	156836733	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2451;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=2;SSF=0.00378;SOR=0;LSEQ=TCAACGCTCTGGAGTCTCTC;RSEQ=CCTGGAAAACTGTGCAGGGC;CSQ=C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|5/17||NM_001007792.1:c.301T>C|NP_001007793.1:p.Ser101Pro|381|301|101|S/P|Tcc/Ccc|CD000267||1||EntrezGene||||||1:g.156836733T>C||||||||||||||1,C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|4/16||NM_001012331.2:c.391T>C|NP_001012331.1:p.Ser131Pro|461|391|131|S/P|Tcc/Ccc|CD000267||1||EntrezGene||||||1:g.156836733T>C||||||||||||||1,C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|4/17||NM_002529.4:c.391T>C|NP_002520.2:p.Ser131Pro|461|391|131|S/P|Tcc/Ccc|CD000267||1||EntrezGene||YES||||1:g.156836733T>C||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2451:0:0,0:1261,1190:2451,0:0:2,0:38.5:1:35.6:1:1:0:60:35.044:1:0:0.4	0/1:161:2:1,1:86,73:159,2:0.0124:2,2:43.5:1:37:0:1:1.17688:60:4:0.0125:0:1
    254. 

  254. 1	156836789	156836789	A	G	intronic	NTRK1	.	.	.	0.012	0.0006	0	0	0	0.0105	0	0	0.0010	rs192153341	rs192153341	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62328078;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU113481002	LAML-KR|1|205|0.00487805	0.25	363	127	1	156836789	.	A	G	363	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2032;VD=998;AF=0.4911;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=inf;LSEQ=CTGTGAGTGGGGGCGCTTCC;RSEQ=GGGGCAAGAGCACCAAGTGT;CSQ=G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||5/16|NM_001007792.1:c.338+19A>G|||||||rs192153341&COSV62328078||1||EntrezGene||||||1:g.156836789A>G|0.000855|0|0|0|0.01153|0|8.791e-06|0.0003258|0|0.01153|gnomAD_EAS||0&1|0&1,G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||4/15|NM_001012331.2:c.428+19A>G|||||||rs192153341&COSV62328078||1||EntrezGene||||||1:g.156836789A>G|0.000855|0|0|0|0.01153|0|8.791e-06|0.0003258|0|0.01153|gnomAD_EAS||0&1|0&1,G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||4/16|NM_002529.4:c.428+19A>G|||||||rs192153341&COSV62328078||1||EntrezGene||YES||||1:g.156836789A>G|0.000855|0|0|0|0.01153|0|8.791e-06|0.0003258|0|0.01153|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2032:998:402,596:442,561:1003,998:0.4911:2,2:39.1:1:36.5:1:0.09393:1.168:60:82.167:0.498:0:1.1	0/0:127:0:0,0:52,75:127,0:0:2,0:36.4:1:36.2:1:1:0:60:62.5:1:0:0.1
    255. 

  255. 1	156837969	156837969	G	T	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon5:c.G502T:p.G168C,NTRK1:NM_002529:exon5:c.G502T:p.G168C,NTRK1:NM_001007792:exon6:c.G412T:p.G138C	.	.	.	.	.	.	.	.	.	.	.	0.099	0.306	T	0.035	0.287	B	0.081	0.337	B	0.202	0.166	N	1	0.090	N	0.57	0.153	N	-2.64	0.902	D	-0.24	0.108	N	0.337	0.398	-0.656	0.625	T	0.329	0.697	T	0.036	0.565	D	1.807	0.278	15.03	0.987	0.448	0.431	0.268	N	c	-0.486	-0.412	0.160	0.176	0.554	0.283	0	2.04	0.257	2.263	0.427	-0.298	0.081	0.955	0.331	0.535	0.277	5.167	0.143	Cysteine-rich flanking region, C-terminal|Leucine-rich repeat domain, L domain-like|Tyrosine-protein kinase receptor NTRK, C2-Ig-like domain;Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	194	1	156837969	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1336;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01601;SOR=0;LSEQ=GCTGGGAGGAGGAGGGACTG;RSEQ=GCGGAGTGCCTGAACAGAAG;CSQ=T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|6/17||NM_001007792.1:c.412G>T|NP_001007793.1:p.Gly138Cys|492|412|138|G/C|Ggc/Tgc|||1||EntrezGene||||||1:g.156837969G>T||||||||||||||,T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|5/16||NM_001012331.2:c.502G>T|NP_001012331.1:p.Gly168Cys|572|502|168|G/C|Ggc/Tgc|||1||EntrezGene||||||1:g.156837969G>T||||||||||||||,T|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|5/17||NM_002529.4:c.502G>T|NP_002520.2:p.Gly168Cys|572|502|168|G/C|Ggc/Tgc|||1||EntrezGene||YES||||1:g.156837969G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1336:0:0,0:746,590:1336,0:0:2,0:37.3:1:36.8:1:1:0:60:266.2:1:0:0.2	0/1:194:2:1,1:118,74:192,2:0.0103:2,2:47:1:37:0:1:1.59057:60:4:0.0104:0:4.5
    256. 

  256. 1	156841946	156841946	C	A	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	104	1	156841946	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=190;VD=2;AF=0.0105;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.41687;SOR=inf;LSEQ=GCCTAATTTCTCTAGATCAG;RSEQ=CAACAAATTATCTTAAATAT;CSQ=A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.760+399C>A|||||||||1||EntrezGene||||||1:g.156841946C>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.850+399C>A|||||||||1||EntrezGene||||||1:g.156841946C>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.850+399C>A|||||||||1||EntrezGene||YES||||1:g.156841946C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:190:2:1,1:63,125:188,2:0.0105:2,2:10:1:37:0:1:1.98:60:4:0.0108:0:1	0/0:104:0:0,0:48,56:104,0:0:2,0:51:0:11:0:1:0:60:0:0:0:1
    257. 

  257. 1	156841970	156841970	A	G	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	110	1	156841970	.	A	G	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=120;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.22764;SOR=0;LSEQ=CAAATTATCTTAAATATTCT;RSEQ=CTTTACATCAGTTTTCTTCT;CSQ=G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.760+423A>G|||||||||1||EntrezGene||||||1:g.156841970A>G||||||||||||||,G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.850+423A>G|||||||||1||EntrezGene||||||1:g.156841970A>G||||||||||||||,G|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.850+423A>G|||||||||1||EntrezGene||YES||||1:g.156841970A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:120:0:0,0:52,68:120,0:0:2,0:26.8:1:35.8:1:1:0:60:119:1:0:0.2	0/1:110:2:1,1:60,48:108,2:0.0182:2,2:26.5:1:25:0:1:1.24744:60:4:0.0183:0:1
    258. 

  258. 1	156842472	156842472	T	-	intronic	NTRK1	.	.	.	.	0.0057	0.0009	0.0357	0.0164	0	0.0454	0.0043	0.0111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU87102992	MALY-DE|1|241|0.00414938	0.25	55	1	1	156842471	.	CT	C	55	MSI12;MSI12	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=10;VD=3;AF=0.3;SHIFT3=13;MSI=14;MSILEN=1;SSF=0.72727;SOR=inf;LSEQ=TTACCAGATTGGGTCTATTT;RSEQ=TTTTTTTTTTTTTGAGATGG;CSQ=-|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.760+938del|||||||rs1300739349||1||EntrezGene||||||1:g.156842485del||||||||||||||,-|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.850+938del|||||||rs1300739349||1||EntrezGene||||||1:g.156842485del||||||||||||||,-|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.850+938del|||||||rs1300739349||1||EntrezGene||YES||||1:g.156842485del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:10:3:2,1:4,2:6,3:0.3:2,2:31.7:1:35.2:1:1:1:60:6:0.3:0.1:0.3	0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    259. 

  259. 1	156842776	156842776	G	T	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	67	53	1	156842776	.	G	T	67	q22.5;SN1.5;Bias	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=976;VD=30;AF=0.0307;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.49901;SOR=0.80885;LSEQ=ACCGCGCCTGGCCCAGATTG;RSEQ=GTCTATTTCAAACGCATATC;CSQ=T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.761-649G>T|||||||||1||EntrezGene||||||1:g.156842776G>T||||||||||||||,T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.851-649G>T|||||||||1||EntrezGene||||||1:g.156842776G>T||||||||||||||,T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.851-649G>T|||||||||1||EntrezGene||YES||||1:g.156842776G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:976:30:0,30:592,351:943,30:0.0307:2,1:29.2:1:13.7:1:0:0:60:0.2:0.006:0:4	0/1:53:2:0,2:37,14:51,2:0.0377:2,0:8.5:1:31:1:0.08708:0:60:4:0.04:0:1.5
    260. 

  260. 1	156842808	156842808	-	GTGT	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	62	68	1	156842808	.	A	AGTGT	62	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=1152;VD=0;AF=0;SHIFT3=1;MSI=5;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACGCATATCTTTTTTCAAAA;RSEQ=GAGTGTGTGTGTGTGTGTGT;CSQ=GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.761-616_761-615insTGTG|||||||||1||EntrezGene||||||1:g.156842809_156842810insTGTG||||||||||||||,GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.851-616_851-615insTGTG|||||||||1||EntrezGene||||||1:g.156842809_156842810insTGTG||||||||||||||,GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.851-616_851-615insTGTG|||||||||1||EntrezGene||YES||||1:g.156842809_156842810insTGTG||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1152:0:0,0:631,504:1135,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:68:4:0,4:44,19:63,4:0.0588:2,0:15.8:1:31.4:1:0.01155:0:60:3:0.0462:0.0441:0.8
    261. 

  261. 1	156842810	156842810	-	GT	intronic	NTRK1	.	.	.	.	0.2616	0.1785	0.1969	0.1651	0.0645	0.3387	0.3206	0.2781	rs55870362	rs71593866	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	325	68	1	156842810	.	A	AGT	325	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=1150;VD=518;AF=0.4504;SHIFT3=44;MSI=23;MSILEN=2;SSF=0;SOR=4.74876;LSEQ=GCATATCTTTTTTCAAAAAG;RSEQ=GTGTGTGTGTGTGTGTGTGT;CSQ=GT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.761-572_761-571dup|||||||rs55870362||1||EntrezGene||||||1:g.156842853_156842854dup||||||||||||||,GT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.851-572_851-571dup|||||||rs55870362||1||EntrezGene||||||1:g.156842853_156842854dup||||||||||||||,GT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.851-572_851-571dup|||||||rs55870362||1||EntrezGene||YES||||1:g.156842853_156842854dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1150:518:236,281:110,65:175,518:0.4504:2,2:48.5:1:36.1:1:0.00011:2.01297:60:1036:0.7:0:0.6	0/1:68:10:3,6:2,2:4,10:0.1471:2,2:57.1:1:38.1:0:1:1.8918:61.8:20:0.1389:0:0
    262. 

  262. 1	156842993	156842993	T	C	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	130	1	156842993	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1037;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=2;SSF=0.01232;SOR=0;LSEQ=GGATTACAGGAGCAAGTCAC;RSEQ=GTGCCTGGCTTTTCCCCAAA;CSQ=C|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||8/16|NM_001007792.1:c.761-432T>C|||||||rs1373981352||1||EntrezGene||||||1:g.156842993T>C||||||||||||||,C|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||7/15|NM_001012331.2:c.851-432T>C|||||||rs1373981352||1||EntrezGene||||||1:g.156842993T>C||||||||||||||,C|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||7/16|NM_002529.4:c.851-432T>C|||||||rs1373981352||1||EntrezGene||YES||||1:g.156842993T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1037:0:0,0:521,516:1037,0:0:2,0:37.3:1:36.1:1:1:0:60:56.611:1:0:0.1	0/1:130:2:1,1:69,59:128,2:0.0154:2,2:29:1:37:0:1:1.16808:60:4:0.0156:0:1
    263. 

  263. 1	156843572	156843572	T	C	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon8:c.T998C:p.L333P,NTRK1:NM_002529:exon8:c.T998C:p.L333P,NTRK1:NM_001007792:exon9:c.T908C:p.L303P	.	.	.	.	.	.	.	.	.	.	.	0.159	0.238	T	0.89	0.764	P	0.712	0.672	P	0.006	0.320	N	1	0.810	D	1.79	0.469	L	1.53	0.304	T	-1.13	0.305	N	0.34	0.733	-1.044	0.162	T	0.115	0.409	T	0.018	0.403	T	4.409	0.590	24.1	0.999	0.948	0.949	0.625	D	c	0.640	0.668	1.000	0.747	0.517	0.208	0	6.17	0.997	1.736	0.376	1.061	0.807	0.968	0.339	0.994	0.587	15.646	0.767	Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	132	1	156843572	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1939;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00403;SOR=0;LSEQ=CTTCATCTTCACTGAGTTCC;RSEQ=GGAGCCGGCAGCCAATGAGA;CSQ=C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|9/17||NM_001007792.1:c.908T>C|NP_001007793.1:p.Leu303Pro|988|908|303|L/P|cTg/cCg|||1||EntrezGene||||||1:g.156843572T>C||||||||||||||,C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|8/16||NM_001012331.2:c.998T>C|NP_001012331.1:p.Leu333Pro|1068|998|333|L/P|cTg/cCg|||1||EntrezGene||||||1:g.156843572T>C||||||||||||||,C|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|8/17||NM_002529.4:c.998T>C|NP_002520.2:p.Leu333Pro|1068|998|333|L/P|cTg/cCg|||1||EntrezGene||YES||||1:g.156843572T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1939:0:0,0:1081,858:1939,0:0:2,0:37:1:36.2:1:1:0:60:57.758:1:0:0.1	0/1:132:2:1,1:69,61:130,2:0.0152:2,2:31:1:37:0:1:1.13009:60:4:0.0155:0:1
    264. 

  264. 1	156843654	156843654	G	A	exonic	NTRK1	.	synonymous SNV	NTRK1:NM_001012331:exon8:c.G1080A:p.T360T,NTRK1:NM_002529:exon8:c.G1080A:p.T360T,NTRK1:NM_001007792:exon9:c.G990A:p.T330T	0.062	0.0019	0	0	0	0.0358	0	0	0.0020	rs2274498	rs2274498	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62327218;OCCURENCE=1(biliary_tract),1(prostate),2(lung),1(endometrium)	277580	Hereditary_insensitivity_to_pain_with_anhidrosis	MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	MU85095182	LICA-CN|2|402|0.00497512,LUSC-KR|2|170|0.0117647,UCEC-US|2|531|0.00376648	0.25	215	140	1	156843654	.	G	A	215	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2140;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCAACAACGGCAACTACAC;RSEQ=CTGCTGGCTGCCAACCCCTT;CSQ=A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|9/17||NM_001007792.1:c.990G>A|NP_001007793.1:p.Thr330%3D|1070|990|330|T|acG/acA|rs2274498&COSV62327218||1||EntrezGene||||||1:g.156843654G>A|0.003193|0|3.05e-05|0.001992|0.03723|0|6.863e-05|0.002111|0.001878|0.03723|gnomAD_EAS|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|8/16||NM_001012331.2:c.1080G>A|NP_001012331.1:p.Thr360%3D|1150|1080|360|T|acG/acA|rs2274498&COSV62327218||1||EntrezGene||||||1:g.156843654G>A|0.003193|0|3.05e-05|0.001992|0.03723|0|6.863e-05|0.002111|0.001878|0.03723|gnomAD_EAS|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding|8/17||NM_002529.4:c.1080G>A|NP_002520.2:p.Thr360%3D|1150|1080|360|T|acG/acA|rs2274498&COSV62327218||1||EntrezGene||YES||||1:g.156843654G>A|0.003193|0|3.05e-05|0.001992|0.03723|0|6.863e-05|0.002111|0.001878|0.03723|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2140:0:0,0:1005,1134:2139,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:140:70:29,41:34,36:70,70:0.5:2,2:38.3:1:35.2:1:0.49696:1.33247:60:22.333:0.4963:0:1.1
    265. 

  265. 1	156843729	156843729	C	T	exonic	NTRK1	.	synonymous SNV	NTRK1:NM_001012331:exon8:c.C1155T:p.F385F,NTRK1:NM_002529:exon8:c.C1155T:p.F385F,NTRK1:NM_001007792:exon9:c.C1065T:p.F355F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	129	1	156843729	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1480;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00638;SOR=0;LSEQ=ATGGACAACCCTTTCGAGTT;RSEQ=AACCCCGAGGACCCCATCCC;CSQ=T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|9/17||NM_001007792.1:c.1065C>T|NP_001007793.1:p.Phe355%3D|1145|1065|355|F|ttC/ttT|COSV62327487||1||EntrezGene||||||1:g.156843729C>T|||||||||||||1|1,T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|8/16||NM_001012331.2:c.1155C>T|NP_001012331.1:p.Phe385%3D|1225|1155|385|F|ttC/ttT|COSV62327487||1||EntrezGene||||||1:g.156843729C>T|||||||||||||1|1,T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding|8/17||NM_002529.4:c.1155C>T|NP_002520.2:p.Phe385%3D|1225|1155|385|F|ttC/ttT|COSV62327487||1||EntrezGene||YES||||1:g.156843729C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1480:0:0,0:673,807:1480,0:0:2,0:33.2:1:36.6:1:1:0:60:147:1:0:0.1	0/1:129:2:1,1:63,64:127,2:0.0155:2,2:20.5:1:31:1:1:1.02:60:4:0.0157:0:2
    266. 

  266. 1	156843761	156843761	C	T	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	130	1	156843761	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1363;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.00753;SOR=0;LSEQ=CCCCATCCCTGGTGCGAGGG;RSEQ=CATCCTGAACCCTGCCCCCA;CSQ=T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||9/16|NM_001007792.1:c.1087+10C>T|||||||||1||EntrezGene||||||1:g.156843761C>T||||||||||||||,T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||8/15|NM_001012331.2:c.1177+10C>T|||||||||1||EntrezGene||||||1:g.156843761C>T||||||||||||||,T|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||8/16|NM_002529.4:c.1177+10C>T|||||||||1||EntrezGene||YES||||1:g.156843761C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1363:0:0,0:633,730:1363,0:0:2,0:34.6:1:36.6:1:1:0:60:112.583:1:0:0.1	0/1:130:2:1,1:67,61:128,2:0.0154:2,2:42.5:1:37:0:1:1.09757:60:4:0.0155:0:1
    267. 

  267. 1	156844613	156844614	TG	CA	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	98	1	156844613	.	TG	CA	37	v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Complex;DP=755;VD=0;AF=0;SHIFT3=4;MSI=1;MSILEN=1;SSF=0.01308;SOR=0;LSEQ=GACCTGGCTCCGGGCTCCCA;RSEQ=CAGGATGAAAAAATGGCTTA;CSQ=CA|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||10/16|NM_001007792.1:c.1144-85_1144-84inv|||||||||1||EntrezGene||||||1:g.156844613_156844614inv||||||||||||||,CA|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||9/15|NM_001012331.2:c.1234-85_1234-84inv|||||||||1||EntrezGene||||||1:g.156844613_156844614inv||||||||||||||,CA|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||10/16|NM_002529.4:c.1252-85_1252-84inv|||||||||1||EntrezGene||YES||||1:g.156844613_156844614inv||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:755:0:0,0:520,234:754,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:98:2:1,1:66,30:96,2:0.0204:2,2:38.5:1:37:0:0.53482:2.1806:60:4:0.0208:0:1
    268. 

  268. 1	156844649	156844649	G	A	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	144	1	156844649	.	G	A	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1340;VD=2;AF=0.0015;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.04922;SOR=0.10646;LSEQ=GGCTTACTACAGGAGGCTCT;RSEQ=AGAGTACAGGAGGAGCCCCT;CSQ=A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||10/16|NM_001007792.1:c.1144-49G>A|||||||||1||EntrezGene||||||1:g.156844649G>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||9/15|NM_001012331.2:c.1234-49G>A|||||||||1||EntrezGene||||||1:g.156844649G>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||10/16|NM_002529.4:c.1252-49G>A|||||||||1||EntrezGene||YES||||1:g.156844649G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1340:2:2,0:951,386:1337,2:0.0015:2,0:24:1:37:0:1:0:60:4:0.0015:0:1.5	0/1:144:2:1,1:93,49:142,2:0.0139:2,2:50:1:37:0:1:1.88903:60:4:0.0139:0:1
    269. 

  269. 1	156845364	156845364	G	A	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon11:c.G1389A:p.M463I,NTRK1:NM_001007792:exon12:c.G1299A:p.M433I,NTRK1:NM_002529:exon12:c.G1407A:p.M469I	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.0	0.253	B	0.002	0.237	B	0.000	0.629	D	1.000	0.548	D	0.775	0.195	N	-0.86	0.749	T	-0.47	0.166	N	0.49	0.550	-0.916	0.461	T	0.111	0.399	T	0.029	0.521	D	1.776	0.274	14.85	0.802	0.127	0.962	0.678	D	c	-0.271	-0.063	0.997	0.352	0.583	0.331	0	4.45	0.532	2.833	0.476	0.953	0.551	1.000	0.715	1.000	0.888	15.814	0.783	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	102	1	156845364	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1257;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00558;SOR=0;LSEQ=GCCATGTCCCTGCATTTCAT;RSEQ=ACATTGGGTGGCAGCTCCCT;CSQ=A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|12/17||NM_001007792.1:c.1299G>A|NP_001007793.1:p.Met433Ile|1379|1299|433|M/I|atG/atA|COSV62326744||1||EntrezGene||||||1:g.156845364G>A|||||||||||||1|1,A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|11/16||NM_001012331.2:c.1389G>A|NP_001012331.1:p.Met463Ile|1459|1389|463|M/I|atG/atA|COSV62326744||1||EntrezGene||||||1:g.156845364G>A|||||||||||||1|1,A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|12/17||NM_002529.4:c.1407G>A|NP_002520.2:p.Met469Ile|1477|1407|469|M/I|atG/atA|COSV62326744||1||EntrezGene||YES||||1:g.156845364G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1257:0:0,0:678,578:1256,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:102:2:1,1:47,53:100,2:0.0196:2,2:66:1:37:0:1:1.13:60:4:0.0196:0:1
    270. 

  270. 1	156845378	156845378	G	A	exonic	NTRK1	.	nonsynonymous SNV	NTRK1:NM_001012331:exon11:c.G1403A:p.S468N,NTRK1:NM_001007792:exon12:c.G1313A:p.S438N,NTRK1:NM_002529:exon12:c.G1421A:p.S474N	.	.	.	.	.	.	.	.	.	.	.	0.742	0.037	T	0.001	0.491	B	0.005	0.476	B	0.000	0.466	N	1.000	0.548	D	2.005	0.547	M	-0.97	0.759	T	0.35	0.038	N	0.148	0.204	-0.899	0.481	T	0.147	0.473	T	0.024	0.474	T	1.130	0.203	11.38	0.945	0.244	0.933	0.576	D	c	-0.226	-0.081	0.960	0.284	0.583	0.331	0	3.72	0.417	0.977	0.289	1.048	0.713	0.998	0.411	0.779	0.330	11.347	0.486	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	103	1	156845378	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1316;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00522;SOR=0;LSEQ=TTTCATGACATTGGGTGGCA;RSEQ=CTCCCTGTCCCCCACCGAGG;CSQ=A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|12/17||NM_001007792.1:c.1313G>A|NP_001007793.1:p.Ser438Asn|1393|1313|438|S/N|aGc/aAc|rs752915558||1||EntrezGene||||||1:g.156845378G>A|3.981e-06|0|0|0|0|0|8.798e-06|0|0|8.798e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|11/16||NM_001012331.2:c.1403G>A|NP_001012331.1:p.Ser468Asn|1473|1403|468|S/N|aGc/aAc|rs752915558||1||EntrezGene||||||1:g.156845378G>A|3.981e-06|0|0|0|0|0|8.798e-06|0|0|8.798e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|NTRK1|4914|Transcript|NM_002529.4|protein_coding|12/17||NM_002529.4:c.1421G>A|NP_002520.2:p.Ser474Asn|1491|1421|474|S/N|aGc/aAc|rs752915558||1||EntrezGene||YES||||1:g.156845378G>A|3.981e-06|0|0|0|0|0|8.798e-06|0|0|8.798e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1316:0:0,0:706,610:1316,0:0:2,0:37.6:1:36.6:1:1:0:60:262.2:1:0:0.1	0/1:103:2:1,1:48,53:101,2:0.0194:2,2:36.5:1:37:0:1:1.1:60:4:0.0194:0:1
    271. 

  271. 1	156845492	156845492	-	GTGT	intronic	NTRK1	.	.	.	0.15	0.4943	0.3289	0.4913	0.5950	0.0551	0.5291	0.6294	0.5330	rs56185968	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU111653654	BTCA-SG|2|71|0.028169	0.25	286	49	1	156845492	.	A	AGTGT	286	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=917;VD=231;AF=0.2519;SHIFT3=36;MSI=20;MSILEN=2;SSF=0;SOR=inf;LSEQ=CTGGGTCAAGGGCAGGGACG;RSEQ=GTGTGTGTGTGTGTGTGTGT;CSQ=GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||12/16|NM_001007792.1:c.1393+67_1393+70dup|||||||rs56185968||1||EntrezGene||||||1:g.156845525_156845528dup||||||||||||||1,GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||11/15|NM_001012331.2:c.1483+67_1483+70dup|||||||rs56185968||1||EntrezGene||||||1:g.156845525_156845528dup||||||||||||||1,GTGT|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||12/16|NM_002529.4:c.1501+67_1501+70dup|||||||rs56185968||1||EntrezGene||YES||||1:g.156845525_156845528dup||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:917:231:75,156:94,90:184,231:0.2519:2,2:53.7:1:36.5:1:0.00014:2.16827:60.2:462:0.357:0:0.5	0/0:49:0:0,0:10,14:24,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    272. 

  272. 1	156846233	156846233	G	A	exonic	NTRK1	.	synonymous SNV	NTRK1:NM_001012331:exon13:c.G1656A:p.Q552Q,NTRK1:NM_001007792:exon14:c.G1566A:p.Q522Q,NTRK1:NM_002529:exon14:c.G1674A:p.Q558Q	0.36	0.1995	0.1354	0.2076	0.2167	0.3626	0.2084	0.2161	0.2055	rs6334	rs6334	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62323674;OCCURENCE=1(large_intestine),1(stomach),7(soft_tissue),1(lung)	276641	Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified	MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU124466	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	210	133	1	156846233	.	G	A	210	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1368;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTGCTCGGCAGGACTTCCA;RSEQ=CGTGAGGCTGAGCTGCTCAC;CSQ=A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|14/17||NM_001007792.1:c.1566G>A|NP_001007793.1:p.Gln522%3D|1646|1566|522|Q|caG/caA|rs6334&COSV62323674||1||EntrezGene||||||1:g.156846233G>A|0.2203|0.1314|0.2163|0.1979|0.3494|0.2018|0.2144|0.2277|0.2352|0.3494|gnomAD_EAS|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|13/16||NM_001012331.2:c.1656G>A|NP_001012331.1:p.Gln552%3D|1726|1656|552|Q|caG/caA|rs6334&COSV62323674||1||EntrezGene||||||1:g.156846233G>A|0.2203|0.1314|0.2163|0.1979|0.3494|0.2018|0.2144|0.2277|0.2352|0.3494|gnomAD_EAS|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding|14/17||NM_002529.4:c.1674G>A|NP_002520.2:p.Gln558%3D|1744|1674|558|Q|caG/caA|rs6334&COSV62323674||1||EntrezGene||YES||||1:g.156846233G>A|0.2203|0.1314|0.2163|0.1979|0.3494|0.2018|0.2144|0.2277|0.2352|0.3494|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1368:0:0,0:694,674:1368,0:0:2,0:39:1:36.7:1:1:0:60:170:1:0:0.1	0/1:133:62:37,25:40,31:71,62:0.4662:2,2:34.4:1:35.4:1:0.72756:1.15:60:30:0.4615:0:1.1
    273. 

  273. 1	156848995	156848995	C	T	exonic	NTRK1	.	synonymous SNV	NTRK1:NM_001012331:exon14:c.C1869T:p.A623A,NTRK1:NM_001007792:exon15:c.C1779T:p.A593A,NTRK1:NM_002529:exon15:c.C1887T:p.A629A	0.73	0.5379	0.2079	0.5919	0.7351	0.0433	0.7278	0.7271	0.6219	rs6337	rs6337	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62325231;OCCURENCE=1(breast),3(lung),2(thyroid)	142267	Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified	MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU687507	LAML-KR|1|205|0.00487805,LUSC-KR|3|170|0.0176471,BRCA-KR|1|50|0.02	0.25	346	140	1	156848995	.	C	T	346	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1622;VD=800;AF=0.4932;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGTCTGGGGCAGCTGCTGGC;RSEQ=GTGGCTAGCCAGGTCGCTGC;CSQ=T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|15/17||NM_001007792.1:c.1779C>T|NP_001007793.1:p.Ala593%3D|1859|1779|593|A|gcC/gcT|rs6337&COSV62325231||1||EntrezGene||||||1:g.156848995C>T|0.5779|0.1981|0.5752|0.7505|0.03955|0.7318|0.7242|0.6379|0.3929|0.7505|gnomAD_ASJ|benign|0&1|1&1,T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|14/16||NM_001012331.2:c.1869C>T|NP_001012331.1:p.Ala623%3D|1939|1869|623|A|gcC/gcT|rs6337&COSV62325231||1||EntrezGene||||||1:g.156848995C>T|0.5779|0.1981|0.5752|0.7505|0.03955|0.7318|0.7242|0.6379|0.3929|0.7505|gnomAD_ASJ|benign|0&1|1&1,T|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding|15/17||NM_002529.4:c.1887C>T|NP_002520.2:p.Ala629%3D|1957|1887|629|A|gcC/gcT|rs6337&COSV62325231||1||EntrezGene||YES||||1:g.156848995C>T|0.5779|0.1981|0.5752|0.7505|0.03955|0.7318|0.7242|0.6379|0.3929|0.7505|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1622:800:504,296:522,298:820,800:0.4932:2,2:38.5:1:35.9:1:0.79669:1.02876:60:46.059:0.4906:0:1.1	0/0:140:0:0,0:92,48:140,0:0:2,0:35.2:1:36.6:1:1:0:60:280:1:0:0.1
    274. 

  274. 1	156849759	156849759	C	A	intronic	NTRK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU79197187	LIRI-JP|1|258|0.00387597	0.25	44	207	1	156849759	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1541;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00164;SOR=0;LSEQ=GACGGGCTGTCCCAGGCGCC;RSEQ=CTGGAATTGATGCAGTGTCC;CSQ=A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||15/16|NM_001007792.1:c.1939-32C>A|||||||||1||EntrezGene||||||1:g.156849759C>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||14/15|NM_001012331.2:c.2029-32C>A|||||||||1||EntrezGene||||||1:g.156849759C>A||||||||||||||,A|intron_variant|MODIFIER|NTRK1|4914|Transcript|NM_002529.4|protein_coding||15/16|NM_002529.4:c.2047-32C>A|||||||||1||EntrezGene||YES||||1:g.156849759C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1541:0:0,0:907,634:1541,0:0:2,0:37.3:1:36.4:1:1:0:60:95.312:1:0:0.1	0/1:207:3:2,1:117,87:204,3:0.0145:2,2:43.7:1:28.3:1:1:1.48:60:2:0.0098:0:2
    275. 

  275. 1	156849780	156849780	G	A	intronic	NTRK1	.	.	.	0.12	0.0063	0.0003	0.0489	0	0.0921	0	0	0.0020	rs79173278	rs79173278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	276646	Hereditary_insensitivity_to_pain_with_anhidrosis	MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU14404261	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526	0.25	242	215	1	156849780	.	G	A	242	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1821;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGAATTGATGCAGTGTCC;RSEQ=CCCGTGGCAGGTGGGAGGCC;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding||15/16|NM_001007792.1:c.1939-11G>A|||||||rs79173278||1||EntrezGene||||||1:g.156849780G>A|0.01269|0.0007512|0.04162|0|0.08873|0|2.658e-05|0.007521|0.001209|0.12|EAS|benign||1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding||14/15|NM_001012331.2:c.2029-11G>A|||||||rs79173278||1||EntrezGene||||||1:g.156849780G>A|0.01269|0.0007512|0.04162|0|0.08873|0|2.658e-05|0.007521|0.001209|0.12|EAS|benign||1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding||15/16|NM_002529.4:c.2047-11G>A|||||||rs79173278||1||EntrezGene||YES||||1:g.156849780G>A|0.01269|0.0007512|0.04162|0|0.08873|0|2.658e-05|0.007521|0.001209|0.12|EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1821:0:0,0:1022,799:1821,0:0:2,0:37.7:1:36.6:1:1:0:60:226.625:1:0:0.1	0/1:215:95:54,41:58,59:117,95:0.4419:2,2:43.6:1:36.9:1:0.33359:1.34:60:190:0.4439:0:1.1
    276. 

  276. 1	156849946	156849946	G	A	exonic	NTRK1	.	synonymous SNV	NTRK1:NM_001012331:exon15:c.G2184A:p.T728T,NTRK1:NM_001007792:exon16:c.G2094A:p.T698T,NTRK1:NM_002529:exon16:c.G2202A:p.T734T	0.033	0.0052	0.0184	0	0	0	0	0	0	rs55668752	rs55668752	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV104662698;OCCURENCE=1(prostate)	276648	Hereditary_insensitivity_to_pain_with_anhidrosis|not_specified|not_provided	MONDO:MONDO:0009746,MedGen:C0020074,OMIM:256800,Orphanet:ORPHA642,SNOMED_CT:62985007|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	115	1	156849946	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1438;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00544;SOR=0;LSEQ=TGGTACCAGCTCTCCAACAC;RSEQ=GAGGTCAGCCCCGGCCCATG;CSQ=A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001007792.1|protein_coding|16/17||NM_001007792.1:c.2094G>A|NP_001007793.1:p.Thr698%3D|2174|2094|698|T|acG/acA|rs55668752&COSV104662698||1||EntrezGene||||||1:g.156849946G>A|0.001236|0.01674|0.0006362|0|0.0001088|0|8.801e-05|0.0006532|0|0.0333|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_001012331.2|protein_coding|15/16||NM_001012331.2:c.2184G>A|NP_001012331.1:p.Thr728%3D|2254|2184|728|T|acG/acA|rs55668752&COSV104662698||1||EntrezGene||||||1:g.156849946G>A|0.001236|0.01674|0.0006362|0|0.0001088|0|8.801e-05|0.0006532|0|0.0333|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|NTRK1|4914|Transcript|NM_002529.4|protein_coding|16/17||NM_002529.4:c.2202G>A|NP_002520.2:p.Thr734%3D|2272|2202|734|T|acG/acA|rs55668752&COSV104662698||1||EntrezGene||YES||||1:g.156849946G>A|0.001236|0.01674|0.0006362|0|0.0001088|0|8.801e-05|0.0006532|0|0.0333|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1438:0:0,0:578,855:1433,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:115:2:1,1:36,77:113,2:0.0174:2,2:19:1:37:0:0.54188:2.12:60:4:0.0182:0:1
    277. 

  277. 1	158581206	158581206	C	T	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	205	1	158581206	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=177;VD=2;AF=0.0113;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.21404;SOR=inf;LSEQ=AGTATAAAAAGAGAAAAATA;RSEQ=AGTTATAGGGATTCAAAATA;CSQ=T|3_prime_UTR_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding|2/2||NM_001004478.2:c.*4036C>T||5225|||||||1||EntrezGene||YES||||1:g.158581206C>T||||||||||||||,T|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||51/51|NM_003126.4:c.7135-27G>A|||||||||-1||EntrezGene||YES||||1:g.158581206C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:177:2:1,1:48,126:174,2:0.0113:2,2:38:1:37:0:0.48045:2.61:60:4:0.0114:0:1	0/0:205:0:0,0:59,146:205,0:0:2,0:36.1:1:36.6:1:1:0:60:101.5:1:0:0.1
    278. 

  278. 1	158582646	158582646	T	C	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon51:c.A7095G:p.A2365A	0.65	0.5331	0.4155	0.5610	0.5861	0.6126	0.6305	0.5642	0.5871	rs2251969	rs2251969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63755039;OCCURENCE=1(large_intestine),1(lung)	249424	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU26751744	LUSC-KR|1|170|0.00588235,COCA-CN|5|321|0.0155763	0.25	242	183	1	158582646	.	T	C	242	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=365;VD=2;AF=0.0055;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00422;LSEQ=GTAATATATGACTTGCCCTC;RSEQ=GCCAGGGCTTGGAAGGCATT;CSQ=C|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding||||||||||rs2251969&COSV63755039|342|1||EntrezGene||YES||||1:g.158582646T>C|0.5417|0.4232|0.5439|0.5798|0.6105|0.6353|0.555|0.5496|0.4302|0.6353|gnomAD_FIN|benign|0&1|1&1,C|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|51/52||NM_003126.4:c.7095A>G|NP_003117.2:p.Ala2365%3D|7293|7095|2365|A|gcA/gcG|rs2251969&COSV63755039||-1||EntrezGene||YES||||1:g.158582646T>C|0.5417|0.4232|0.5439|0.5798|0.6105|0.6353|0.555|0.5496|0.4302|0.6353|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:365:2:1,1:202,161:363,2:0.0055:2,2:25.5:1:31:1:1:1.25387:60:4:0.0055:0:1	1/0:183:104:53,51:39,40:79,104:0.5683:2,2:35.6:1:36.2:1:0.88184:1.07:60:103:0.5659:0:1.1
    279. 

  279. 1	158583506	158583506	C	A	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	164	1	158583506	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=2;AF=0.0135;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.22421;SOR=inf;LSEQ=GTCTGACCCTTAGTCTTGTT;RSEQ=CTACCTCCCTGGATCCACAG;CSQ=A|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding|||||||||||1202|1||EntrezGene||YES||||1:g.158583506C>A||||||||||||||,A|splice_donor_5th_base_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||50/51|NM_003126.4:c.6989+5G>T|||||||||-1||EntrezGene||YES||||1:g.158583506C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:148:2:1,1:83,63:146,2:0.0135:2,2:48:0:37:0:1:1.31497:60:4:0.0136:0:1	0/0:164:0:0,0:101,63:164,0:0:2,0:38.4:1:36.3:1:1:0:60:81:1:0:0.1
    280. 

  280. 1	158583526	158583526	G	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon50:c.C6974T:p.A2325V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.0	0.026	B	0.001	0.040	B	0.007	0.319	N	0.601	0.309	N	1.21	0.306	L	.	.	.	.	.	.	0.067	0.072	-0.933	0.437	T	0.008	0.028	T	0.015	0.363	T	1.177	0.208	11.63	0.915	0.201	0.850	0.438	D	c	-0.638	-0.507	0.000	0.058	0.487	0.133	0	0.847	0.180	2.473	0.446	0.953	0.551	0.997	0.399	0.998	0.697	5.990	0.186	EF-hand domain|EF-hand domain pair	.	.	ID=COSV63752982;OCCURENCE=1(stomach),1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	204	1	158583526	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20727;SOR=inf;LSEQ=CCTACCTCCCTGGATCCACA;RSEQ=CATCCAGGAACTTCTCAAAC;CSQ=A|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding||||||||||rs1472406241&COSV63752982|1222|1||EntrezGene||YES||||1:g.158583526G>A|4.014e-06|0|0|0|0|0|8.858e-06|0|0|8.858e-06|gnomAD_NFE||0&1|0&1,A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|50/52||NM_003126.4:c.6974C>T|NP_003117.2:p.Ala2325Val|7172|6974|2325|A/V|gCt/gTt|rs1472406241&COSV63752982||-1||EntrezGene||YES||||1:g.158583526G>A|4.014e-06|0|0|0|0|0|8.858e-06|0|0|8.858e-06|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:89,80:169,2:0.0117:2,2:43:0:37:0:1:1.1118:60:4:0.0118:0:1	0/0:204:0:0,0:111,93:204,0:0:2,0:36.4:1:35.6:1:1:0:60:21.667:1:0:0.1
    281. 

  281. 1	158584029	158584029	G	A	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	27	1	158584029	.	G	A	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=3;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAGAAGCAGTTAACTAT;RSEQ=AAATTATACTCACTTATAGA;CSQ=A|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding||||||||||rs1290622900|1725|1||EntrezGene||YES||||1:g.158584029G>A||||||||||||||,A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||49/51|NM_003126.4:c.6842+14C>T|||||||rs1290622900||-1||EntrezGene||YES||||1:g.158584029G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:27:2:1,1:16,9:25,2:0.0741:2,2:26:1:37:0:1:1.73837:60:4:0.08:0:1
    282. 

  282. 1	158584091	158584091	A	G	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon49:c.T6794C:p.I2265T	0.65	0.5290	0.4127	0.5595	0.5867	0.6088	0.6259	0.5602	0.5842	rs952094	rs952094	.	.	.	0.0	0.026	B	0.0	0.013	B	.	.	.	1.000	0.186	P	-0.955	0.012	N	.	.	.	.	.	.	0.039	0.028	-0.960	0.392	T	0.013	0.053	T	.	.	.	-0.738	0.043	0.059	0.115	0.002	0.052	0.108	N	c	-1.129	-0.943	0.000	0.053	0.487	0.133	0	1.28	0.206	2.960	0.486	-0.230	0.094	1.000	0.715	0.989	0.536	7.241	0.251	EF-hand domain pair	ENSG00000163554.7|ENSG00000163554.7	Artery_Tibial|Muscle_Skeletal	ID=COSV63754417;OCCURENCE=1(large_intestine),1(biliary_tract),2(pancreas),1(thyroid)	249425	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU4557910	COCA-CN|6|321|0.0186916,BTCA-JP|1|239|0.0041841	0.25	135	43	1	158584091	.	A	G	135	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.38182;SOR=0;LSEQ=TCTCTTCACTCACACCTTTG;RSEQ=TGTCCCTGAAAGAAAAAAAA;CSQ=G|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding||||||||||rs952094&COSV63754417|1787|1||EntrezGene||YES||||1:g.158584091A>G|0.5373|0.4214|0.5381|0.5756|0.6057|0.6346|0.5515|0.5438|0.4175|0.6346|gnomAD_FIN|benign|0&1|1&1,G|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|49/52||NM_003126.4:c.6794T>C|NP_003117.2:p.Ile2265Thr|6992|6794|2265|I/T|aTc/aCc|rs952094&COSV63754417||-1||EntrezGene||YES||||1:g.158584091A>G|0.5373|0.4214|0.5381|0.5756|0.6057|0.6346|0.5515|0.5438|0.4175|0.6346|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:41:0:37:0:1:0:60:4:1:0:0	0/1:43:17:8,9:14,12:26,17:0.3953:2,2:39.3:1:33.2:1:0.75967:1.30418:60:7.5:0.3846:0:1.2
    283. 

  283. 1	158584103	158584103	-	A	intronic	SPTA1	.	.	.	0.27	0.2868	0.2598	0.2102	0.3440	0.1688	0.3286	0.3080	0.3326	rs57778257	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	277526	Elliptocytosis|Hereditary_pyropoikilocytosis|not_specified|Spherocytosis,_Recessive	Human_Phenotype_Ontology:HP:0004445,Human_Phenotype_Ontology:HP:0004837,MedGen:C0427480|Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MedGen:CN169374|MedGen:CN239472	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU111654029	BTCA-SG|3|71|0.0422535	0.25	152	42	1	158584103	.	G	GA	152	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2;VD=0;AF=0;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.37104;SOR=0;LSEQ=CACCTTTGATGTCCCTGAAA;RSEQ=AAAAAAAAAAAACATGAATT;CSQ=A|downstream_gene_variant|MODIFIER|OR10Z1|128368|Transcript|NM_001004478.2|protein_coding||||||||||rs5778083|1799|1||EntrezGene||YES||||1:g.158584115dup|0.3206|0.3249|0.262|0.364|0.2605|0.3312|0.3337|0.3255|0.3453|0.364|gnomAD_ASJ|uncertain_significance&benign&likely_benign||1,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||48/51|NM_003126.4:c.6789-8dup|||||||rs5778083||-1||EntrezGene||YES||||1:g.158584115dup|0.3206|0.3249|0.262|0.364|0.2605|0.3312|0.3337|0.3255|0.3453|0.364|gnomAD_ASJ|uncertain_significance&benign&likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:53:0:24:1:1:0:60:1:1:0:0	0/1:42:17:7,9:13,12:25,17:0.4048:2,2:43.7:1:37.4:1:0.75132:1.38159:60.6:34:0.5484:0.0238:1.1
    284. 

  284. 1	158587390	158587390	C	T	intronic	SPTA1	.	.	.	0.65	0.5224	0.3782	0.5540	0.59	0.6122	0.6307	0.5641	0.5859	rs857716	rs857716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249427	Hemolytic_anemia|Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified	Human_Phenotype_Ontology:HP:0001878,Human_Phenotype_Ontology:HP:0001910,Human_Phenotype_Ontology:HP:0004827,Human_Phenotype_Ontology:HP:0004853,Human_Phenotype_Ontology:HP:0004868,Human_Phenotype_Ontology:HP:0005503,MONDO:MONDO:0003664,MedGen:C0002878|Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU26751814	COCA-CN|5|321|0.0155763	0.25	175	69	1	158587390	.	C	T	175	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00377;SOR=0;LSEQ=AGCAATGATCTAGTTAAGAA;RSEQ=CGAAGGAAATCATTATGCAT;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||46/51|NM_003126.4:c.6549-12G>A|||||||rs857716||-1||EntrezGene||YES||||1:g.158587390C>T|0.5376|0.3812|0.5398|0.5852|0.608|0.6342|0.5535|0.5466|0.4291|0.6342|gnomAD_FIN|benign&likely_pathogenic&conflicting_interpretations_of_pathogenicity||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:7,5:12,0:0:2,0:48.2:1:37:0:1:0:60:24:1:0:0	0/1:69:28:13,15:21,20:41,28:0.4058:2,2:44.6:1:36.6:1:0.80752:1.20816:60:56:0.4058:0:1.1
    285. 

  285. 1	158587784	158587784	T	G	intronic	SPTA1	.	.	.	1.	0.9997	0.9990	1	1	1	1	0.9999	1	rs857717	rs857717	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81713328	COCA-CN|5|321|0.0155763	0.5	241	109	1	158587784	.	T	G	241	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=3;SSF=1;SOR=0;LSEQ=TTTCTTAACGAATTCTTCCA;RSEQ=AATAATATAATAAAGCAAAC;CSQ=G|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||46/51|NM_003126.4:c.6548+45A>C|||||||rs857717||-1||EntrezGene||YES||||1:g.158587784T>G|0.9998|0.9981|0.9999|1|1|1|1|1|1|1|AMR&EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:109:109:73,36:0,0:0,109:1:0,2:36.3:1:35.7:1:1:0:60:26.25:1:0:1.4
    286. 

  286. 1	158587858	158587858	G	A	intronic	SPTA1	.	.	.	0.3	0.2607	0.2008	0.1850	0.3609	0.1716	0.2918	0.2965	0.3149	rs28525570	rs28525570	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63760163;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	249428	Hemolytic_anemia|Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified	Human_Phenotype_Ontology:HP:0001878,Human_Phenotype_Ontology:HP:0001910,Human_Phenotype_Ontology:HP:0004827,Human_Phenotype_Ontology:HP:0004853,Human_Phenotype_Ontology:HP:0004868,Human_Phenotype_Ontology:HP:0005503,MONDO:MONDO:0003664,MedGen:C0002878|Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11288459	LAML-KR|3|205|0.0146341,COCA-CN|4|321|0.0124611	0.25	197	157	1	158587858	.	G	A	197	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.33325;SOR=0;LSEQ=AAGTAAGCCCTGGACATGGA;RSEQ=GTCCGGAACAGGAATCACAT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||45/51|NM_003126.4:c.6531-12C>T|||||||rs28525570&CS995155&COSV63760163||-1||EntrezGene||YES||||1:g.158587858G>A|0.2544|0.198|0.1711|0.3488|0.1855|0.2916|0.284|0.2593|0.2499|0.3488|gnomAD_ASJ|conflicting_interpretations_of_pathogenicity&likely_pathogenic&likely_benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:2,0:2,0:0:0,0:64:1:37:0:1:0:60:4:1:0:0	0/1:157:67:31,36:42,48:90,67:0.4268:2,2:41.7:1:32.5:1:1:1.01603:60:8.571:0.4027:0:1.6
    287. 

  287. 1	158589959	158589959	C	T	splicing	SPTA1	NM_003126:exon44:c.6417+1G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.846	0.651	24.8	0.995	0.653	0.996	0.979	D	c	1.070	0.890	1.000	0.747	0.054	0.004	0	5.25	0.731	7.536	0.808	0.807	0.329	1.000	0.715	0.218	0.221	17.582	0.878	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	126	1	158589959	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.33067;SOR=inf;LSEQ=TTCTGCCGTGTTCCAGGTTA;RSEQ=CTCAATGATGTCAGATAGGT;CSQ=T|splice_donor_variant|HIGH|SPTA1|6708|Transcript|NM_003126.4|protein_coding||44/51|NM_003126.4:c.6417+1G>A|||||||||-1||EntrezGene||YES||||1:g.158589959C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:139,30:169,2:0.0117:2,2:22.5:1:37:0:0.33058:4.57438:60:4:0.0118:0:2	0/0:126:0:0,0:91,35:126,0:0:2,0:37.6:1:36:1:1:0:60:41:1:0:0.1
    288. 

  288. 1	158590248	158590248	G	A	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon44:c.C6129T:p.D2043D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	180	1	158590248	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=533;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06347;SOR=0;LSEQ=TGTGCAAATTCCACGAACAG;RSEQ=TCCTCAGCCTGCAGAGAGAA;CSQ=A|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|44/52||NM_003126.4:c.6129C>T|NP_003117.2:p.Asp2043%3D|6327|6129|2043|D|gaC/gaT|||-1||EntrezGene||YES||||1:g.158590248G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:533:0:0,0:198,334:532,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:180:2:1,1:63,114:177,2:0.0111:2,2:69:1:37:0:1:1.8:60:4:0.0114:0:1
    289. 

  289. 1	158590266	158590266	-	A	intronic	SPTA1	.	.	.	0.008	.	.	.	.	.	.	.	.	rs761012566	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	61	146	1	158590266	.	G	GA	61	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=424;VD=3;AF=0.0071;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.38018;SOR=0.51372;LSEQ=AGGTCCTCAGCCTGCAGAGA;RSEQ=AAAAAAAAGACACTACCATC;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||43/51|NM_003126.4:c.6121-11dup|||||||rs548425429||-1||EntrezGene||YES||||1:g.158590274dup|1.647e-05|0|0|0|0.0001732|0|9.117e-06|0|0|0.0001732|gnomAD_EAS|likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:424:3:0,3:135,266:401,3:0.0071:2,0:23.4:1:38.7:0:0.5539:0:62.8:6:0.0079:0:1	0/1:146:2:1,1:44,93:137,2:0.0137:2,2:33.5:1:38.7:0:0.54426:2.1:62.8:4:0.0161:0:0
    290. 

  290. 1	158592935	158592935	G	A	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon43:c.C5958T:p.P1986P	0.44	0.3339	0.4272	0.2122	0.4040	0.1718	0.3010	0.3095	0.3460	rs3753068	rs3753068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63748986;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),2(urinary_tract),2(lung),2(large_intestine)	249433	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU79745	LAML-KR|3|205|0.0146341,LUSC-KR|2|170|0.0117647,COCA-CN|4|321|0.0124611	0.25	248	261	1	158592935	.	G	A	248	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=790;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=TCCTTCAGGTCAGTGATCTC;RSEQ=GGAAGTCTCTCTTGCTGGAA;CSQ=A|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|43/52||NM_003126.4:c.5958C>T|NP_003117.2:p.Pro1986%3D|6156|5958|1986|P|ccC/ccT|rs3753068&COSV63748986&COSV63751777||-1||EntrezGene||YES||||1:g.158592935G>A|0.2901|0.43|0.1969|0.4008|0.1857|0.2997|0.3014|0.292|0.3006|0.4387|AFR|benign|0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:790:0:0,0:341,449:790,0:0:2,0:37.8:1:36.5:1:1:0:60:196.5:1:0:0.1	0/1:261:117:47,70:69,75:144,117:0.4483:2,2:38.2:1:36.1:1:0.25963:1.36854:60:57.5:0.4457:0:1.1
    291. 

  291. 1	158596695	158596695	G	A	exonic	SPTA1	.	stopgain	SPTA1:NM_003126:exon41:c.C5767T:p.Q1923X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.009	0.308	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.022	0.988	40	0.997	0.824	0.944	0.607	D	c	0.736	0.555	0.743	0.232	0.487	0.133	0	5.41	0.782	6.581	0.737	1.048	0.713	1.000	0.715	0.973	0.468	11.513	0.496	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	174	1	158596695	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=174;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.24928;SOR=0;LSEQ=GGCATAATCGTCTTCCAATT;RSEQ=CAACTTCCAAGCAGCTATTG;CSQ=A|stop_gained|HIGH|SPTA1|6708|Transcript|NM_003126.4|protein_coding|41/52||NM_003126.4:c.5767C>T|NP_003117.2:p.Gln1923Ter|5965|5767|1923|Q/*|Caa/Taa|||-1||EntrezGene||YES||||1:g.158596695G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:174:0:0,0:79,95:174,0:0:2,0:37.5:1:36.2:1:1:0:60:57:1:0:0.1	0/1:174:2:1,1:87,85:172,2:0.0115:2,2:38:1:37:0:1:1.0234:60:4:0.0116:0:1
    292. 

  292. 1	158597464	158597464	T	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon40:c.A5615G:p.E1872G	.	.	.	.	.	.	.	.	.	.	.	0.207	0.198	T	0.008	0.135	B	0.008	0.127	B	0.091	0.203	N	0.682	0.302	N	2.13	0.595	M	0.6	0.537	T	-2.86	0.601	D	0.255	0.320	-1.073	0.089	T	0.067	0.276	T	0.039	0.585	D	4.695	0.629	24.6	0.998	0.928	0.919	0.543	D	c	-0.124	0.052	0.574	0.215	0.554	0.246	0	5.42	0.786	4.873	0.625	1.061	0.807	1.000	0.715	0.682	0.305	14.438	0.667	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	1	158597464	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=104;VD=2;AF=0.0192;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.14426;SOR=inf;LSEQ=ACACATTTTGTACTCGGGTC;RSEQ=CATGGACAGCAAAGTCATTT;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|40/52||NM_003126.4:c.5615A>G|NP_003117.2:p.Glu1872Gly|5813|5615|1872|E/G|gAg/gGg|||-1||EntrezGene||YES||||1:g.158597464T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:104:2:1,1:47,55:102,2:0.0192:2,2:45.5:1:37:0:1:1.17:60:4:0.0192:0:1	0/0:169:0:0,0:85,84:169,0:0:2,0:40.3:1:36.9:1:1:0:60:338:1:0:0.4
    293. 

  293. 1	158597507	158597507	G	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon40:c.C5572G:p.L1858V	0.3	0.2604	0.2005	0.1838	0.3609	0.1694	0.2911	0.2966	0.3149	rs3737515	rs3737515	0.009	0.574	D	0.601	0.375	P	0.395	0.425	B	0.296	0.147	N	0.032	0.386	P	2.66	0.781	M	0.82	0.481	T	-2.39	0.526	N	0.16	0.192	-1.004	0.286	T	0.100	0.372	T	.	.	.	4.359	0.584	24.1	0.991	0.510	0.972	0.730	D	c	-0.088	-0.104	0.001	0.083	0.554	0.246	0	2.68	0.307	2.724	0.467	0.142	0.226	1.000	0.715	0.917	0.393	10.249	0.423	.	.	.	ID=COSV63752283;OCCURENCE=2(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(lung)	249434	Hemolytic_anemia|Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified	Human_Phenotype_Ontology:HP:0001878,Human_Phenotype_Ontology:HP:0001910,Human_Phenotype_Ontology:HP:0004827,Human_Phenotype_Ontology:HP:0004853,Human_Phenotype_Ontology:HP:0004868,Human_Phenotype_Ontology:HP:0005503,MONDO:MONDO:0003664,MedGen:C0002878|Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU79760	LAML-KR|3|205|0.0146341,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.25	225	156	1	158597507	.	G	C	225	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAAGCTTCATGCTTCATTA;RSEQ=CAAGCTCTGCATAAATAAGT;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|40/52||NM_003126.4:c.5572C>G|NP_003117.2:p.Leu1858Val|5770|5572|1858|L/V|Cta/Gta|rs3737515&COSV63752283||-1||EntrezGene||YES||||1:g.158597507G>C|0.2545|0.1982|0.171|0.3499|0.1856|0.292|0.2843|0.2606|0.2502|0.3499|gnomAD_ASJ|benign/likely_benign&benign&likely_pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:71:0:0,0:25,46:71,0:0:2,0:36.8:1:35.7:1:1:0:60:22.667:1:0:0.1	1/0:156:78:32,46:33,45:78,78:0.5:2,2:40.3:1:35.9:1:1:1.05378:60:38:0.4967:0:1
    294. 

  294. 1	158606449	158606449	G	T	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon37:c.C5292A:p.A1764A	0.47	0.3434	0.4621	0.2105	0.4040	0.1706	0.3008	0.3091	0.3446	rs3738791	rs3738791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63752352;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),3(lung)	249437	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU79783	LAML-KR|3|205|0.0146341,LUSC-KR|3|170|0.0176471,COCA-CN|4|321|0.0124611	0.25	237	187	1	158606449	.	G	T	237	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=208;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCTGGATGGCAGGCTCATG;RSEQ=GCCACCAGCTCCCCCTCTAG;CSQ=T|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|37/52||NM_003126.4:c.5292C>A|NP_003117.2:p.Ala1764%3D|5490|5292|1764|A|gcC/gcA|rs3738791&COSV63752352||-1||EntrezGene||YES||||1:g.158606449G>T|0.2922|0.4614|0.1977|0.4015|0.1857|0.2998|0.3014|0.2929|0.3002|0.4743|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:208:0:0,0:129,79:208,0:0:2,0:31.5:1:36.7:1:1:0:60:207:1:0:0.1	0/1:187:89:59,30:47,51:98,89:0.4759:2,2:40:1:36.6:1:0.01254:2.13:60:178:0.4785:0:1.2
    295. 

  295. 1	158609807	158609807	G	T	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	160	1	158609807	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=400;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.08127;SOR=0;LSEQ=TCCAGTTGCTCCTAACCCAA;RSEQ=GAGAGTGAGGAGTCATTACA;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||33/51|NM_003126.4:c.4738-10C>A|||||||COSV63753139||-1||EntrezGene||YES||||1:g.158609807G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:400:0:0,0:139,261:400,0:0:2,0:35.8:1:35.9:1:1:0:60:99:1:0:0.1	0/1:160:2:1,1:63,95:158,2:0.0125:2,2:58:1:37:0:1:1.5:60:4:0.0129:0:1
    296. 

  296. 1	158612152	158612152	G	T	intronic	SPTA1	.	.	.	0.	.	.	.	.	.	.	.	.	rs749088747	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	132	1	158612152	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=90;VD=2;AF=0.0222;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.16326;SOR=inf;LSEQ=AAAAAAAAGAAAGAGTAAAT;RSEQ=ATTCCTCTTCATGTGACTTT;CSQ=T|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||33/51|NM_003126.4:c.4737+49C>A|||||||rs749088747||-1||EntrezGene||YES||||1:g.158612152G>T|8.251e-06|0|0|0|0|0|1.819e-05|0|0|1.819e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:90:2:1,1:61,25:86,2:0.0222:2,2:10:0:37:0:0.50601:2.41216:60:4:0.0225:0:1	0/0:132:0:0,0:102,30:132,0:0:2,0:35.2:1:34.7:1:1:0:60:17.857:1:0:0.5
    297. 

  297. 1	158612236	158612236	A	G	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon33:c.T4702C:p.C1568R	0.69	0.6122	0.6602	0.5825	0.6324	0.6214	0.6409	0.5774	0.6194	rs863931	rs863931	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.009	0.307	N	0.997	0.229	P	-2.8	0.000	N	0.87	0.464	T	4.11	0.001	N	0.067	0.072	-0.946	0.416	T	0.008	0.028	T	.	.	.	-1.334	0.021	0.004	0.221	0.009	0.110	0.162	N	c	-1.280	-1.120	0.005	0.108	0.554	0.246	0	1.01	0.190	0.976	0.289	0.138	0.222	0.735	0.287	0.314	0.240	10.075	0.413	.	ENSG00000163554.7	Muscle_Skeletal	ID=COSV63754161;OCCURENCE=1(large_intestine),1(pancreas)	249440	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU81713356	COCA-CN|5|321|0.0155763	0.25	249	249	1	158612236	.	A	G	249	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=343;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=ATTGCCATCACAAGCGCTAC;RSEQ=CTCAATCAGGGAGTTCCCCA;CSQ=G|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|33/52||NM_003126.4:c.4702T>C|NP_003117.2:p.Cys1568Arg|4900|4702|1568|C/R|Tgt/Cgt|rs863931&COSV63754161||-1||EntrezGene||YES||||1:g.158612236A>G|0.578|0.6659|0.5651|0.6399|0.6155|0.6432|0.5723|0.5814|0.4803|0.6853|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:343:0:0,0:177,166:343,0:0:2,0:42.4:1:36.1:1:1:0:60:67.6:1:0:0.1	0/1:249:115:64,51:69,65:134,115:0.4618:2,2:40.2:1:36.4:1:0.52663:1.18:60:114:0.4634:0:1.1
    298. 

  298. 1	158613116	158613116	C	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon31:c.G4438T:p.D1480Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.971	0.552	D	0.895	0.617	P	0.004	0.339	N	0.997	0.438	D	2.95	0.852	M	1.22	0.370	T	-5.86	0.885	D	0.696	0.705	-0.911	0.467	T	0.131	0.442	T	0.092	0.760	D	5.869	0.804	27.4	0.992	0.543	0.965	0.690	D	c	0.245	0.145	0.991	0.322	0.554	0.246	0	2.38	0.283	3.045	0.493	0.013	0.140	0.995	0.385	0.992	0.562	9.597	0.386	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	167	1	158613116	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=366;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.09777;SOR=0;LSEQ=ATCACTCAGGCCTGACCTGT;RSEQ=TAGTACACGTTGGAGCCGCG;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|31/52||NM_003126.4:c.4438G>T|NP_003117.2:p.Asp1480Tyr|4636|4438|1480|D/Y|Gac/Tac|COSV63753396||-1||EntrezGene||YES||||1:g.158613116C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:366:0:0,0:223,143:366,0:0:2,0:38.3:1:36.5:1:1:0:60:121:1:0:0.1	0/1:167:2:1,1:99,66:165,2:0.012:2,2:29:1:37:0:1:1.49623:60:4:0.012:0:1
    299. 

  299. 1	158614023	158614023	C	A	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	113	1	158614023	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=155;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.07381;SOR=0;LSEQ=TACGGATTATTATTTTAATT;RSEQ=CTTTACTAGTCATTATTACC;CSQ=A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||30/51|NM_003126.4:c.4338+20G>T|||||||||-1||EntrezGene||YES||||1:g.158614023C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:155:0:0,0:120,35:155,0:0:2,0:23.6:1:35.7:1:1:0:60:310:1:0:0.4	0/1:113:3:2,1:85,25:110,3:0.0265:2,2:35:1:28.3:1:0.54729:1.69099:60:2:0.0192:0:1.7
    300. 

  300. 1	158614075	158614075	G	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon30:c.C4306T:p.R1436W	0.001	3.233e-05	0	0	0	0.0006	0	0	0	rs570224404	.	0.001	0.784	D	0.999	0.764	D	0.932	0.650	D	0.137	0.184	N	0.985	0.402	D	2.6	0.763	M	0.76	0.499	T	-3.11	0.636	D	0.425	0.497	-0.724	0.593	T	0.214	0.575	T	0.249	0.891	D	6.844	0.928	33	0.999	0.977	0.991	0.909	D	c	0.637	0.583	1.000	0.747	0.487	0.133	0	5.33	0.756	7.742	0.838	0.998	0.613	1.000	0.715	0.815	0.341	17.768	0.883	.	.	.	ID=COSV63751852;OCCURENCE=1(stomach),1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	MU4668528	COAD-US|1|402|0.00248756,STAD-US|1|439|0.0022779	0.25	271	192	1	158614075	.	G	A	271	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=425;VD=169;AF=0.3976;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGCTTTGTCCAAATCGTCCC;RSEQ=TTTCTTCATCAAAGCCTCCA;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|30/52||NM_003126.4:c.4306C>T|NP_003117.2:p.Arg1436Trp|4504|4306|1436|R/W|Cgg/Tgg|rs570224404&COSV63751852&COSV63754974||-1||EntrezGene||YES||||1:g.158614075G>A|3.612e-05|0|0|0|0.0004453|0|8.848e-06|0|0|0.001|EAS||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:425:169:102,67:157,99:256,169:0.3976:2,2:34.3:1:36.7:1:0.83983:1.04162:60:338:0.3986:0:1.1	0/0:192:0:0,0:127,65:192,0:0:2,0:36.3:1:36:1:1:0:60:63:1:0:0.3
    301. 

  301. 1	158614198	158614198	C	T	intronic	SPTA1	.	.	.	0.47	0.3433	0.4614	0.2112	0.4040	0.1694	0.3010	0.3091	0.3476	rs6702040	rs6702040	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63760177;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	249446	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU19591023	LAML-KR|3|205|0.0146341,COCA-CN|4|321|0.0124611	0.25	245	234	1	158614198	.	C	T	245	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=364;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGAACATCTATGAGGAAT;RSEQ=AAATGAGAGGGGTATGGTAT;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||29/51|NM_003126.4:c.4195-12G>A|||||||rs6702040&COSV63760177||-1||EntrezGene||YES||||1:g.158614198C>T|0.2918|0.4614|0.1976|0.4011|0.1824|0.2997|0.3008|0.2928|0.3013|0.4743|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:364:0:0,0:129,235:364,0:0:2,0:34.9:1:36.6:1:1:0:60:120.333:1:0:0.2	0/1:234:112:49,63:48,74:122,112:0.4786:2,2:39.9:1:36:1:0.50942:1.2:60:55:0.4783:0:1.1
    302. 

  302. 1	158617393	158617393	T	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon27:c.A3832G:p.T1278A	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.032	0.189	B	0.071	0.265	B	.	.	.	1	0.090	N	0.745	0.190	N	0.9	0.453	T	1.78	0.005	N	0.134	0.166	-0.935	0.434	T	0.013	0.049	T	0.009	0.245	T	-1.935	0.009	0.001	0.570	0.055	0.428	0.267	N	c	-1.004	-0.942	0.994	0.335	0.487	0.133	0	0.734	0.174	1.941	0.396	1.058	0.762	0.950	0.328	0.006	0.095	3.667	0.077	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	120	1	158617393	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=264;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.0971;SOR=0;LSEQ=GCTCTCCTTACGATCCTTTG;RSEQ=ACGCCCCTGCAGGTCTTCCC;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|27/52||NM_003126.4:c.3832A>G|NP_003117.2:p.Thr1278Ala|4030|3832|1278|T/A|Aca/Gca|||-1||EntrezGene||YES||||1:g.158617393T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:264:0:0,0:128,136:264,0:0:2,0:33.6:1:35.9:1:1:0:60:65:1:0:0.1	0/1:120:2:1,1:68,50:118,2:0.0167:2,2:34.5:1:37:0:1:1.35645:60:4:0.0168:0:1
    303. 

  303. 1	158618455	158618455	G	A	intronic	SPTA1	.	.	.	0.4	0.2354	0.1232	0.3313	0.2119	0.4370	0.3325	0.2500	0.2592	rs2246434	rs2246434	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63755347;OCCURENCE=1(large_intestine),1(biliary_tract)	249450	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU30433178	LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BTCA-JP|1|239|0.0041841	0.25	173	73	1	158618455	.	G	A	173	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=217;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=TCTGCTTCTCTGGTATACAA;RSEQ=AGAGTAGAGAGTTCAAAAGT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||25/51|NM_003126.4:c.3570-12C>T|||||||rs2246434&COSV63755347||-1||EntrezGene||YES||||1:g.158618455G>A|0.2598|0.1181|0.3359|0.2134|0.409|0.3373|0.2506|0.2581|0.1534|0.409|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:217:0:0,0:73,144:217,0:0:2,0:36.7:1:36:1:1:0:60:53.25:1:0:0.1	0/1:73:28:6,22:10,34:44,28:0.3836:2,2:35.5:1:36.1:1:1:1.07733:60:56:0.3944:0:1.2
    304. 

  304. 1	158619721	158619721	C	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon25:c.G3494T:p.W1165L	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.999	0.764	D	0.995	0.818	D	0.010	0.302	N	1.000	0.588	D	3.315	0.908	M	-0.33	0.683	T	-11.55	0.995	D	0.885	0.873	-0.074	0.807	T	0.445	0.782	T	0.171	0.849	D	7.030	0.939	33	0.986	0.433	0.978	0.770	D	c	0.773	0.711	1.000	0.747	0.487	0.133	0	5.08	0.682	7.194	0.771	0.935	0.490	1.000	0.715	0.583	0.285	17.234	0.868	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	85	1	158619721	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=133;VD=2;AF=0.015;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37112;SOR=inf;LSEQ=CAAGCCTCTGCAAAGAACCC;RSEQ=AGCGGGAATTCAATTCCTAA;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|25/52||NM_003126.4:c.3494G>T|NP_003117.2:p.Trp1165Leu|3692|3494|1165|W/L|tGg/tTg|COSV100934283||-1||EntrezGene||YES||||1:g.158619721C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:133:2:1,1:72,59:131,2:0.015:2,2:27.5:1:37:0:1:1.2185:60:4:0.015:0:2	0/0:85:0:0,0:34,51:85,0:0:2,0:34.8:1:36.4:1:1:0:60:84:1:0:1
    305. 

  305. 1	158619728	158619728	A	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon25:c.T3487G:p.S1163A	1.	0.9936	0.9773	1	1	1	1	1	0.9990	rs2482965	rs2482965	0.488	0.080	T	0.0	0.026	B	0.001	0.040	B	0.869	0.088	N	1	0.090	P	-0.69	0.019	N	-0.22	0.665	T	-0.65	0.189	N	0.012	0.001	-1.062	0.113	T	0.030	0.130	T	.	.	.	0.038	0.097	2.956	0.953	0.260	0.098	0.153	N	c	-1.135	-1.005	0.007	0.113	0.487	0.133	0	-1.91	0.072	0.317	0.191	-0.667	0.040	0.889	0.309	0.543	0.278	6.955	0.236	.	.	.	.	249451	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU81713367	COCA-CN|5|321|0.0155763	1	259	79	1	158619728	.	A	C	259	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=135;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAAGAACCCCAGCGGG;RSEQ=ATTCAATTCCTAAAAGAGGC;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|25/52||NM_003126.4:c.3487T>G|NP_003117.2:p.Ser1163Ala|3685|3487|1163|S/A|Tcc/Gcc|rs2482965||-1||EntrezGene||YES||||1:g.158619728A>C|0.9985|0.9779|0.9989|1|1|1|1|0.9997|0.9999|1|AMR&EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:135:135:72,63:0,0:0,135:1:0,2:43.5:1:36.6:1:1:0:60:134:1:0:1.1	1/1:79:79:31,48:0,0:0,79:1:0,2:36.2:1:36.2:1:1:0:60:78:1:0:1.1
    306. 

  306. 1	158623027	158623027	C	T	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	108	1	158623027	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=179;VD=2;AF=0.0112;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.38817;SOR=inf;LSEQ=CTTTGGCGAAAAATGTCTGA;RSEQ=CAAATACTGTTCAGTTCTCC;CSQ=T|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||22/51|NM_003126.4:c.3188+37G>A|||||||||-1||EntrezGene||YES||||1:g.158623027C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:179:2:1,1:127,50:177,2:0.0112:2,2:29.5:1:37:0:0.4898:2.52487:60:4:0.0113:0:1	0/0:108:0:0,0:83,25:108,0:0:2,0:32.2:1:36.3:1:1:0:60:107:1:0:0.1
    307. 

  307. 1	158623182	158623182	C	T	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon22:c.G3070A:p.G1024S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.006	0.327	N	1.000	0.588	D	4.03	0.970	H	-2.34	0.880	D	-5.41	0.851	D	0.68	0.694	0.840	0.949	D	0.856	0.952	D	0.071	0.713	D	6.471	0.892	29.9	0.999	0.937	0.976	0.756	D	c	0.879	0.745	1.000	0.747	0.554	0.283	0	5.15	0.702	7.324	0.782	0.935	0.490	1.000	0.715	0.954	0.431	17.367	0.872	SH3 domain|Spectrin alpha chain, SH3 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	257	1	158623182	.	C	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=494;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.03977;SOR=0;LSEQ=ATAGACAGCTGGGACAATGC;RSEQ=CTGATGATCAGCAGCTTCCA;CSQ=T|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|22/52||NM_003126.4:c.3070G>A|NP_003117.2:p.Gly1024Ser|3268|3070|1024|G/S|Ggc/Agc|||-1||EntrezGene||YES||||1:g.158623182C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:494:0:0,0:230,264:494,0:0:2,0:36:1:36.7:1:1:0:60:246:1:0:0.1	0/1:257:3:1,2:115,138:253,3:0.0117:2,2:29.7:1:28.3:1:1:1.66348:60:2:0.0079:0:1
    308. 

  308. 1	158624364	158624364	G	A	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	187	1	158624364	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11586;SOR=inf;LSEQ=GGAGAGATGGTTCTGAAAGA;RSEQ=CCACTTTTTGATGGAAAGAT;CSQ=A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||21/51|NM_003126.4:c.3036+37C>T|||||||rs1488849920||-1||EntrezGene||YES||||1:g.158624364G>A|4.01e-06|0|0|0|0|0|0|0|3.268e-05|3.268e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:70,25:95,2:0.0206:2,2:21:1:37:0:0.46628:2.76517:60:4:0.0208:0:1	0/0:187:0:0,0:121,66:187,0:0:2,0:40.2:1:35.9:1:1:0:60:61.333:1:0:0.1
    309. 

  309. 1	158624376	158624376	T	C	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	199	1	158624376	.	T	C	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=113;VD=2;AF=0.0177;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13043;SOR=inf;LSEQ=CTGAAAGAGCCACTTTTTGA;RSEQ=GGAAAGATTAGAAGGAAAAG;CSQ=C|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||21/51|NM_003126.4:c.3036+25A>G|||||||||-1||EntrezGene||YES||||1:g.158624376T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:113:2:1,1:79,32:111,2:0.0177:2,2:34:1:25:0:0.50063:2.44641:60:4:0.018:0:1	0/0:199:0:0,0:128,71:199,0:0:2,0:41.8:1:35.4:1:1:0:60:38.8:1:0:0.1
    310. 

  310. 1	158626357	158626357	G	A	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon20:c.C2895T:p.C965C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	150	1	158626357	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=22;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.75989;SOR=0;LSEQ=CGCTAAGTTAGTCTTACCTG;RSEQ=CAGGCGTTTGCCTGATTCCG;CSQ=A|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|20/52||NM_003126.4:c.2895C>T|NP_003117.2:p.Cys965%3D|3093|2895|965|C|tgC/tgT|rs1404053718||-1||EntrezGene||YES||||1:g.158626357G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:22:0:0,0:9,13:22,0:0:2,0:38.4:1:37:0:1:0:60:44:1:0:0.1	0/1:150:2:1,1:88,60:148,2:0.0133:2,2:38:1:37:0:1:1.4628:60:4:0.0134:0:2
    311. 

  311. 1	158626378	158626378	C	T	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon20:c.G2874A:p.L958L	0.79	0.4052	0.7057	0.3852	0.2285	0.4462	0.3308	0.2552	0.2949	rs857691	rs857691	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63748240;OCCURENCE=1(stomach),2(haematopoietic_and_lymphoid_tissue),1(lung),6(large_intestine)	249454	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU25267234	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|7|321|0.0218069	0.25	232	172	1	158626378	.	C	T	232	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=24;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGCGTTTGCCTGATTCCG;RSEQ=AGAGCTTTCATACTGTCTCC;CSQ=T|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|20/52||NM_003126.4:c.2874G>A|NP_003117.2:p.Leu958%3D|3072|2874|958|L|ctG/ctA|rs857691&COSV63748240||-1||EntrezGene||YES||||1:g.158626378C>T|0.3069|0.7212|0.3717|0.2383|0.4254|0.3346|0.2542|0.2868|0.1568|0.7935|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:24:0:0,0:10,14:24,0:0:2,0:37.4:1:37:0:1:0:60:48:1:0:0.1	0/1:172:84:47,37:46,41:87,84:0.4884:2,2:39.1:1:36.4:1:0.75924:1.13:60:83:0.4911:0:1.1
    312. 

  312. 1	158627260	158627263	ACCT	CCCA	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	85	46	1	158627260	.	ACCT	CCCA	85	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Complex;DP=54;VD=10;AF=0.1852;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00138;SOR=inf;LSEQ=ACAATGTTAAACCCACCCCC;RSEQ=TACCCCAGCTGCTTCTTCAT;CSQ=CCCA|splice_donor_region_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||19/51|NM_003126.4:c.2805+4_2805+7delinsTGGG|||||||||-1||EntrezGene||YES||||1:g.158627260_158627263delinsCCCA||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:54:10:10,0:23,20:43,10:0.1852:2,0:40.8:1:25.8:1:0.00845:0:60:9:0.2195:0.1481:1	0/0:46:0:0,0:19,24:43,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    313. 

  313. 1	158627266	158627266	C	A	splicing	SPTA1	NM_003126:exon19:c.2805+1G>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.896	0.658	24.9	0.994	0.644	0.994	0.955	D	c	1.055	0.863	1.000	0.747	0.054	0.004	0	4.79	0.608	7.402	0.790	0.935	0.490	1.000	0.715	0.970	0.461	16.924	0.860	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	25	48	1	158627266	.	C	A	25	v3;pSTD;q22.5;SN1.5;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=48;VD=1;AF=0.0208;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.5;SOR=0.49289;LSEQ=TTAAACCCACCCCCACCTTA;RSEQ=CCCAGCTGCTTCTTCATCAG;CSQ=A|splice_donor_variant|HIGH|SPTA1|6708|Transcript|NM_003126.4|protein_coding||19/51|NM_003126.4:c.2805+1G>T|||||||||-1||EntrezGene||YES||||1:g.158627266C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:48:1:1,0:25,22:47,1:0.0208:2,0:38:0:11:0:1:0:60:0:0:0:7	0/1:48:2:2,0:22,24:46,2:0.0417:2,0:34:1:25:0:0.48936:0:60:4:0.05:0:7.5
    314. 

  314. 1	158631136	158631136	G	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon18:c.C2528T:p.A843V	0.0003	.	.	.	.	.	.	.	.	rs369695627	.	0.014	0.531	D	0.106	0.245	B	0.201	0.352	B	.	.	.	1	0.090	N	2.28	0.651	M	0.58	0.542	T	-2.24	0.501	N	0.059	0.075	-0.864	0.510	T	0.069	0.282	T	0.020	0.425	T	0.573	0.149	7.971	0.981	0.374	0.617	0.313	D	c	-0.811	-0.898	0.039	0.144	0.487	0.133	0	-4.48	0.032	2.195	0.421	0.112	0.206	1.000	0.715	0.960	0.441	6.235	0.198	.	.	.	ID=COSV100935527;OCCURENCE=1(upper_aerodigestive_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	MU131228316	HNSC-US|1|508|0.0019685	0.25	37	200	1	158631136	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=68;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.55621;SOR=0;LSEQ=GAATGCGTGGTTCATGGCTG;RSEQ=CAATGTTCTCCAGGATGACT;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|18/52||NM_003126.4:c.2528C>T|NP_003117.2:p.Ala843Val|2726|2528|843|A/V|gCc/gTc|rs369695627&COSV100935527||-1||EntrezGene||YES||||1:g.158631136G>A|1.604e-05|6.461e-05|2.897e-05|0|5.565e-05|0|0|0|3.268e-05|0.0002579|AA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:68:0:0,0:35,33:68,0:0:2,0:37.8:1:36.5:1:1:0:60:136:1:0:0	0/1:200:2:1,1:100,98:198,2:0.01:2,2:52:0:37:0:1:1.02031:60:4:0.01:0:2
    315. 

  315. 1	158631171	158631171	A	C	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon18:c.T2493G:p.L831L	0.41	0.2532	0.1719	0.3549	0.2185	0.4460	0.3334	0.2554	0.2668	rs2518493	rs2518493	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63748244;OCCURENCE=1(stomach),2(haematopoietic_and_lymphoid_tissue),5(large_intestine)	249458	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU29727630	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|6|321|0.0186916	0.25	237	213	1	158631171	.	A	C	237	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGACTCTATGCCTATTCAG;RSEQ=AGCTTTTTGGAAGCAATCAG;CSQ=C|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|18/52||NM_003126.4:c.2493T>G|NP_003117.2:p.Leu831%3D|2691|2493|831|L|ctT/ctG|rs2518493&COSV63748244||-1||EntrezGene||YES||||1:g.158631171A>C|0.2677|0.1741|0.3432|0.2216|0.4253|0.3389|0.254|0.2652|0.1543|0.4253|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:71:0:0,0:32,39:71,0:0:2,0:39.1:1:36.7:1:1:0:60:142:1:0:0	0/1:213:106:50,56:45,62:107,106:0.4977:2,2:43.5:1:35.3:1:0.49204:1.23:60:25.5:0.4928:0:1.1
    316. 

  316. 1	158632694	158632694	T	C	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon17:c.A2262G:p.E754E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63751761;OCCURENCE=1(large_intestine),1(stomach)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU4668865	STAD-US|1|439|0.0022779	0.25	37	226	1	158632694	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=160;VD=2;AF=0.0125;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.17119;SOR=inf;LSEQ=GAATCAGGATGGCCTATTTC;RSEQ=TCAAAATATGCAGCCAGGTC;CSQ=C|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|17/52||NM_003126.4:c.2262A>G|NP_003117.2:p.Glu754%3D|2460|2262|754|E|gaA/gaG|COSV63751761||-1||EntrezGene||YES||||1:g.158632694T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:160:2:1,1:60,98:158,2:0.0125:2,2:56:1:37:0:1:1.63:60:4:0.0126:0:1	0/0:226:0:0,0:91,135:226,0:0:2,0:39.9:1:36.6:1:1:0:60:225:1:0:0.1
    317. 

  317. 1	158632750	158632750	G	T	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	1	158632750	.	G	T	37	v3;NM5.25	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=2;AF=0.0267;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.10356;SOR=inf;LSEQ=CTGATCCTAAGGGAGAAATA;RSEQ=AATGAATGCGAAGAAATCCC;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||16/51|NM_003126.4:c.2221-15C>A|||||||||-1||EntrezGene||YES||||1:g.158632750G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:75:2:1,1:21,52:73,2:0.0267:2,2:54.5:1:37:0:0.50342:2.44:60:4:0.0267:0:6	0/0:157:0:0,0:55,102:157,0:0:2,0:34.4:1:36.2:1:1:0:60:314:1:0:0.1
    318. 

  318. 1	158632761	158632761	A	G	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	138	1	158632761	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=67;VD=2;AF=0.0299;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.10574;SOR=inf;LSEQ=GGAGAAATAGAATGAATGCG;RSEQ=AGAAATCCCATCATTTAGTA;CSQ=G|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||16/51|NM_003126.4:c.2221-26T>C|||||||||-1||EntrezGene||YES||||1:g.158632761A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:67:2:1,1:20,44:64,2:0.0299:2,2:18:0:37:0:0.53846:2.17:60:4:0.0303:0:1	0/0:138:0:0,0:47,91:138,0:0:2,0:33.6:1:36.4:1:1:0:60:68:1:0:0.1
    319. 

  319. 1	158636087	158636087	C	A	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	160	1	158636087	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=85;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.42556;SOR=0;LSEQ=ACCCATTGCTTATGGCTGGC;RSEQ=AAAGAGCTAACAACAAACCT;CSQ=A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||16/51|NM_003126.4:c.2220+19G>T|||||||||-1||EntrezGene||YES||||1:g.158636087C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:85:0:0,0:63,22:85,0:0:2,0:33.7:1:36.7:1:1:0:60:170:1:0:0.2	0/1:160:2:1,1:101,57:158,2:0.0125:2,2:5:0:37:0:1:1.76517:60:4:0.0127:0:1
    320. 

  320. 1	158636312	158636312	A	G	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	243	1	158636312	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=2;AF=0.0606;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01391;SOR=inf;LSEQ=GAGAAGACATAAGGTAGAAG;RSEQ=CATTAGGTACCATAACTATT;CSQ=G|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||15/51|NM_003126.4:c.2039-25T>C|||||||||-1||EntrezGene||YES||||1:g.158636312A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:33:2:1,1:8,23:31,2:0.0606:2,2:24.5:1:37:0:0.47727:2.77:60:4:0.0625:0:1	0/0:243:0:0,0:99,144:243,0:0:2,0:38:1:36.4:1:1:0:60:80:1:0:0.1
    321. 

  321. 1	158637689	158637689	G	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon15:c.C1997T:p.A666V	0.0001	.	.	.	.	.	.	.	.	rs766916369	.	0.309	0.140	T	0.0	0.026	B	0.001	0.040	B	0.233	0.035	N	1	0.090	N	0.11	0.085	N	0.72	0.510	T	0.32	0.040	N	0.139	0.162	-1.085	0.064	T	0.021	0.089	T	0.005	0.113	T	-0.454	0.058	0.286	0.770	0.113	0.022	0.063	N	c	-1.636	-1.701	0.068	0.154	0.487	0.133	0	-7.26	0.013	-0.269	0.086	-0.939	0.025	0.000	0.063	0.027	0.143	6.127	0.193	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	183	1	158637689	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=91;VD=2;AF=0.022;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.10949;SOR=inf;LSEQ=GCAACTCCTCCCAGAGGCTG;RSEQ=CAACTTCACTCAGACGAGTG;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|15/52||NM_003126.4:c.1997C>T|NP_003117.2:p.Ala666Val|2195|1997|666|A/V|gCc/gTc|rs766916369||-1||EntrezGene||YES||||1:g.158637689G>A|4.011e-06|0|2.9e-05|0|0|0|0|0|0|2.9e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:91:2:1,1:57,32:89,2:0.022:2,2:69:1:37:0:1:1.76928:60:4:0.0227:0:1	0/0:183:0:0,0:113,70:183,0:0:2,0:37.3:1:36.3:1:1:0:60:90.5:1:0:0.1
    322. 

  322. 1	158637755	158637755	C	T	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon15:c.G1931A:p.G644D	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.995	0.818	D	0.096	0.201	N	1.000	0.548	D	3.82	0.957	H	0.91	0.449	T	-6.67	0.923	D	0.857	0.844	-0.262	0.761	T	0.281	0.653	T	0.129	0.812	D	5.463	0.741	26.1	0.998	0.877	0.942	0.602	D	c	0.646	0.503	0.658	0.222	0.487	0.133	0	4.03	0.459	4.495	0.598	0.852	0.362	1.000	0.715	0.996	0.625	13.507	0.608	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	232	1	158637755	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=118;VD=2;AF=0.0169;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11302;SOR=inf;LSEQ=CACCCTCAATCATCTCTTGG;RSEQ=CAGTTTTCTGTATGTTTTCC;CSQ=T|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|15/52||NM_003126.4:c.1931G>A|NP_003117.2:p.Gly644Asp|2129|1931|644|G/D|gGc/gAc|||-1||EntrezGene||YES||||1:g.158637755C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:118:2:1,1:57,59:116,2:0.0169:2,2:33.5:1:37:0:1:1.03:60:4:0.0174:0:1	0/0:232:0:0,0:112,119:231,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    323. 

  323. 1	158637866	158637868	AAA	-	intronic	SPTA1	.	.	.	0.22	0.3183	0.1932	0.4141	0.4023	0.4683	0.4430	0.3537	0.3388	rs140998442	rs140998442	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	276726	Elliptocytosis|Hereditary_pyropoikilocytosis|Spherocytosis,_Recessive	Human_Phenotype_Ontology:HP:0004445,Human_Phenotype_Ontology:HP:0004837,MedGen:C0427480|Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MedGen:CN239472	criteria_provided,_single_submitter	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	205	125	1	158637865	.	GAAA	G	205	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=25;VD=0;AF=0;SHIFT3=13;MSI=16;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TGTATGTCCTGAGATAAGAT;RSEQ=AAAAAAAAAAAAACCATTAC;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||14/51|NM_003126.4:c.1834-16_1834-14del|||||||rs3039789||-1||EntrezGene||YES||||1:g.158637879_158637881del|0.2815|0.1764|0.3275|0.2972|0.3379|0.3556|0.286|0.2962|0.184|0.4018|EAS|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:25:0:0,0:7,17:24,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:125:48:18,30:23,33:56,48:0.384:2,2:49.6:1:36.8:1:0.84075:1.15994:60:96:0.3871:0:0.5
    324. 

  324. 1	158641183	158641183	T	A	exonic	SPTA1	.	stopgain	SPTA1:NM_003126:exon12:c.A1549T:p.K517X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.052	0.980	38	0.997	0.794	0.979	0.774	D	c	0.884	0.759	1.000	0.480	0.487	0.133	0	5.17	0.707	7.425	0.793	1.061	0.807	1.000	0.715	0.999	0.750	13.990	0.637	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	150	1	158641183	.	T	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=272;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04433;SOR=0;LSEQ=TTCCTCAAAGTCTTCATGCT;RSEQ=CTGAAGAAGGGCTTCTGCAC;CSQ=A|stop_gained|HIGH|SPTA1|6708|Transcript|NM_003126.4|protein_coding|12/52||NM_003126.4:c.1549A>T|NP_003117.2:p.Lys517Ter|1747|1549|517|K/*|Aag/Tag|||-1||EntrezGene||YES||||1:g.158641183T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:272:0:0,0:156,116:272,0:0:2,0:38.3:1:36.6:1:1:0:60:544:1:0:0	0/1:150:3:2,1:79,68:147,3:0.02:2,2:46.7:1:28.3:1:1:1.72:60:2:0.0135:0:1.3
    325. 

  325. 1	158641986	158641986	T	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon11:c.A1351T:p.M451L	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.003	0.102	B	0.007	0.121	B	0.002	0.387	N	1	0.810	D	0.71	0.187	N	1.01	0.411	T	0.63	0.024	N	0.606	0.648	-1.033	0.195	T	0.020	0.084	T	.	.	.	0.402	0.133	6.631	0.582	0.058	0.934	0.579	D	c	-0.489	-0.275	0.373	0.199	0.487	0.133	0	5.24	0.728	4.215	0.581	1.061	0.807	1.000	0.715	0.865	0.361	9.790	0.397	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	258	1	158641986	.	T	A	31	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=183;VD=2;AF=0.0109;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.17165;SOR=inf;LSEQ=GTTGTTGTCAAGTATTTCCA;RSEQ=CTTTGGAAAGAAGGAGATAA;CSQ=A|missense_variant&splice_region_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|11/52||NM_003126.4:c.1351A>T|NP_003117.2:p.Met451Leu|1549|1351|451|M/L|Atg/Ttg|||-1||EntrezGene||YES||||1:g.158641986T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:183:2:1,1:61,120:181,2:0.0109:2,2:7:0:31:1:1:1.96:60:4:0.0112:0:1	0/0:258:0:0,0:99,159:258,0:0:2,0:36.5:1:36.1:1:1:0:60:128:1:0:0.1
    326. 

  326. 1	158644144	158644144	T	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon10:c.A1325G:p.E442G	.	.	.	.	.	.	.	.	.	.	.	0.276	0.157	T	0.578	0.369	P	0.388	0.423	B	0.086	0.206	N	0.995	0.423	D	2.255	0.644	M	0.68	0.520	T	-2.11	0.480	N	0.208	0.266	-1.048	0.149	T	0.088	0.340	T	0.053	0.652	D	4.768	0.640	24.7	0.999	0.972	0.947	0.617	D	c	0.331	0.420	1.000	0.747	0.500	0.196	0	5.28	0.740	5.607	0.671	1.058	0.762	1.000	0.715	0.591	0.287	13.222	0.591	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	194	1	158644144	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=211;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.22884;SOR=0;LSEQ=CCCGAACTTCATCAGAGGCT;RSEQ=CATGATTGGCATTCACGAGG;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|10/52||NM_003126.4:c.1325A>G|NP_003117.2:p.Glu442Gly|1523|1325|442|E/G|gAa/gGa|||-1||EntrezGene||YES||||1:g.158644144T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:211:0:0,0:150,61:211,0:0:2,0:27.3:1:36.7:1:1:0:60:422:1:0:0.2	0/1:194:2:1,1:118,74:192,2:0.0103:2,2:42.5:1:37:0:1:1.59057:60:4:0.0104:0:1.5
    327. 

  327. 1	158644167	158644167	T	C	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon10:c.A1302G:p.Q434Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	55	220	1	158644167	.	T	C	55	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=328;VD=4;AF=0.0122;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.1274;SOR=inf;LSEQ=TGATTGGCATTCACGAGGTC;RSEQ=TGACCAGTCTCATCAGCAGA;CSQ=C|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|10/52||NM_003126.4:c.1302A>G|NP_003117.2:p.Gln434%3D|1500|1302|434|Q|caA/caG|||-1||EntrezGene||YES||||1:g.158644167T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:328:4:2,2:206,118:324,4:0.0122:2,2:30.2:1:27.5:1:0.62536:1.74256:60:3:0.0092:0:1	0/0:220:0:0,0:122,97:219,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    328. 

  328. 1	158644473	158644473	A	-	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	169	1	158644472	.	GA	G	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=303;VD=4;AF=0.0132;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.16862;SOR=inf;LSEQ=AAAATCGATGGTACCTGTGG;RSEQ=AAAGTGAGGTAAAAGACAGG;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||8/51|NM_003126.4:c.1113-8del|||||||||-1||EntrezGene||YES||||1:g.158644476del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:303:4:2,2:113,186:299,4:0.0132:2,2:31.5:1:37:0:0.63597:1.64:60:8:0.0134:0:0	0/0:169:0:0,0:69,100:169,0:0:2,0:39.7:1:36.6:1:1:0:60:83.5:1:0:0.1
    329. 

  329. 1	158644491	158644491	A	G	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	1	158644491	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=243;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.15346;SOR=0;LSEQ=GGAAAAGTGAGGTAAAAGAC;RSEQ=GGAAGGAGAAACCAGATATG;CSQ=G|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||8/51|NM_003126.4:c.1113-26T>C|||||||||-1||EntrezGene||YES||||1:g.158644491A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:243:0:0,0:81,162:243,0:0:2,0:38.8:1:36.1:1:1:0:60:120.5:1:0:0.1	0/1:157:2:1,1:60,95:155,2:0.0127:2,2:25.5:1:37:0:1:1.58:60:4:0.0128:0:1
    330. 

  330. 1	158647495	158647495	A	T	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon7:c.T942A:p.A314A	1.	0.9564	0.8613	0.9893	1	1	0.9874	0.9952	0.9857	rs325996	rs325996	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249465	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU81713407	COCA-CN|5|321|0.0155763	1	319	182	1	158647495	.	A	T	319	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=423;VD=423;AF=1;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACCTTGTCACTCATGAC;RSEQ=GCAAGATTTCTCTCAAGTCC;CSQ=T|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|7/52||NM_003126.4:c.942T>A|NP_003117.2:p.Ala314%3D|1140|942|314|A|gcT/gcA|rs325996||-1||EntrezGene||YES||||1:g.158647495A>T|0.9869|0.8585|0.9916|0.9989|1|0.9853|0.9964|0.9932|0.9994|1|EAS&SAS&gnomAD_EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:423:423:268,155:0,0:0,423:1:0,2:39.9:1:36.6:1:1:0:60:210.5:1:0:1.7	1/1:182:182:120,62:0,0:0,182:1:0,2:36.9:1:36.6:1:1:0:60:90:1:0:1.2
    331. 

  331. 1	158647522	158647522	A	G	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon7:c.T915C:p.S305S	0.63	0.5122	0.2803	0.5561	0.5497	0.5537	0.6304	0.6065	0.5890	rs703121	rs703121	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63750610;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(urinary_tract)	249466	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU16355391	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.25	298	220	1	158647522	.	A	G	298	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=525;VD=301;AF=0.5733;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TTTCTCTCAAGTCCCTTGTG;RSEQ=CTGTGAAACAGTCCTTCAGA;CSQ=G|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|7/52||NM_003126.4:c.915T>C|NP_003117.2:p.Ser305%3D|1113|915|305|S|agT/agC|rs703121&COSV63750610||-1||EntrezGene||YES||||1:g.158647522A>G|0.55|0.2674|0.5456|0.5791|0.5499|0.6296|0.5959|0.5721|0.4585|0.6296|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:525:301:177,124:133,91:224,301:0.5733:2,2:38.8:1:36.3:1:0.92861:1.02386:60:99.333:0.5753:0:2.1	0/0:220:0:0,0:132,88:220,0:0:2,0:39.1:1:36.3:1:1:0:60:54:1:0:1.2
    332. 

  332. 1	158647631	158647631	T	A	intronic	SPTA1	.	.	.	1.	0.9565	0.8613	0.9893	1	1	0.9874	0.9953	0.9857	rs325995	rs325995	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249468	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81713444	COCA-CN|5|321|0.0155763	1	328	229	1	158647631	.	T	A	328	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=535;VD=534;AF=0.9981;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.70026;SOR=0;LSEQ=CTTCAGTCACATCCCTGCAG;RSEQ=CATTAACAAGAGCTCCAACC;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||6/51|NM_003126.4:c.813-7A>T|||||||rs325995||-1||EntrezGene||YES||||1:g.158647631T>A|0.9869|0.8582|0.9917|0.9989|1|0.9853|0.9964|0.9932|0.9994|1|EAS&SAS&gnomAD_EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:535:534:204,330:0,0:0,534:0.9981:0,2:40.1:1:36.3:1:1:0:60:105.8:0.9981:0:1.7	1/1:229:229:88,141:0,0:0,229:1:0,2:37.1:1:36.6:1:1:0:60:228:1:0:1.1
    333. 

  333. 1	158647669	158647669	T	C	intronic	SPTA1	.	.	.	0.63	0.5124	0.2812	0.5561	0.5497	0.5551	0.6309	0.6064	0.5886	rs703122	rs703122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63753726;OCCURENCE=1(lung),1(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU724064	ESAD-UK|1|409|0.00244499,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235	0.25	279	177	1	158647669	.	T	C	279	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=383;VD=200;AF=0.5222;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=ACCAAAGAAGATAGCAAGCA;RSEQ=TACAGGGCAAACGGTCCAAC;CSQ=C|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||6/51|NM_003126.4:c.813-45A>G|||||||rs703122&COSV63753726||-1||EntrezGene||YES||||1:g.158647669T>C|0.5501|0.2675|0.5457|0.5791|0.5504|0.6306|0.5963|0.5727|0.4585|0.6306|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:383:200:64,136:60,123:183,200:0.5222:2,2:37.4:1:36.6:1:0.9131:1.03651:60:400:0.5305:0:2.1	0/0:177:0:0,0:51,126:177,0:0:2,0:38:1:36.3:1:1:0:60:354:1:0:0.9
    334. 

  334. 1	158648251	158648251	C	A	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon6:c.G752T:p.G251V	.	.	.	.	.	.	.	.	.	.	.	0.141	0.255	T	0.028	0.184	B	0.071	0.265	B	0.907	0.074	N	0.801	0.291	N	1.905	0.510	L	0.78	0.494	T	-2.74	0.582	D	0.245	0.314	-0.980	0.350	T	0.067	0.274	T	0.041	0.598	D	2.963	0.416	22.1	0.987	0.451	0.306	0.239	N	c	-0.748	-0.824	0.014	0.125	0.487	0.133	0	0.603	0.166	1.375	0.337	0.065	0.171	0.001	0.137	0.188	0.214	9.461	0.378	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	44	299	1	158648251	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=319;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11267;SOR=0;LSEQ=TCTGTCTCTGGAGAGCCAAA;RSEQ=CACGAAGGCGCTCCCAGGCA;CSQ=A|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|6/52||NM_003126.4:c.752G>T|NP_003117.2:p.Gly251Val|950|752|251|G/V|gGt/gTt|||-1||EntrezGene||YES||||1:g.158648251C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:319:0:0,0:152,167:319,0:0:2,0:39.8:1:36.5:1:1:0:60:318:1:0:0.1	0/1:299:3:2,1:154,142:296,3:0.01:2,2:38:1:28.3:1:1:1.84:60:2:0.0068:0:2.7
    335. 

  335. 1	158648303	158648303	A	G	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon6:c.T700C:p.L234L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	266	1	158648303	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=180;VD=2;AF=0.0111;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.16234;SOR=inf;LSEQ=ATTTTGCTTAGACTGAATTA;RSEQ=GGGTAGGTCAGGATGGTTTT;CSQ=G|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|6/52||NM_003126.4:c.700T>C|NP_003117.2:p.Leu234%3D|898|700|234|L|Tta/Cta|||-1||EntrezGene||YES||||1:g.158648303A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:180:2:1,1:63,115:178,2:0.0111:2,2:49.5:1:37:0:1:1.82:60:4:0.0116:0:1	0/0:266:0:0,0:105,161:266,0:0:2,0:40:1:35.5:1:1:0:60:43.333:1:0:0.1
    336. 

  336. 1	158653119	158653119	T	C	intronic	SPTA1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	85	1	158653119	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=19;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.66654;SOR=0;LSEQ=CAGTTAAAACCCTGATAACA;RSEQ=AATCAATAATTGGAAACTTC;CSQ=C|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||3/51|NM_003126.4:c.390+42A>G|||||||||-1||EntrezGene||YES||||1:g.158653119T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:19:0:0,0:16,3:19,0:0:2,0:24.7:1:35.7:1:1:0:60:38:1:0:0.3	0/1:85:2:1,1:52,31:83,2:0.0235:2,2:63:1:37:0:1:1.66673:60:4:0.0241:0:1
    337. 

  337. 1	158653235	158653235	T	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon3:c.A316G:p.R106G	.	3.233e-05	0	0	0	0	0	6.673e-05	0	.	.	0.62	0.053	T	0.0	0.026	B	0.004	0.093	B	0.003	0.352	N	1	0.090	N	1.295	0.326	L	1.45	0.325	T	-0.24	0.108	N	0.106	0.157	-0.962	0.388	T	0.018	0.075	T	0.018	0.399	T	-0.895	0.036	0.026	0.206	0.008	0.118	0.167	N	c	-1.023	-1.005	1.000	0.747	0.487	0.133	0	2.58	0.299	0.960	0.286	0.123	0.211	0.004	0.165	0.578	0.284	4.250	0.101	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU70995324	ESAD-UK|1|409|0.00244499	0.25	37	106	1	158653235	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=68;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.36974;SOR=0;LSEQ=TTCCAGTTCAGACATGAGTC;RSEQ=TGATTTTGTTTGCACCTCTG;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|3/52||NM_003126.4:c.316A>G|NP_003117.2:p.Arg106Gly|514|316|106|R/G|Aga/Gga|rs1321388973||-1||EntrezGene||YES||||1:g.158653235T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:68:0:0,0:35,32:67,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:106:2:1,1:44,60:104,2:0.0189:2,2:47.5:1:37:0:1:1.36:60:4:0.0194:0:1
    338. 

  338. 1	158654852	158654852	A	G	intronic	SPTA1	.	.	.	0.63	0.5185	0.3031	0.5576	0.5497	0.5570	0.6304	0.6060	0.5910	rs857937	rs857937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63750615;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(pancreas),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU16355568	ESAD-UK|1|409|0.00244499,PACA-CA|1|268|0.00373134,LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.25	106	82	1	158654852	.	A	G	106	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=8;AF=0.7273;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=AAAAACCTATTTCCTTCTCT;RSEQ=GAGATCTTAGGGTCTGCTCT;CSQ=G|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||2/51|NM_003126.4:c.264+46T>C|||||||rs857937&COSV63750615||-1||EntrezGene||YES||||1:g.158654852A>G|0.5508|0.2894|0.5467|0.5791|0.5501|0.6291|0.5954|0.5731|0.4585|0.6291|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:11:8:7,1:3,0:3,8:0.7273:0,2:28.2:1:35.5:1:1:0:60:16:0.7273:0:1.5	0/0:82:0:0,0:70,12:82,0:0:2,0:30.1:1:35.6:1:1:0:60:40:1:0:0.3
    339. 

  339. 1	158654980	158654980	T	C	exonic	SPTA1	.	nonsynonymous SNV	SPTA1:NM_003126:exon2:c.A182G:p.D61G	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	1.0	0.899	D	0.998	0.875	D	0.005	0.331	N	1	0.810	D	3.23	0.897	M	0.49	0.558	T	-5.58	0.864	D	0.65	0.688	-0.309	0.747	T	0.313	0.683	T	0.131	0.813	D	5.544	0.754	26.4	0.998	0.925	0.935	0.581	D	c	0.707	0.623	1.000	0.747	0.487	0.133	0	5.18	0.710	7.674	0.830	1.011	0.635	1.000	0.715	0.965	0.450	14.016	0.639	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	263	1	158654980	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=2;AF=0.0144;SHIFT3=2;MSI=2;MSILEN=2;SSF=0.11899;SOR=inf;LSEQ=ACTTCCCCAGATCATCTGCA;RSEQ=CTCGCTTGAAAACTTGTAAG;CSQ=C|missense_variant|MODERATE|SPTA1|6708|Transcript|NM_003126.4|protein_coding|2/52||NM_003126.4:c.182A>G|NP_003117.2:p.Asp61Gly|380|182|61|D/G|gAt/gGt|||-1||EntrezGene||YES||||1:g.158654980T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:139:2:1,1:85,52:137,2:0.0144:2,2:36.5:1:37:0:1:1.62855:60:4:0.0144:0:2.5	0/0:263:0:0,0:157,105:262,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    340. 

  340. 1	158655036	158655036	G	A	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon2:c.C126T:p.V42V	1.	0.9740	0.9094	0.9928	1	1	1	0.9999	0.9939	rs435080	rs435080	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249471	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU81713460	COCA-CN|5|321|0.0155763	1	302	306	1	158655036	.	G	A	302	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=240;VD=237;AF=0.9875;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.22691;SOR=0.25962;LSEQ=AGCTTCTGACCCCTCTCAGC;RSEQ=ACCCGCTCCTTGAAACTTTG;CSQ=A|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|2/52||NM_003126.4:c.126C>T|NP_003117.2:p.Val42%3D|324|126|42|V|gtC/gtT|rs435080||-1||EntrezGene||YES||||1:g.158655036G>A|0.9931|0.9056|0.9946|1|1|1|0.9997|0.9967|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:240:237:118,119:0,0:0,237:0.9875:0,2:34.8:1:36.4:1:1:0:60:117.5:0.9874:0:1.2	1/1:306:305:142,163:0,0:0,305:0.9967:0,2:40.5:1:36.6:1:1:0:60:304:1:0:1.2
    341. 

  341. 1	158655126	158655126	G	A	exonic	SPTA1	.	synonymous SNV	SPTA1:NM_003126:exon2:c.C36T:p.S12S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	230	1	158655126	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=173;VD=2;AF=0.0116;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.18367;SOR=inf;LSEQ=TCCAAAACCTTTGGCCCACT;RSEQ=CTCTCCACAACCTGCAAGTT;CSQ=A|synonymous_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding|2/52||NM_003126.4:c.36C>T|NP_003117.2:p.Ser12%3D|234|36|12|S|agC/agT|||-1||EntrezGene||YES||||1:g.158655126G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:173:2:1,1:67,104:171,2:0.0116:2,2:5:0:37:0:1:1.55:60:4:0.0117:0:2	0/0:230:0:0,0:81,149:230,0:0:2,0:39.8:1:36:1:1:0:60:75.667:1:0:1.2
    342. 

  342. 1	158655162	158655162	C	A	intronic	SPTA1	.	.	.	1.	0.9741	0.9095	0.9928	1	1	1	0.9999	0.9939	rs2564859	rs2564859	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81713470	COCA-CN|5|321|0.0155763	1	266	158	1	158655162	.	C	A	266	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=77;VD=77;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTAAAAAGATTCTGTTA;RSEQ=TTGCTAGTTCTCAAATATTT;CSQ=A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||1/51|NM_003126.4:c.25-25G>T|||||||rs2564859||-1||EntrezGene||YES||||1:g.158655162C>A|0.993|0.9057|0.9945|1|1|1|0.9997|0.9967|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:77:77:25,52:0,0:0,77:1:0,2:32.4:1:34.7:1:1:0:60:14.4:1:0:1.4	1/1:158:158:50,108:0,0:0,158:1:0,2:35.5:1:36.5:1:1:0:60:157:1:0:1.3
    343. 

  343. 1	158655196	158655196	G	A	intronic	SPTA1	.	.	.	0.0015	0.0006	0.0023	0	0	0	0	0	0	rs116802150	rs116802150	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	84	1	158655196	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=32;VD=2;AF=0.0625;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07436;SOR=inf;LSEQ=AATATTTAACATGTTGCCCC;RSEQ=CTTATATGTGTCAAGGTGTT;CSQ=A|intron_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding||1/51|NM_003126.4:c.25-59C>T|||||||rs116802150||-1||EntrezGene||YES||||1:g.158655196G>A||||||||||0.0015|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:32:2:1,1:7,23:30,2:0.0625:2,2:31:1:37:0:0.44355:3.14:60:4:0.0667:0:2	0/0:84:0:0,0:25,59:84,0:0:2,0:32:1:35.8:1:1:0:60:83:1:0:1.1
    344. 

  344. 1	158656281	158656281	T	C	intronic	SPTA1	.	.	.	1.	0.9738	0.9088	0.9928	1	1	1	0.9999	0.9928	rs2564858	rs2564858	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249472	Hereditary_pyropoikilocytosis|Elliptocytosis_2|Spherocytosis_type_3|not_specified|none_provided	Human_Phenotype_Ontology:HP:0004805,Human_Phenotype_Ontology:HP:0004839,MONDO:MONDO:0009948,MedGen:C0520739,OMIM:266140,Orphanet:ORPHA98867,SNOMED_CT:9434008|MONDO:MONDO:0007533,MedGen:C1851741,OMIM:130600|MONDO:MONDO:0010053,MedGen:C2678338,OMIM:270970|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81713483	COCA-CN|5|321|0.0155763	0.5	204	50	1	158656281	.	T	C	204	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAGAGAAATATGTACT;RSEQ=ACGGTTTCCTTTGGAAATTG;CSQ=C|splice_donor_region_variant&intron_variant|LOW|SPTA1|6708|Transcript|NM_003126.4|protein_coding||1/51|NM_003126.4:c.24+3A>G|||||||rs2564858||-1||EntrezGene||YES||||1:g.158656281T>C|0.9931|0.9054|0.9945|1|1|1|0.9997|0.9967|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:50:50:32,18:0,0:0,50:1:0,2:36.8:1:36.2:1:1:0:60:49:1:0:1.1
    345. 

  345. 1	158656347	158656347	-	AGAG	UTR5	SPTA1	NM_003126:c.-41_-40insCTCT	.	.	0.62	0.9185	0.8954	0.9207	0.9394	0.9943	0.8423	0.9353	0.9171	rs111674514	rs111674514	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	197	60	1	158656347	.	C	CAGAG	197	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=Insertion;DP=0;VD=0;AF=0;SHIFT3=19;MSI=11;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGGCAAGATAAAATGTGT;RSEQ=AGAGAGAGAGAGAGAGAGAA;CSQ=AGAG|5_prime_UTR_variant|MODIFIER|SPTA1|6708|Transcript|NM_003126.4|protein_coding|1/52||NM_003126.4:c.-44_-41dup||158-159|||||rs111674514||-1||EntrezGene||YES||||1:g.158656363_158656366dup||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:60:49:19,30:8,3:11,49:0.8167:2,2:49.2:1:35.1:1:0.05127:4.10859:60.3:23.5:0.7833:0:0.7
    346. 

  346. 1	161293411	161293411	G	A	exonic	SDHC	.	nonsynonymous SNV	SDHC:NM_001035511:exon2:c.G28A:p.G10S,SDHC:NM_001035512:exon2:c.G28A:p.G10S,SDHC:NM_001278172:exon2:c.G28A:p.G10S,SDHC:NM_003001:exon2:c.G28A:p.G10S	.	.	.	.	.	.	.	.	.	.	.	0.263	0.912	T	0.522	0.466	P	0.156	0.430	B	0.001	0.398	N	1	0.810	D	1.4	0.355	L	-3.99	0.963	D	-0.3	0.420	N	0.359	0.447	0.230	0.864	D	0.679	0.889	D	0.099	0.771	D	1.245	0.215	11.98	0.984	0.403	0.783	0.383	D	c	-0.363	-0.288	0.998	0.366	0.732	0.924	0	3.62	0.405	1.384	0.338	-0.690	0.038	0.999	0.424	0.964	0.448	10.748	0.452	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	113	1	161293411	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=2;AF=0.0156;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.28105;SOR=inf;LSEQ=TCTTATCTTGCAGACACGTT;RSEQ=GTCGTCATTGCCTCCGAGCC;CSQ=A|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001035511.2|protein_coding|2/5||NM_001035511.2:c.28G>A|NP_001030588.1:p.Gly10Ser|53|28|10|G/S|Ggt/Agt|||1||EntrezGene||||||1:g.161293411G>A||||||||||||||,A|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001035512.2|protein_coding|2/5||NM_001035512.2:c.28G>A|NP_001030589.1:p.Gly10Ser|53|28|10|G/S|Ggt/Agt|||1||EntrezGene||||||1:g.161293411G>A||||||||||||||,A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035513.2|protein_coding||1/3|NM_001035513.2:c.20+9196G>A|||||||||1||EntrezGene||||||1:g.161293411G>A||||||||||||||,A|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001278172.2|protein_coding|2/4||NM_001278172.2:c.28G>A|NP_001265101.1:p.Gly10Ser|53|28|10|G/S|Ggt/Agt|||1||EntrezGene||||||1:g.161293411G>A||||||||||||||,A|missense_variant|MODERATE|SDHC|6391|Transcript|NM_003001.5|protein_coding|2/6||NM_003001.5:c.28G>A|NP_002992.1:p.Gly10Ser|53|28|10|G/S|Ggt/Agt|||1||EntrezGene||YES||||1:g.161293411G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SDHC|6391|Transcript|NR_103459.2|misc_RNA|2/7||NR_103459.2:n.53G>A||53|||||||1||EntrezGene||||||1:g.161293411G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:128:2:1,1:76,50:126,2:0.0156:2,2:21:1:37:0:1:1.51485:60:4:0.0161:0:2	0/0:113:0:0,0:60,53:113,0:0:2,0:46.2:1:35.3:1:1:0:60:27.25:1:0:0.2
    347. 

  347. 1	161293424	161293424	T	C	exonic	SDHC	.	nonsynonymous SNV	SDHC:NM_001035511:exon2:c.T41C:p.L14P,SDHC:NM_001035512:exon2:c.T41C:p.L14P,SDHC:NM_001278172:exon2:c.T41C:p.L14P,SDHC:NM_003001:exon2:c.T41C:p.L14P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.629	D	1	0.810	D	2.42	0.702	M	-4.26	0.971	D	-3.29	0.711	D	0.946	0.955	1.087	0.991	D	0.920	0.974	D	0.470	0.947	D	5.151	0.695	25.4	0.999	0.960	0.960	0.667	D	c	0.575	0.534	1.000	0.747	0.732	0.924	0	5.51	0.817	4.679	0.611	1.056	0.757	1.000	0.715	0.995	0.604	13.576	0.612	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	110	1	161293424	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.20558;SOR=0;LSEQ=ACACGTTGGTCGTCATTGCC;RSEQ=CCGAGCCCACTTTAGCCCTC;CSQ=C|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001035511.2|protein_coding|2/5||NM_001035511.2:c.41T>C|NP_001030588.1:p.Leu14Pro|66|41|14|L/P|cTc/cCc|||1||EntrezGene||||||1:g.161293424T>C||||||||||||||,C|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001035512.2|protein_coding|2/5||NM_001035512.2:c.41T>C|NP_001030589.1:p.Leu14Pro|66|41|14|L/P|cTc/cCc|||1||EntrezGene||||||1:g.161293424T>C||||||||||||||,C|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035513.2|protein_coding||1/3|NM_001035513.2:c.20+9209T>C|||||||||1||EntrezGene||||||1:g.161293424T>C||||||||||||||,C|missense_variant|MODERATE|SDHC|6391|Transcript|NM_001278172.2|protein_coding|2/4||NM_001278172.2:c.41T>C|NP_001265101.1:p.Leu14Pro|66|41|14|L/P|cTc/cCc|||1||EntrezGene||||||1:g.161293424T>C||||||||||||||,C|missense_variant|MODERATE|SDHC|6391|Transcript|NM_003001.5|protein_coding|2/6||NM_003001.5:c.41T>C|NP_002992.1:p.Leu14Pro|66|41|14|L/P|cTc/cCc|||1||EntrezGene||YES||||1:g.161293424T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|SDHC|6391|Transcript|NR_103459.2|misc_RNA|2/7||NR_103459.2:n.66T>C||66|||||||1||EntrezGene||||||1:g.161293424T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:132:0:0,0:79,53:132,0:0:2,0:38.8:1:36:1:1:0:60:65:1:0:0.7	0/1:110:2:1,1:53,55:108,2:0.0182:2,2:21.5:1:31:1:1:1.04:60:4:0.0185:0:1
    348. 

  348. 1	161309335	161309335	-	T	intronic	SDHC	.	.	.	0.2	0.0075	0.0207	0.0077	0	0	0.0067	0.0007	0.0066	rs746552469	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU111660902	BTCA-SG|2|71|0.028169	0.25	110	60	1	161309335	.	A	AT	110	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=133;VD=7;AF=0.0526;SHIFT3=11;MSI=12;MSILEN=1;SSF=0.07017;SOR=inf;LSEQ=AGGAGTTTTGAGTTATAATC;RSEQ=TTTTTTTTTTTCTCAGCCCT;CSQ=T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035511.2|protein_coding||3/4|NM_001035511.2:c.180-1038dup|||||||rs369711016||1||EntrezGene||||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035512.2|protein_coding||2/4|NM_001035512.2:c.78-1038dup|||||||rs369711016||1||EntrezGene||||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035513.2|protein_coding||1/3|NM_001035513.2:c.21-1038dup|||||||rs369711016||1||EntrezGene||||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001278172.2|protein_coding||2/3|NM_001278172.2:c.78-1038dup|||||||rs369711016||1||EntrezGene||||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_003001.5|protein_coding||3/5|NM_003001.5:c.180-1038dup|||||||rs369711016||1||EntrezGene||YES||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||,T|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|SDHC|6391|Transcript|NR_103459.2|misc_RNA||3/6|NR_103459.2:n.205-6dup|||||||rs369711016||1||EntrezGene||||||1:g.161309346dup|0.07255|0.1484|0.08793|0.05542|0.1002|0.04106|0.06421|0.08156|0.05505|0.1484|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:133:7:2,5:42,75:117,7:0.0526:2,2:27.7:1:39.5:1:1:1.39639:64:14:0.0574:0.015:0	0/0:60:0:0,0:34,26:60,0:0:2,0:37.4:1:35.7:1:1:0:60:29:1:0:0.1
    349. 

  349. 1	161309366	161309366	C	T	intronic	SDHC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	57	1	161309366	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14093;SOR=0;LSEQ=TCTCAGCCCTATCAGTGATG;RSEQ=AGTCTGGTAAAGGTAGGGAT;CSQ=T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035511.2|protein_coding||3/4|NM_001035511.2:c.180-1018C>T|||||||||1||EntrezGene||||||1:g.161309366C>T||||||||||||||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035512.2|protein_coding||2/4|NM_001035512.2:c.78-1018C>T|||||||||1||EntrezGene||||||1:g.161309366C>T||||||||||||||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035513.2|protein_coding||1/3|NM_001035513.2:c.21-1018C>T|||||||||1||EntrezGene||||||1:g.161309366C>T||||||||||||||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001278172.2|protein_coding||2/3|NM_001278172.2:c.78-1018C>T|||||||||1||EntrezGene||||||1:g.161309366C>T||||||||||||||,T|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_003001.5|protein_coding||3/5|NM_003001.5:c.180-1018C>T|||||||||1||EntrezGene||YES||||1:g.161309366C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SDHC|6391|Transcript|NR_103459.2|misc_RNA|4/7||NR_103459.2:n.219C>T||219|||||||1||EntrezGene||||||1:g.161309366C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:94:0:0,0:25,68:93,0:0:2,0:30.4:1:36.2:1:1:0:60:92:1:0:0.2	0/1:57:2:1,1:27,28:55,2:0.0351:2,2:33:0:37:0:1:1.04:60:4:0.0357:0:1
    350. 

  350. 1	161310455	161310455	T	A	intronic	SDHC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	139	1	161310455	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=588;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.03634;SOR=0;LSEQ=TTTGAGTGCAGGTATGTATA;RSEQ=GTGTTTTTACACACACATAT;CSQ=A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035511.2|protein_coding||4/4|NM_001035511.2:c.241+10T>A|||||||||1||EntrezGene||||||1:g.161310455T>A||||||||||||||,A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035512.2|protein_coding||3/4|NM_001035512.2:c.139+10T>A|||||||||1||EntrezGene||||||1:g.161310455T>A||||||||||||||,A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001035513.2|protein_coding||2/3|NM_001035513.2:c.82+10T>A|||||||||1||EntrezGene||||||1:g.161310455T>A||||||||||||||,A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_001278172.2|protein_coding||3/3|NM_001278172.2:c.139+10T>A|||||||||1||EntrezGene||||||1:g.161310455T>A||||||||||||||,A|intron_variant|MODIFIER|SDHC|6391|Transcript|NM_003001.5|protein_coding||4/5|NM_003001.5:c.241+10T>A|||||||||1||EntrezGene||YES||||1:g.161310455T>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|SDHC|6391|Transcript|NR_103459.2|misc_RNA||5/6|NR_103459.2:n.293+10T>A|||||||||1||EntrezGene||||||1:g.161310455T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:588:0:0,0:286,302:588,0:0:2,0:46.4:1:36.6:1:1:0:60:195:1:0:0.1	0/1:139:2:1,1:58,79:137,2:0.0144:2,2:42.5:1:37:0:1:1.36:60:4:0.0145:0:1
    351. 

  351. 1	161332121	161332121	G	A	exonic	SDHC	.	nonsynonymous SNV	SDHC:NM_001035513:exon4:c.G249A:p.M83I,SDHC:NM_001278172:exon4:c.G142A:p.V48M,SDHC:NM_001035511:exon5:c.G244A:p.V82M,SDHC:NM_001035512:exon5:c.G306A:p.M102I,SDHC:NM_003001:exon6:c.G408A:p.M136I	.	.	.	.	.	.	.	.	.	.	.	0.404	0.103	T	0.0	0.026	B	0.001	0.040	B	0.398	0.132	N	0.968	0.386	D	.	.	.	-3.47	0.945	D	-0.54	0.208	N	0.226	0.277	0.030	0.829	D	0.711	0.901	D	0.151	0.833	D	1.610	0.255	13.91	0.787	0.120	0.158	0.189	N	c	0.033	-0.140	0.019	0.132	0.732	0.924	0	-2.52	0.059	-0.410	0.072	-0.102	0.116	0.167	0.237	0.796	0.335	7.620	0.272	Succinate dehydrogenase, cytochrome b subunit, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	179	1	161332121	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=322;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12719;SOR=0;LSEQ=TTTTTGCTTTGTCCACAGAT;RSEQ=TGGGACCTAGGAAAAGGCCT;CSQ=A|downstream_gene_variant|MODIFIER|CFAP126|257177|Transcript|NM_001013625.4|protein_coding|||||||||||2402|-1||EntrezGene||YES||||1:g.161332121G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|SDHC|6391|Transcript|NM_001035511.2|protein_coding|5/5||NM_001035511.2:c.244G>A|NP_001030588.1:p.Val82Met|269|244|82|V/M|Gtg/Atg|||1||EntrezGene||||||1:g.161332121G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|SDHC|6391|Transcript|NM_001035512.2|protein_coding|5/5||NM_001035512.2:c.306G>A|NP_001030589.1:p.Met102Ile|331|306|102|M/I|atG/atA|||1||EntrezGene||||||1:g.161332121G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|SDHC|6391|Transcript|NM_001035513.2|protein_coding|4/4||NM_001035513.2:c.249G>A|NP_001030590.1:p.Met83Ile|274|249|83|M/I|atG/atA|||1||EntrezGene||||||1:g.161332121G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|SDHC|6391|Transcript|NM_001278172.2|protein_coding|4/4||NM_001278172.2:c.142G>A|NP_001265101.1:p.Val48Met|167|142|48|V/M|Gtg/Atg|||1||EntrezGene||||||1:g.161332121G>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|SDHC|6391|Transcript|NM_003001.5|protein_coding|6/6||NM_003001.5:c.408G>A|NP_002992.1:p.Met136Ile|433|408|136|M/I|atG/atA|||1||EntrezGene||YES||||1:g.161332121G>A||||||||||||||,A|splice_region_variant&non_coding_transcript_exon_variant|LOW|SDHC|6391|Transcript|NR_103459.2|misc_RNA|7/7||NR_103459.2:n.460G>A||460|||||||1||EntrezGene||||||1:g.161332121G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:322:0:0,0:184,138:322,0:0:2,0:28.9:1:33.1:1:1:0:56:9.062:1:0:0.3	0/1:179:2:1,1:107,69:176,2:0.0112:2,2:45.5:1:31:1:1:1.54674:60:4:0.013:0:1
    352. 

  352. 1	161514542	161514542	A	C	exonic	FCGR3A	.	nonsynonymous SNV	FCGR3A:NM_000569:exon4:c.T841G:p.F281V,FCGR3A:NM_001127592:exon4:c.T838G:p.F280V,FCGR3A:NM_001127593:exon5:c.T526G:p.F176V,FCGR3A:NM_001127595:exon5:c.T526G:p.F176V,FCGR3A:NM_001127596:exon5:c.T523G:p.F175V,FCGR3A:NM_001329120:exon5:c.T526G:p.F176V	0.35	0.3243	0.3307	0.2716	0.4291	0.3291	0.2771	0.3331	0.3076	rs396991	rs396991	0.212	0.270	T	0.0	0.026	B	0.0	0.013	B	0.034	0.248	N	1	0.090	P	0.16	0.090	N	2.76	0.115	T	2.46	0.003	N	0.066	0.370	-0.916	0.462	T	0.003	0.011	T	.	.	.	-1.789	0.011	0.002	0.380	0.025	0.017	0.053	N	c	-2.225	-2.151	0.978	0.298	0.447	0.083	0	-0.103	0.129	-0.375	0.075	-3.170	0.001	0.000	0.063	0.000	0.016	0.356	0.003	Immunoglobulin subtype|Immunoglobulin-like domain|Immunoglobulin-like fold	ENSG00000244682.3|ENSG00000225217.1|ENSG00000225217.1|ENSG00000244682.3|ENSG00000225217.1|ENSG00000244682.3|ENSG00000225217.1|ENSG00000244682.3|ENSG00000244682.3|ENSG00000225217.1|ENSG00000244682.3|ENSG00000225217.1|ENSG00000225217.1|ENSG00000224203.2	Adipose_Subcutaneous|Adipose_Subcutaneous|Artery_Tibial|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Esophagus_Muscularis|Esophagus_Muscularis|Lung|Muscle_Skeletal|Muscle_Skeletal|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Thyroid|Whole_Blood	ID=COSV63459276;OCCURENCE=1(breast),7(soft_tissue),2(skin),3(lung),1(thyroid)	227742	not_specified|rituximab_response_-_Efficacy|trastuzumab_response_-_Efficacy	MedGen:CN169374|MedGen:CN236577|MedGen:CN236585	reviewed_by_expert_panel	drug_response	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU4547350	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|4|170|0.0235294,COCA-CN|2|321|0.00623053	0.75	327	108	1	161514542	.	A	C	327	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1032;VD=485;AF=0.47;SHIFT3=0;MSI=5;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACACATTTTTACTCCCAA;RSEQ=AAGCCCCCTGCAGAAGTAGG;CSQ=C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_000569.8|protein_coding|4/5||NM_000569.8:c.526T>G|NP_000560.7:p.Phe176Val|608|526|176|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127592.2|protein_coding|4/5||NM_001127592.2:c.838T>G|NP_001121064.2:p.Phe280Val|890|838|280|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||YES||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127593.1|protein_coding|5/6||NM_001127593.1:c.526T>G|NP_001121065.1:p.Phe176Val|681|526|176|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127595.2|protein_coding|5/6||NM_001127595.2:c.526T>G|NP_001121067.1:p.Phe176Val|661|526|176|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127596.2|protein_coding|5/6||NM_001127596.2:c.523T>G|NP_001121068.1:p.Phe175Val|658|523|175|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001329120.2|protein_coding|5/6||NM_001329120.2:c.526T>G|NP_001316049.1:p.Phe176Val|672|526|176|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|intron_variant|MODIFIER|FCGR3A|2214|Transcript|NM_001329122.1|protein_coding||3/3|NM_001329122.1:c.635-1553T>G|||||||rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1,C|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001386450.1|protein_coding|5/6||NM_001386450.1:c.523T>G|NP_001373379.1:p.Phe175Val|669|523|175|F/V|Ttt/Gtt|rs396991&CM992625&COSV63459276||-1||EntrezGene||||||1:g.161514542A>C|0.325|0.3291|0.239|0.416|0.3373|0.2789|0.3443|0.3415|0.3414|0.416|gnomAD_ASJ|likely_benign&drug_response|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1032:485:282,203:296,248:544,485:0.47:2,2:39.3:1:36.7:1:0.23248:1.16:42.8:484:0.4802:0:1.1	1/1:108:108:60,48:0,0:0,108:1:0,2:34.9:1:36.4:1:1:0:45.1:53:1:0:1.2
    353. 

  353. 1	161514585	161514585	T	G	exonic	FCGR3A	.	nonsynonymous SNV	FCGR3A:NM_000569:exon4:c.A798C:p.K266N,FCGR3A:NM_001127592:exon4:c.A795C:p.K265N,FCGR3A:NM_001127593:exon5:c.A483C:p.K161N,FCGR3A:NM_001127595:exon5:c.A483C:p.K161N,FCGR3A:NM_001127596:exon5:c.A480C:p.K160N,FCGR3A:NM_001329120:exon5:c.A483C:p.K161N	.	.	.	.	.	.	.	.	.	.	.	0.259	0.268	T	0.0	0.067	B	0.003	0.080	B	0.270	0.038	N	1	0.090	N	0.89	0.217	L	2.91	0.100	T	-1.77	0.418	N	0.024	0.100	-0.965	0.382	T	0.009	0.031	T	0.003	0.056	T	0.315	0.124	5.834	0.951	0.255	0.019	0.057	N	c	-0.779	-0.939	0.998	0.365	0.447	0.083	0	-4.45	0.033	-0.982	0.038	0.095	0.197	0.001	0.137	0.005	0.090	1.104	0.016	Immunoglobulin subtype|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	129	1	161514585	.	T	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1138;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01029;SOR=0;LSEQ=CCGCTGTCTTTGAGTGTGGC;RSEQ=TTTGGAATGTAGAAGTCAGA;CSQ=G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_000569.8|protein_coding|4/5||NM_000569.8:c.483A>C|NP_000560.7:p.Lys161Asn|565|483|161|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127592.2|protein_coding|4/5||NM_001127592.2:c.795A>C|NP_001121064.2:p.Lys265Asn|847|795|265|K/N|aaA/aaC|||-1||EntrezGene||YES||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127593.1|protein_coding|5/6||NM_001127593.1:c.483A>C|NP_001121065.1:p.Lys161Asn|638|483|161|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127595.2|protein_coding|5/6||NM_001127595.2:c.483A>C|NP_001121067.1:p.Lys161Asn|618|483|161|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001127596.2|protein_coding|5/6||NM_001127596.2:c.480A>C|NP_001121068.1:p.Lys160Asn|615|480|160|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001329120.2|protein_coding|5/6||NM_001329120.2:c.483A>C|NP_001316049.1:p.Lys161Asn|629|483|161|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|intron_variant|MODIFIER|FCGR3A|2214|Transcript|NM_001329122.1|protein_coding||3/3|NM_001329122.1:c.635-1596A>C|||||||||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||,G|missense_variant|MODERATE|FCGR3A|2214|Transcript|NM_001386450.1|protein_coding|5/6||NM_001386450.1:c.480A>C|NP_001373379.1:p.Lys160Asn|626|480|160|K/N|aaA/aaC|||-1||EntrezGene||||||1:g.161514585T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1138:0:0,0:558,580:1138,0:0:2,0:35.1:1:35.2:1:1:0:56.1:25.465:1:0:0.5	0/1:129:2:1,1:67,60:127,2:0.0155:2,2:30.5:1:37:0:1:1.11571:53.5:4:0.0159:0:2.5
    354. 

  354. 1	162688838	162688838	A	-	UTR5	DDR2	NM_001014796:c.-16del-;NM_006182:c.-16del-	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	151	1	162688837	.	CA	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=170;VD=2;AF=0.0118;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.27969;SOR=inf;LSEQ=TTGGTGGCAGACTCCAGTTC;RSEQ=ACACCATCTTCTGAGATGAT;CSQ=-|5_prime_UTR_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding|4/19||NM_001014796.3:c.-15del||424|||||||1||EntrezGene||||||1:g.162688839del||||||||||||||,-|5_prime_UTR_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding|3/18||NM_001354982.2:c.-15del||295|||||||1||EntrezGene||||||1:g.162688839del||||||||||||||,-|5_prime_UTR_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding|3/18||NM_001354983.2:c.-15del||761|||||||1||EntrezGene||YES||||1:g.162688839del||||||||||||||,-|5_prime_UTR_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding|3/18||NM_006182.4:c.-15del||344|||||||1||EntrezGene||||||1:g.162688839del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:170:2:1,1:97,71:168,2:0.0118:2,2:45.5:1:37:0:1:1.36363:60:4:0.0118:0:0	0/0:151:0:0,0:83,68:151,0:0:2,0:37:1:36.6:1:1:0:60:150:1:0:0.1
    355. 

  355. 1	162688914	162688914	G	T	exonic	DDR2	.	nonsynonymous SNV	DDR2:NM_006182:exon3:c.G61T:p.A21S,DDR2:NM_001014796:exon4:c.G61T:p.A21S	.	.	.	.	.	.	.	.	.	.	.	0.298	0.183	T	0.041	0.200	B	0.016	0.166	B	0.202	0.166	N	0.985	0.248	N	1.345	0.336	L	-4.28	0.977	D	-0.73	0.206	N	0.298	0.362	-0.403	0.720	T	0.595	0.856	D	0.051	0.647	D	1.463	0.238	13.12	0.974	0.334	0.501	0.283	D	c	-0.510	-0.384	0.992	0.326	0.626	0.397	0	1.23	0.203	0.853	0.272	0.902	0.416	1.000	0.715	0.998	0.697	3.012	0.056	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	161	1	162688914	.	G	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.30625;SOR=inf;LSEQ=TGCTGCCTATCTTGAGTTCT;RSEQ=CAAAAGCTCAGGTTAATCCA;CSQ=T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001014796.3|protein_coding|4/19||NM_001014796.3:c.61G>T|NP_001014796.1:p.Ala21Ser|500|61|21|A/S|Gca/Tca|||1||EntrezGene||||||1:g.162688914G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354982.2|protein_coding|3/18||NM_001354982.2:c.61G>T|NP_001341911.1:p.Ala21Ser|371|61|21|A/S|Gca/Tca|||1||EntrezGene||||||1:g.162688914G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354983.2|protein_coding|3/18||NM_001354983.2:c.61G>T|NP_001341912.1:p.Ala21Ser|837|61|21|A/S|Gca/Tca|||1||EntrezGene||YES||||1:g.162688914G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_006182.4|protein_coding|3/18||NM_006182.4:c.61G>T|NP_006173.2:p.Ala21Ser|420|61|21|A/S|Gca/Tca|||1||EntrezGene||||||1:g.162688914G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:83,115:198,2:0.01:2,2:37.5:1:31:1:1:1.38:60:4:0.0102:0:1.5	0/0:161:0:0,0:74,87:161,0:0:2,0:2:0:11:0:1:0:60:0:0:0:8
    356. 

  356. 1	162730972	162730972	T	C	intronic	DDR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	1	162730972	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=956;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01979;SOR=0;LSEQ=GCACCTTAGCAGGGCCAACC;RSEQ=ATCACTCACATGCCTCTTTC;CSQ=C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||9/18|NM_001014796.3:c.856-29T>C|||||||||1||EntrezGene||||||1:g.162730972T>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||8/17|NM_001354982.2:c.856-29T>C|||||||||1||EntrezGene||||||1:g.162730972T>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||8/17|NM_001354983.2:c.856-29T>C|||||||||1||EntrezGene||YES||||1:g.162730972T>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||8/17|NM_006182.4:c.856-29T>C|||||||||1||EntrezGene||||||1:g.162730972T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:956:0:0,0:602,354:956,0:0:2,0:38.5:1:36.3:1:1:0:60:67.286:1:0:0.1	0/1:157:2:1,1:106,49:155,2:0.0127:2,2:32.5:1:37:0:0.53691:2.15165:60:4:0.013:0:1
    357. 

  357. 1	162735763	162735763	G	A	intronic	DDR2	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs770289851	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	170	1	162735763	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=2;AF=0.0101;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.29016;SOR=inf;LSEQ=AGCTGTCTGTCTTCTCCCTG;RSEQ=CTCTGACTCACCCTTGTTTT;CSQ=A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||10/18|NM_001014796.3:c.1100-28G>A|||||||rs770289851||1||EntrezGene||||||1:g.162735763G>A|3.985e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||9/17|NM_001354982.2:c.1100-28G>A|||||||rs770289851||1||EntrezGene||||||1:g.162735763G>A|3.985e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||9/17|NM_001354983.2:c.1100-28G>A|||||||rs770289851||1||EntrezGene||YES||||1:g.162735763G>A|3.985e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||9/17|NM_006182.4:c.1100-28G>A|||||||rs770289851||1||EntrezGene||||||1:g.162735763G>A|3.985e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:199:2:1,1:120,77:197,2:0.0101:2,2:13.5:1:37:0:1:1.55481:60:4:0.0101:0:1	0/0:170:0:0,0:106,64:170,0:0:2,0:38.8:1:36.6:1:1:0:60:169:1:0:0
    358. 

  358. 1	162735862	162735862	G	T	intronic	DDR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	188	1	162735862	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=305;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05491;SOR=0;LSEQ=CCACAACCTATGGTATATGT;RSEQ=ATTCCTAATTACACAAATTA;CSQ=T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||11/18|NM_001014796.3:c.1162+9G>T|||||||||1||EntrezGene||||||1:g.162735862G>T||||||||||||||,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||10/17|NM_001354982.2:c.1162+9G>T|||||||||1||EntrezGene||||||1:g.162735862G>T||||||||||||||,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||10/17|NM_001354983.2:c.1162+9G>T|||||||||1||EntrezGene||YES||||1:g.162735862G>T||||||||||||||,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||10/17|NM_006182.4:c.1162+9G>T|||||||||1||EntrezGene||||||1:g.162735862G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:305:0:0,0:156,149:305,0:0:2,0:38.2:1:36.4:1:1:0:60:75.25:1:0:0.1	0/1:188:3:1,2:84,101:185,3:0.016:2,2:15.7:1:28.3:1:1:1.65905:60:2:0.0108:0:1
    359. 

  359. 1	162737116	162737116	C	G	exonic	DDR2	.	synonymous SNV	DDR2:NM_006182:exon11:c.C1260G:p.L420L,DDR2:NM_001014796:exon12:c.C1260G:p.L420L	0.5	0.2473	0.4814	0.3890	0.1391	0.3938	0.0808	0.1358	0.1386	rs2298258	rs2298258	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63369342;OCCURENCE=1(breast),1(stomach),2(haematopoietic_and_lymphoid_tissue),1(lung),23(meninges)	249492	Squamous_cell_lung_carcinoma|Spondyloepimetaphyseal_dysplasia-short_limb-abnormal_calcification_syndrome|not_specified	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0010077,MedGen:C1849011,OMIM:271665,Orphanet:ORPHA93358|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU647178	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.25	253	246	1	162737116	.	C	G	253	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=567;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=GCCATCATTGTCATCATCCT;RSEQ=TGGAGGCAGTTCTGGCAGAA;CSQ=G|synonymous_variant|LOW|DDR2|4921|Transcript|NM_001014796.3|protein_coding|12/19||NM_001014796.3:c.1260C>G|NP_001014796.1:p.Leu420%3D|1699|1260|420|L|ctC/ctG|rs2298258&COSV63369342||1||EntrezGene||||||1:g.162737116C>G|0.2269|0.4774|0.4054|0.1008|0.3975|0.07439|0.1403|0.1892|0.2679|0.5023|AFR|likely_benign&benign|0&1|1&1,G|synonymous_variant|LOW|DDR2|4921|Transcript|NM_001354982.2|protein_coding|11/18||NM_001354982.2:c.1260C>G|NP_001341911.1:p.Leu420%3D|1570|1260|420|L|ctC/ctG|rs2298258&COSV63369342||1||EntrezGene||||||1:g.162737116C>G|0.2269|0.4774|0.4054|0.1008|0.3975|0.07439|0.1403|0.1892|0.2679|0.5023|AFR|likely_benign&benign|0&1|1&1,G|synonymous_variant|LOW|DDR2|4921|Transcript|NM_001354983.2|protein_coding|11/18||NM_001354983.2:c.1260C>G|NP_001341912.1:p.Leu420%3D|2036|1260|420|L|ctC/ctG|rs2298258&COSV63369342||1||EntrezGene||YES||||1:g.162737116C>G|0.2269|0.4774|0.4054|0.1008|0.3975|0.07439|0.1403|0.1892|0.2679|0.5023|AFR|likely_benign&benign|0&1|1&1,G|synonymous_variant|LOW|DDR2|4921|Transcript|NM_006182.4|protein_coding|11/18||NM_006182.4:c.1260C>G|NP_006173.2:p.Leu420%3D|1619|1260|420|L|ctC/ctG|rs2298258&COSV63369342||1||EntrezGene||||||1:g.162737116C>G|0.2269|0.4774|0.4054|0.1008|0.3975|0.07439|0.1403|0.1892|0.2679|0.5023|AFR|likely_benign&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:567:0:0,0:252,315:567,0:0:2,0:40.6:1:36.7:1:1:0:60:282.5:1:0:0.1	0/1:246:115:54,61:59,72:131,115:0.4675:2,2:37.3:1:37:0:0.79837:1.08:60:230:0.4675:0:1.1
    360. 

  360. 1	162737188	162737188	T	A	intronic	DDR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	156	1	162737188	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=185;VD=2;AF=0.0108;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.2936;SOR=inf;LSEQ=GTCATGATATAAGAAACTGC;RSEQ=CCTTTCTTTCTTAAGCCACT;CSQ=A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||12/18|NM_001014796.3:c.1293+39T>A|||||||||1||EntrezGene||||||1:g.162737188T>A||||||||||||||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||11/17|NM_001354982.2:c.1293+39T>A|||||||||1||EntrezGene||||||1:g.162737188T>A||||||||||||||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||11/17|NM_001354983.2:c.1293+39T>A|||||||||1||EntrezGene||YES||||1:g.162737188T>A||||||||||||||,A|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||11/17|NM_006182.4:c.1293+39T>A|||||||||1||EntrezGene||||||1:g.162737188T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:185:2:1,1:49,134:183,2:0.0108:2,2:20.5:1:37:0:0.46857:2.72:60:4:0.0109:0:1	0/0:156:0:0,0:46,109:155,0:0:2,0:36.5:1:36.9:1:1:0:60:310:1:0:0.4
    361. 

  361. 1	162743245	162743245	T	A	intronic	DDR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	218	1	162743245	.	T	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=130;VD=2;AF=0.0154;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13888;SOR=inf;LSEQ=ATGATGATGCTGAGACTAGA;RSEQ=GACTTTTGTCTAGGTTCATC;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|DDR2|4921|Transcript|NM_001014796.3|protein_coding||14/18|NM_001014796.3:c.1729-14T>A|||||||||1||EntrezGene||||||1:g.162743245T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|DDR2|4921|Transcript|NM_001354982.2|protein_coding||13/17|NM_001354982.2:c.1729-14T>A|||||||||1||EntrezGene||||||1:g.162743245T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|DDR2|4921|Transcript|NM_001354983.2|protein_coding||13/17|NM_001354983.2:c.1729-14T>A|||||||||1||EntrezGene||YES||||1:g.162743245T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|DDR2|4921|Transcript|NM_006182.4|protein_coding||13/17|NM_006182.4:c.1729-14T>A|||||||||1||EntrezGene||||||1:g.162743245T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:130:2:1,1:92,36:128,2:0.0154:2,2:41:0:37:0:0.4898:2.53446:60:4:0.0155:0:1	0/0:218:0:0,0:140,78:218,0:0:2,0:37.2:1:36.8:1:1:0:60:436:1:0:0.1
    362. 

  362. 1	162743418	162743418	G	T	intronic	DDR2	.	.	.	1.	0.9958	0.9855	1	1	1	1	1	0.9980	rs1355287	rs1355287	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	249495	Squamous_cell_lung_carcinoma|not_specified	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81714582	COCA-CN|5|321|0.0155763	1	275	197	1	162743418	.	G	T	275	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=170;VD=170;AF=1;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTTGAATTTTCCTTTA;RSEQ=GTATTTCATCTTTAGGACCA;CSQ=T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||15/18|NM_001014796.3:c.1856+32G>T|||||||rs1355287||1||EntrezGene||||||1:g.162743418G>T|0.9989|0.9857|0.9993|1|1|1|1|0.9992|0.9996|1|EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE|benign&uncertain_significance||1,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||14/17|NM_001354982.2:c.1856+32G>T|||||||rs1355287||1||EntrezGene||||||1:g.162743418G>T|0.9989|0.9857|0.9993|1|1|1|1|0.9992|0.9996|1|EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE|benign&uncertain_significance||1,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||14/17|NM_001354983.2:c.1856+32G>T|||||||rs1355287||1||EntrezGene||YES||||1:g.162743418G>T|0.9989|0.9857|0.9993|1|1|1|1|0.9992|0.9996|1|EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE|benign&uncertain_significance||1,T|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||14/17|NM_006182.4:c.1856+32G>T|||||||rs1355287||1||EntrezGene||||||1:g.162743418G>T|0.9989|0.9857|0.9993|1|1|1|1|0.9992|0.9996|1|EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE|benign&uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:170:170:69,101:0,0:0,170:1:0,2:33.8:1:36.2:1:1:0:60:340:1:0:1.1	1/1:197:197:63,134:0,0:0,197:1:0,2:37:1:36.1:1:1:0:60:97.5:1:0:1
    363. 

  363. 1	162743440	162743440	G	C	intronic	DDR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	1	162743440	.	G	C	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=2;AF=0.0163;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.19209;SOR=inf;LSEQ=TATTTCATCTTTAGGACCAG;RSEQ=AATACTCCTGGATACTTCTG;CSQ=C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||15/18|NM_001014796.3:c.1856+54G>C|||||||||1||EntrezGene||||||1:g.162743440G>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||14/17|NM_001354982.2:c.1856+54G>C|||||||||1||EntrezGene||||||1:g.162743440G>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||14/17|NM_001354983.2:c.1856+54G>C|||||||||1||EntrezGene||YES||||1:g.162743440G>C||||||||||||||,C|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||14/17|NM_006182.4:c.1856+54G>C|||||||||1||EntrezGene||||||1:g.162743440G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:43,78:121,2:0.0163:2,2:5:0:37:0:1:1.8:60:4:0.0163:0:2	0/0:157:0:0,0:39,118:157,0:0:2,0:32.6:1:36.8:1:1:0:60:314:1:0:1
    364. 

  364. 1	162745457	162745457	G	T	exonic	DDR2	.	nonsynonymous SNV	DDR2:NM_006182:exon15:c.G1872T:p.K624N,DDR2:NM_001014796:exon16:c.G1872T:p.K624N	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1.000	0.588	D	0.62	0.158	N	-1.67	0.828	D	-4.1	0.749	D	0.394	0.453	-0.348	0.736	T	0.377	0.735	T	0.092	0.759	D	6.119	0.843	28.3	0.998	0.926	0.944	0.609	D	c	0.237	0.214	0.008	0.115	0.732	0.924	0	2.24	0.271	2.017	0.404	0.108	0.203	1.000	0.715	1.000	0.888	7.677	0.275	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	198	1	162745457	.	G	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=3;AF=0.016;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11364;SOR=inf;LSEQ=CCAAGGAATGATTTTCTTAA;RSEQ=GAGATAAAGATCATGTCTCG;CSQ=T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001014796.3|protein_coding|16/19||NM_001014796.3:c.1872G>T|NP_001014796.1:p.Lys624Asn|2311|1872|624|K/N|aaG/aaT|||1||EntrezGene||||||1:g.162745457G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354982.2|protein_coding|15/18||NM_001354982.2:c.1872G>T|NP_001341911.1:p.Lys624Asn|2182|1872|624|K/N|aaG/aaT|||1||EntrezGene||||||1:g.162745457G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354983.2|protein_coding|15/18||NM_001354983.2:c.1872G>T|NP_001341912.1:p.Lys624Asn|2648|1872|624|K/N|aaG/aaT|||1||EntrezGene||YES||||1:g.162745457G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_006182.4|protein_coding|15/18||NM_006182.4:c.1872G>T|NP_006173.2:p.Lys624Asn|2231|1872|624|K/N|aaG/aaT|||1||EntrezGene||||||1:g.162745457G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:187:3:2,1:115,69:184,3:0.016:2,2:38:1:37:0:1:1.2:60:6:0.0163:0:1	0/0:198:0:0,0:128,70:198,0:0:2,0:36.9:1:35.4:1:1:0:60:32:1:0:0.1
    365. 

  365. 1	162745460	162745460	G	T	exonic	DDR2	.	nonsynonymous SNV	DDR2:NM_006182:exon15:c.G1875T:p.E625D,DDR2:NM_001014796:exon16:c.G1875T:p.E625D	.	.	.	.	.	.	.	.	.	.	.	0.241	0.176	T	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1.000	0.588	D	2.905	0.843	M	-4.0	0.963	D	-2.26	0.505	N	0.967	0.967	1.041	0.979	D	0.928	0.976	D	0.486	0.949	D	5.184	0.700	25.5	0.998	0.868	0.954	0.643	D	c	0.666	0.563	0.086	0.160	0.732	0.924	0	4.19	0.485	2.422	0.441	0.998	0.613	1.000	0.715	1.000	0.888	7.686	0.275	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	203	1	162745460	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=194;VD=2;AF=0.0103;SHIFT3=2;MSI=2;MSILEN=2;SSF=0.23816;SOR=inf;LSEQ=AGGAATGATTTTCTTAAGGA;RSEQ=ATAAAGATCATGTCTCGGCT;CSQ=T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001014796.3|protein_coding|16/19||NM_001014796.3:c.1875G>T|NP_001014796.1:p.Glu625Asp|2314|1875|625|E/D|gaG/gaT|||1||EntrezGene||||||1:g.162745460G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354982.2|protein_coding|15/18||NM_001354982.2:c.1875G>T|NP_001341911.1:p.Glu625Asp|2185|1875|625|E/D|gaG/gaT|||1||EntrezGene||||||1:g.162745460G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_001354983.2|protein_coding|15/18||NM_001354983.2:c.1875G>T|NP_001341912.1:p.Glu625Asp|2651|1875|625|E/D|gaG/gaT|||1||EntrezGene||YES||||1:g.162745460G>T||||||||||||||,T|missense_variant|MODERATE|DDR2|4921|Transcript|NM_006182.4|protein_coding|15/18||NM_006182.4:c.1875G>T|NP_006173.2:p.Glu625Asp|2234|1875|625|E/D|gaG/gaT|||1||EntrezGene||||||1:g.162745460G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:194:2:1,1:122,70:192,2:0.0103:2,2:64.5:1:37:0:1:1.73753:60:4:0.0103:0:1	0/0:203:0:0,0:128,75:203,0:0:2,0:37.3:1:36.4:1:1:0:60:100.5:1:0:0.1
    366. 

  366. 1	162749856	162749857	TC	-	intronic	DDR2	.	.	.	0.041	0	0	0	0	0	0	0	0	rs745385978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	861295	Squamous_cell_lung_carcinoma	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782	no_assertion_criteria_provided	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU74889529	BTCA-SG|2|71|0.028169,GACA-JP|3|585|0.00512821	0.25	115	75	1	162749855	.	TTC	T	115	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=223;VD=9;AF=0.0404;SHIFT3=15;MSI=8;MSILEN=2;SSF=0.07059;SOR=inf;LSEQ=TTTCCCCCGTCTTTGTAATA;RSEQ=TCTCTCTCTCTCTCTTTTGT;CSQ=-|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001014796.3|protein_coding||18/18|NM_001014796.3:c.2434-31_2434-30del|||||||rs555765842||1||EntrezGene||||||1:g.162749871_162749872del|0.0004728|0.0002686|3.205e-05|0|5.978e-05|0.003995|0.000284|0|7.736e-05|0.00797|AA|||,-|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354982.2|protein_coding||17/17|NM_001354982.2:c.2434-31_2434-30del|||||||rs555765842||1||EntrezGene||||||1:g.162749871_162749872del|0.0004728|0.0002686|3.205e-05|0|5.978e-05|0.003995|0.000284|0|7.736e-05|0.00797|AA|||,-|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_001354983.2|protein_coding||17/17|NM_001354983.2:c.2434-31_2434-30del|||||||rs555765842||1||EntrezGene||YES||||1:g.162749871_162749872del|0.0004728|0.0002686|3.205e-05|0|5.978e-05|0.003995|0.000284|0|7.736e-05|0.00797|AA|||,-|intron_variant|MODIFIER|DDR2|4921|Transcript|NM_006182.4|protein_coding||17/17|NM_006182.4:c.2434-31_2434-30del|||||||rs555765842||1||EntrezGene||||||1:g.162749871_162749872del|0.0004728|0.0002686|3.205e-05|0|5.978e-05|0.003995|0.000284|0|7.736e-05|0.00797|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:223:9:6,3:151,63:214,9:0.0404:2,2:32.2:1:36.5:1:0.72621:1.19738:60:18:0.0417:0.0045:0	0/0:75:0:0,0:54,21:75,0:0:2,0:27.9:1:36.4:1:1:0:60:150:1:0:0.5
    367. 

  367. 1	176175795	176175795	C	T	exonic	RFWD2	.	nonsynonymous SNV	RFWD2:NM_001001740:exon1:c.G320A:p.G107D,RFWD2:NM_022457:exon1:c.G320A:p.G107D	.	.	.	.	.	.	.	.	.	.	.	0.069	0.369	T	0.0	0.026	B	0.001	0.040	B	0.006	0.326	N	0.582	0.324	D	0	0.065	N	0.34	0.597	T	-1.12	0.299	N	0.174	0.383	-0.917	0.460	T	0.109	0.394	T	0.083	0.741	D	2.430	0.353	19.02	0.993	0.588	0.656	0.325	D	c	-0.414	-0.288	1.000	0.747	0.442	0.072	0	2.84	0.321	1.976	0.400	0.864	0.376	0.774	0.292	0.910	0.387	10.390	0.432	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	0	1	176175795	.	C	T	37	v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCGCTTCCTGCTGCCGCTG;RSEQ=CTAGGCTGGAGCTGCTGCCT;CSQ=T|missense_variant|MODERATE|RFWD2|64326|Transcript|NM_001001740.4|protein_coding|1/19||NM_001001740.4:c.320G>A|NP_001001740.1:p.Gly107Asp|628|320|107|G/D|gGc/gAc|||-1||EntrezGene||||||1:g.176175795C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|RFWD2|64326|Transcript|NM_001286644.2|protein_coding|1/18||NM_001286644.2:c.-204G>A||628|||||||-1||EntrezGene||||||1:g.176175795C>T||||||||||||||,T|missense_variant|MODERATE|RFWD2|64326|Transcript|NM_022457.7|protein_coding|1/20||NM_022457.7:c.320G>A|NP_071902.2:p.Gly107Asp|628|320|107|G/D|gGc/gAc|||-1||EntrezGene||YES||||1:g.176175795C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:1,3:4,2:0.3333:2,2:42.5:1:37:0:1:2.45:60:4:0.3333:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    368. 

  368. 1	179076821	179076821	A	G	UTR3	ABL2	NM_001168239:c.*32T>C;NM_001168236:c.*32T>C;NM_001168237:c.*32T>C;NM_001168238:c.*32T>C;NM_007314:c.*32T>C;NM_005158:c.*32T>C;NM_001136000:c.*32T>C	.	.	0.039	0.0019	0	0	0	0.0358	0	0	0	rs28913893	rs28913893	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61013442;OCCURENCE=1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU21792658	LUSC-KR|2|170|0.0117647,COCA-CN|1|321|0.00311526	0.25	259	242	1	179076821	.	A	G	259	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1378;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTTCCCTCTCCCCTCAGAA;RSEQ=TGTGTGCATTTTCCCACCAG;CSQ=G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding|13/13||NM_001136000.3:c.*32T>C||3259|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|downstream_gene_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding||||||||||rs28913893&COSV61013442|2895|-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_001168236.2|protein_coding|11/11||NM_001168236.2:c.*32T>C||3798|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding|13/13||NM_001168237.2:c.*32T>C||3552|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding|12/12||NM_001168238.2:c.*32T>C||3489|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding|12/12||NM_001168239.2:c.*32T>C||3196|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_005158.5|protein_coding|12/12||NM_005158.5:c.*32T>C||3568|||||rs28913893&COSV61013442||-1||EntrezGene||||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1,G|3_prime_UTR_variant|MODIFIER|ABL2|27|Transcript|NM_007314.4|protein_coding|12/12||NM_007314.4:c.*32T>C||3861|||||rs28913893&COSV61013442||-1||EntrezGene||YES||||1:g.179076821A>G|0.003433|0|3.539e-05|0|0.04066|0|9.971e-06|0.0005887|0.0006065|0.04066|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1378:0:0,0:983,393:1376,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:242:130:90,40:81,30:111,130:0.5372:2,2:36.2:1:36.9:1:0.57047:1.19909:60:260:0.5417:0:1.1
    369. 

  369. 1	179078279	179078279	T	C	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001168236:exon11:c.A2060G:p.Q687R,ABL2:NM_005158:exon12:c.A2078G:p.Q693R,ABL2:NM_007314:exon12:c.A2123G:p.Q708R	.	.	.	.	.	.	.	.	.	.	.	0.521	0.087	T	0.744	0.411	P	0.196	0.350	B	0.000	0.447	D	1	0.810	D	0.345	0.112	N	3.0	0.092	T	-0.57	0.195	N	0.209	0.341	-1.046	0.156	T	0.018	0.075	T	0.004	0.086	T	0.766	0.167	9.252	0.929	0.218	0.935	0.581	D	c	-0.052	0.144	1.000	0.747	0.672	0.522	0	5.7	0.886	3.387	0.520	1.011	0.635	1.000	0.715	1.000	0.888	13.705	0.620	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	166	1	179078279	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2045;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00561;SOR=0;LSEQ=GTGGCACCAGATTCGCCTCT;RSEQ=GCTGGGCAGGAGTGAAAGAG;CSQ=C|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding||12/12|NM_001136000.3:c.2014+64A>G|||||||||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding|||||||||||1437|-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|11/11||NM_001168236.2:c.2060A>G|NP_001161708.1:p.Gln687Arg|2340|2060|687|Q/R|cAa/cGa|||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding||12/12|NM_001168237.2:c.2059+64A>G|||||||||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding||11/11|NM_001168238.2:c.1996+64A>G|||||||||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding||11/11|NM_001168239.2:c.1951+64A>G|||||||||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|12/12||NM_005158.5:c.2078A>G|NP_005149.4:p.Gln693Arg|2110|2078|693|Q/R|cAa/cGa|||-1||EntrezGene||||||1:g.179078279T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|12/12||NM_007314.4:c.2123A>G|NP_009298.1:p.Gln708Arg|2403|2123|708|Q/R|cAa/cGa|||-1||EntrezGene||YES||||1:g.179078279T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2045:0:0,0:1128,914:2042,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:166:2:1,1:95,69:164,2:0.012:2,2:54.5:1:37:0:1:1.3741:60:4:0.0123:0:1
    370. 

  370. 1	179078284	179078284	G	A	exonic	ABL2	.	synonymous SNV	ABL2:NM_001168236:exon11:c.C2055T:p.A685A,ABL2:NM_005158:exon12:c.C2073T:p.A691A,ABL2:NM_007314:exon12:c.C2118T:p.A706A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100772572;OCCURENCE=1(endometrium)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129102349	UCEC-US|1|531|0.00188324	0.25	37	176	1	179078284	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2139;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.00575;SOR=0;LSEQ=ACCAGATTCGCCTCTTGCTG;RSEQ=GCAGGAGTGAAAGAGAACCC;CSQ=A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding||12/12|NM_001136000.3:c.2014+59C>T|||||||COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|downstream_gene_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding||||||||||COSV100772572|1432|-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|synonymous_variant|LOW|ABL2|27|Transcript|NM_001168236.2|protein_coding|11/11||NM_001168236.2:c.2055C>T|NP_001161708.1:p.Ala685%3D|2335|2055|685|A|gcC/gcT|COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding||12/12|NM_001168237.2:c.2059+59C>T|||||||COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding||11/11|NM_001168238.2:c.1996+59C>T|||||||COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding||11/11|NM_001168239.2:c.1951+59C>T|||||||COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|synonymous_variant|LOW|ABL2|27|Transcript|NM_005158.5|protein_coding|12/12||NM_005158.5:c.2073C>T|NP_005149.4:p.Ala691%3D|2105|2073|691|A|gcC/gcT|COSV100772572||-1||EntrezGene||||||1:g.179078284G>A|||||||||||||1|1,A|synonymous_variant|LOW|ABL2|27|Transcript|NM_007314.4|protein_coding|12/12||NM_007314.4:c.2118C>T|NP_009298.1:p.Ala706%3D|2398|2118|706|A|gcC/gcT|COSV100772572||-1||EntrezGene||YES||||1:g.179078284G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2139:0:0,0:1175,964:2139,0:0:2,0:36.9:1:36.5:1:1:0:60:105.95:1:0:0.2	0/1:176:2:1,1:99,75:174,2:0.0114:2,2:32:0:37:0:1:1.31788:60:4:0.0115:0:1
    371. 

  371. 1	179079656	179079656	A	G	intronic	ABL2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	123	1	179079656	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=288;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.08905;SOR=0;LSEQ=AGAAAAAGGGAGTTCTTTTC;RSEQ=GAAAAGGCACACAACTGAGA;CSQ=G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding||10/12|NM_001136000.3:c.1607-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|downstream_gene_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding|||||||||||60|-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168236.2|protein_coding||9/10|NM_001168236.2:c.1589-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding||10/12|NM_001168237.2:c.1652-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding||9/11|NM_001168238.2:c.1589-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding||9/11|NM_001168239.2:c.1544-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_005158.5|protein_coding||10/11|NM_005158.5:c.1607-66T>C|||||||||-1||EntrezGene||||||1:g.179079656A>G||||||||||||||,G|intron_variant|MODIFIER|ABL2|27|Transcript|NM_007314.4|protein_coding||10/11|NM_007314.4:c.1652-66T>C|||||||||-1||EntrezGene||YES||||1:g.179079656A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:288:0:0,0:61,227:288,0:0:2,0:30.9:1:36.4:1:1:0:60:95:1:0:0.1	0/1:123:2:1,1:20,101:121,2:0.0163:2,2:28.5:1:31:1:0.31347:4.95:60:4:0.0163:0:1
    372. 

  372. 1	179081507	179081507	G	A	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon9:c.C1525T:p.P509S,ABL2:NM_001168236:exon9:c.C1525T:p.P509S,ABL2:NM_001168238:exon9:c.C1525T:p.P509S,ABL2:NM_001168239:exon9:c.C1480T:p.P494S,ABL2:NM_001136000:exon10:c.C1543T:p.P515S,ABL2:NM_001168237:exon10:c.C1588T:p.P530S,ABL2:NM_005158:exon10:c.C1543T:p.P515S,ABL2:NM_007314:exon10:c.C1588T:p.P530S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.971	D	0.000	0.523	D	1	0.810	D	3.785	0.954	H	-2.2	0.869	D	-7.81	0.964	D	0.963	0.963	1.026	0.976	D	0.878	0.960	D	0.281	0.903	D	6.290	0.869	29.1	0.999	0.982	0.993	0.944	D	c	1.090	0.987	1.000	0.747	0.672	0.522	0	5.14	0.699	10.003	0.997	1.048	0.713	1.000	0.715	0.999	0.750	17.949	0.889	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV61012246;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	180	1	179081507	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=547;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.06105;SOR=0;LSEQ=GTGTGTTTCAGCAAAAGAGG;RSEQ=CCTATCGGCAGGGCTCCACT;CSQ=A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|10/13||NM_001136000.3:c.1543C>T|NP_001129472.1:p.Pro515Ser|1575|1543|515|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|9/10||NM_001136001.2:c.1525C>T|NP_001129473.1:p.Pro509Ser|1805|1525|509|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|9/11||NM_001168236.2:c.1525C>T|NP_001161708.1:p.Pro509Ser|1805|1525|509|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|10/13||NM_001168237.2:c.1588C>T|NP_001161709.1:p.Pro530Ser|1868|1588|530|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|9/12||NM_001168238.2:c.1525C>T|NP_001161710.1:p.Pro509Ser|1805|1525|509|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|9/12||NM_001168239.2:c.1480C>T|NP_001161711.1:p.Pro494Ser|1512|1480|494|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|10/12||NM_005158.5:c.1543C>T|NP_005149.4:p.Pro515Ser|1575|1543|515|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||||||1:g.179081507G>A|||||||||||||1|1,A|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|10/12||NM_007314.4:c.1588C>T|NP_009298.1:p.Pro530Ser|1868|1588|530|P/S|Ccc/Tcc|COSV61012246||-1||EntrezGene||YES||||1:g.179081507G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:547:0:0,0:230,316:546,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:180:2:1,1:79,99:178,2:0.0111:2,2:51.5:1:37:0:1:1.25:60:4:0.0113:0:1
    373. 

  373. 1	179084018	179084018	C	T	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon8:c.G1493A:p.R498K,ABL2:NM_001168236:exon8:c.G1493A:p.R498K,ABL2:NM_001168238:exon8:c.G1493A:p.R498K,ABL2:NM_001168239:exon8:c.G1448A:p.R483K,ABL2:NM_001136000:exon9:c.G1511A:p.R504K,ABL2:NM_001168237:exon9:c.G1556A:p.R519K,ABL2:NM_005158:exon9:c.G1511A:p.R504K,ABL2:NM_007314:exon9:c.G1556A:p.R519K	.	.	.	.	.	.	.	.	.	.	.	0.068	0.357	T	0.841	0.445	P	0.413	0.431	B	0.000	0.629	D	1	0.810	D	-0.22	0.040	N	-1.51	0.814	D	-2.23	0.526	N	0.767	0.789	-0.394	0.722	T	0.311	0.681	T	0.035	0.561	D	3.669	0.498	23.2	0.986	0.425	0.957	0.657	D	c	0.029	0.268	1.000	0.747	0.672	0.522	0	5.99	0.973	4.996	0.634	0.816	0.334	1.000	0.715	1.000	0.888	19.446	0.948	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	233	1	179084018	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=2;AF=0.0267;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.0587;SOR=inf;LSEQ=TGCAAAAATACTCACATGCT;RSEQ=TCATAAGTTCATAAACCTTA;CSQ=T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|9/13||NM_001136000.3:c.1511G>A|NP_001129472.1:p.Arg504Lys|1543|1511|504|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|8/10||NM_001136001.2:c.1493G>A|NP_001129473.1:p.Arg498Lys|1773|1493|498|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|8/11||NM_001168236.2:c.1493G>A|NP_001161708.1:p.Arg498Lys|1773|1493|498|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|9/13||NM_001168237.2:c.1556G>A|NP_001161709.1:p.Arg519Lys|1836|1556|519|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|8/12||NM_001168238.2:c.1493G>A|NP_001161710.1:p.Arg498Lys|1773|1493|498|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|8/12||NM_001168239.2:c.1448G>A|NP_001161711.1:p.Arg483Lys|1480|1448|483|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|9/12||NM_005158.5:c.1511G>A|NP_005149.4:p.Arg504Lys|1543|1511|504|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||||||1:g.179084018C>T|||||||||||||1|1,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|9/12||NM_007314.4:c.1556G>A|NP_009298.1:p.Arg519Lys|1836|1556|519|R/K|aGa/aAa|COSV61022468||-1||EntrezGene||YES||||1:g.179084018C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:75:2:1,1:50,23:73,2:0.0267:2,2:17.5:1:37:0:0.54054:2.14936:60:4:0.027:0:1	0/0:233:0:0,0:139,93:232,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    374. 

  374. 1	179084042	179084042	G	T	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon8:c.C1469A:p.P490H,ABL2:NM_001168236:exon8:c.C1469A:p.P490H,ABL2:NM_001168238:exon8:c.C1469A:p.P490H,ABL2:NM_001168239:exon8:c.C1424A:p.P475H,ABL2:NM_001136000:exon9:c.C1487A:p.P496H,ABL2:NM_001168237:exon9:c.C1532A:p.P511H,ABL2:NM_005158:exon9:c.C1487A:p.P496H,ABL2:NM_007314:exon9:c.C1532A:p.P511H	.	.	.	.	.	.	.	.	.	.	.	0.009	0.574	D	1.0	0.899	D	1.0	0.971	D	0.000	0.523	D	1	0.810	D	2.865	0.834	M	-0.17	0.656	T	-8.48	0.976	D	0.886	0.880	0.040	0.831	D	0.506	0.814	D	0.151	0.834	D	6.310	0.871	29.2	0.997	0.811	0.993	0.938	D	c	1.015	0.992	1.000	0.747	0.672	0.522	0	5.99	0.973	9.926	0.988	0.912	0.422	1.000	0.715	0.999	0.750	19.446	0.948	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	265	1	179084042	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=110;VD=2;AF=0.0182;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.08549;SOR=inf;LSEQ=TAAGTTCATAAACCTTAGGG;RSEQ=GGCATCCCTCAGGCTGTTCC;CSQ=T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|9/13||NM_001136000.3:c.1487C>A|NP_001129472.1:p.Pro496His|1519|1487|496|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|8/10||NM_001136001.2:c.1469C>A|NP_001129473.1:p.Pro490His|1749|1469|490|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|8/11||NM_001168236.2:c.1469C>A|NP_001161708.1:p.Pro490His|1749|1469|490|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|9/13||NM_001168237.2:c.1532C>A|NP_001161709.1:p.Pro511His|1812|1532|511|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|8/12||NM_001168238.2:c.1469C>A|NP_001161710.1:p.Pro490His|1749|1469|490|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|8/12||NM_001168239.2:c.1424C>A|NP_001161711.1:p.Pro475His|1456|1424|475|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|9/12||NM_005158.5:c.1487C>A|NP_005149.4:p.Pro496His|1519|1487|496|P/H|cCc/cAc|||-1||EntrezGene||||||1:g.179084042G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|9/12||NM_007314.4:c.1532C>A|NP_009298.1:p.Pro511His|1812|1532|511|P/H|cCc/cAc|||-1||EntrezGene||YES||||1:g.179084042G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:110:2:1,1:65,43:108,2:0.0182:2,2:23:0:37:0:1:1.50576:60:4:0.0187:0:1	0/0:265:0:0,0:150,115:265,0:0:2,0:36.8:1:36.6:1:1:0:60:264:1:0:0
    375. 

  375. 1	179084043	179084043	G	T	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon8:c.C1468A:p.P490T,ABL2:NM_001168236:exon8:c.C1468A:p.P490T,ABL2:NM_001168238:exon8:c.C1468A:p.P490T,ABL2:NM_001168239:exon8:c.C1423A:p.P475T,ABL2:NM_001136000:exon9:c.C1486A:p.P496T,ABL2:NM_001168237:exon9:c.C1531A:p.P511T,ABL2:NM_005158:exon9:c.C1486A:p.P496T,ABL2:NM_007314:exon9:c.C1531A:p.P511T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.523	D	1	0.810	D	2.475	0.721	M	-0.11	0.645	T	-7.4	0.953	D	0.839	0.850	-0.141	0.792	T	0.454	0.787	T	0.036	0.571	D	5.995	0.824	27.8	0.998	0.869	0.993	0.938	D	c	0.943	0.945	1.000	0.747	0.672	0.522	0	5.99	0.973	9.926	0.988	0.912	0.422	1.000	0.715	0.999	0.750	19.446	0.948	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	265	1	179084043	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=110;VD=2;AF=0.0182;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.08549;SOR=inf;LSEQ=AAGTTCATAAACCTTAGGGG;RSEQ=GCATCCCTCAGGCTGTTCCA;CSQ=T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|9/13||NM_001136000.3:c.1486C>A|NP_001129472.1:p.Pro496Thr|1518|1486|496|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|8/10||NM_001136001.2:c.1468C>A|NP_001129473.1:p.Pro490Thr|1748|1468|490|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|8/11||NM_001168236.2:c.1468C>A|NP_001161708.1:p.Pro490Thr|1748|1468|490|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|9/13||NM_001168237.2:c.1531C>A|NP_001161709.1:p.Pro511Thr|1811|1531|511|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|8/12||NM_001168238.2:c.1468C>A|NP_001161710.1:p.Pro490Thr|1748|1468|490|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|8/12||NM_001168239.2:c.1423C>A|NP_001161711.1:p.Pro475Thr|1455|1423|475|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|9/12||NM_005158.5:c.1486C>A|NP_005149.4:p.Pro496Thr|1518|1486|496|P/T|Ccc/Acc|||-1||EntrezGene||||||1:g.179084043G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|9/12||NM_007314.4:c.1531C>A|NP_009298.1:p.Pro511Thr|1811|1531|511|P/T|Ccc/Acc|||-1||EntrezGene||YES||||1:g.179084043G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:110:2:1,1:65,43:108,2:0.0182:2,2:51:1:37:0:1:1.50576:60:4:0.0182:0:1	0/0:265:0:0,0:150,115:265,0:0:2,0:36.8:1:36.5:1:1:0:60:264:1:0:0
    376. 

  376. 1	179084045	179084045	C	T	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon8:c.G1466A:p.C489Y,ABL2:NM_001168236:exon8:c.G1466A:p.C489Y,ABL2:NM_001168238:exon8:c.G1466A:p.C489Y,ABL2:NM_001168239:exon8:c.G1421A:p.C474Y,ABL2:NM_001136000:exon9:c.G1484A:p.C495Y,ABL2:NM_001168237:exon9:c.G1529A:p.C510Y,ABL2:NM_005158:exon9:c.G1484A:p.C495Y,ABL2:NM_007314:exon9:c.G1529A:p.C510Y	.	.	.	.	.	.	.	.	.	rs1055810841	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.559	D	1	0.810	D	2.485	0.726	M	-1.85	0.843	D	-10.4	0.991	D	0.986	0.989	0.747	0.938	D	0.806	0.935	D	0.356	0.924	D	6.426	0.887	29.7	0.998	0.890	0.984	0.827	D	c	0.904	0.893	1.000	0.747	0.672	0.522	0	5.99	0.973	7.847	0.851	0.816	0.334	1.000	0.715	0.995	0.604	19.446	0.948	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	261	1	179084045	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=111;VD=2;AF=0.018;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08847;SOR=inf;LSEQ=GTTCATAAACCTTAGGGGGG;RSEQ=ATCCCTCAGGCTGTTCCATT;CSQ=T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|9/13||NM_001136000.3:c.1484G>A|NP_001129472.1:p.Cys495Tyr|1516|1484|495|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|8/10||NM_001136001.2:c.1466G>A|NP_001129473.1:p.Cys489Tyr|1746|1466|489|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|8/11||NM_001168236.2:c.1466G>A|NP_001161708.1:p.Cys489Tyr|1746|1466|489|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|9/13||NM_001168237.2:c.1529G>A|NP_001161709.1:p.Cys510Tyr|1809|1529|510|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|8/12||NM_001168238.2:c.1466G>A|NP_001161710.1:p.Cys489Tyr|1746|1466|489|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|8/12||NM_001168239.2:c.1421G>A|NP_001161711.1:p.Cys474Tyr|1453|1421|474|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|9/12||NM_005158.5:c.1484G>A|NP_005149.4:p.Cys495Tyr|1516|1484|495|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||||||1:g.179084045C>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|9/12||NM_007314.4:c.1529G>A|NP_009298.1:p.Cys510Tyr|1809|1529|510|C/Y|tGc/tAc|rs1055810841||-1||EntrezGene||YES||||1:g.179084045C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:111:2:1,1:65,44:109,2:0.018:2,2:30:1:31:1:1:1.47193:60:4:0.018:0:1	0/0:261:0:0,0:145,116:261,0:0:2,0:37.5:1:36.7:1:1:0:60:522:1:0:0
    377. 

  377. 1	179086656	179086656	G	T	intronic	ABL2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	115	1	179086656	.	G	T	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=275;VD=3;AF=0.0109;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.34946;SOR=inf;LSEQ=ACGAGCTGCAAGATCTCTGT;RSEQ=GGAAAGAGAACCCTAATGTG;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001136000.3|protein_coding||7/12|NM_001136000.3:c.1179-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001136001.2|protein_coding||6/9|NM_001136001.2:c.1161-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001168236.2|protein_coding||6/10|NM_001168236.2:c.1161-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001168237.2|protein_coding||7/12|NM_001168237.2:c.1224-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001168238.2|protein_coding||6/11|NM_001168238.2:c.1161-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_001168239.2|protein_coding||6/11|NM_001168239.2:c.1116-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_005158.5|protein_coding||7/11|NM_005158.5:c.1179-5C>A|||||||||-1||EntrezGene||||||1:g.179086656G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ABL2|27|Transcript|NM_007314.4|protein_coding||7/11|NM_007314.4:c.1224-5C>A|||||||||-1||EntrezGene||YES||||1:g.179086656G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:275:3:1,2:76,196:272,3:0.0109:2,2:25:1:28.3:1:1:1.29:60:2:0.0074:0:2.7	0/0:115:0:0,0:24,91:115,0:0:2,0:37.6:1:36.6:1:1:0:60:230:1:0:0.1
    378. 

  378. 1	179086679	179086679	T	A	intronic	ABL2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	86	1	179086679	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=141;VD=2;AF=0.0142;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.38478;SOR=inf;LSEQ=AAAGAGAACCCTAATGTGAT;RSEQ=CCATTCAGATGGTGAGGAAA;CSQ=A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding||7/12|NM_001136000.3:c.1179-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding||6/9|NM_001136001.2:c.1161-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168236.2|protein_coding||6/10|NM_001168236.2:c.1161-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding||7/12|NM_001168237.2:c.1224-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding||6/11|NM_001168238.2:c.1161-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding||6/11|NM_001168239.2:c.1116-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_005158.5|protein_coding||7/11|NM_005158.5:c.1179-28A>T|||||||||-1||EntrezGene||||||1:g.179086679T>A||||||||||||||,A|intron_variant|MODIFIER|ABL2|27|Transcript|NM_007314.4|protein_coding||7/11|NM_007314.4:c.1224-28A>T|||||||||-1||EntrezGene||YES||||1:g.179086679T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:141:2:0,2:32,107:139,2:0.0142:2,0:8.5:1:37:0:1:0:60:4:0.0142:0:1	0/0:86:0:0,0:17,69:86,0:0:2,0:33.4:1:36.7:1:1:0:60:172:1:0:0.1
    379. 

  379. 1	179090945	179090945	A	G	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon4:c.T682C:p.S228P,ABL2:NM_001168236:exon4:c.T682C:p.S228P,ABL2:NM_001168238:exon4:c.T682C:p.S228P,ABL2:NM_001168239:exon4:c.T637C:p.S213P,ABL2:NM_001136000:exon5:c.T700C:p.S234P,ABL2:NM_001168237:exon5:c.T745C:p.S249P,ABL2:NM_005158:exon5:c.T700C:p.S234P,ABL2:NM_007314:exon5:c.T745C:p.S249P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.899	D	0.992	0.790	D	0.000	0.513	D	1	0.810	D	2.87	0.836	M	1.68	0.272	T	-4.38	0.782	D	0.93	0.959	-0.423	0.713	T	0.232	0.598	T	0.016	0.375	T	6.272	0.866	29.0	0.999	0.951	0.953	0.640	D	c	0.941	0.863	1.000	0.747	0.632	0.406	0	5.2	0.716	9.234	0.944	1.199	0.960	1.000	0.715	1.000	0.888	14.234	0.653	SH2 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	197	1	179090945	.	A	G	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1340;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01636;SOR=0;LSEQ=CAGCCCATCAGCCACTGTGG;RSEQ=GTGATGGTGTACAAGCTCTG;CSQ=G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|5/13||NM_001136000.3:c.700T>C|NP_001129472.1:p.Ser234Pro|732|700|234|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|4/10||NM_001136001.2:c.682T>C|NP_001129473.1:p.Ser228Pro|962|682|228|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|4/11||NM_001168236.2:c.682T>C|NP_001161708.1:p.Ser228Pro|962|682|228|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|5/13||NM_001168237.2:c.745T>C|NP_001161709.1:p.Ser249Pro|1025|745|249|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|4/12||NM_001168238.2:c.682T>C|NP_001161710.1:p.Ser228Pro|962|682|228|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|4/12||NM_001168239.2:c.637T>C|NP_001161711.1:p.Ser213Pro|669|637|213|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|5/12||NM_005158.5:c.700T>C|NP_005149.4:p.Ser234Pro|732|700|234|S/P|Tcc/Ccc|||-1||EntrezGene||||||1:g.179090945A>G||||||||||||||,G|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|5/12||NM_007314.4:c.745T>C|NP_009298.1:p.Ser249Pro|1025|745|249|S/P|Tcc/Ccc|||-1||EntrezGene||YES||||1:g.179090945A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1340:0:0,0:487,837:1324,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:197:2:1,1:68,126:194,2:0.0102:2,2:46.5:1:31:1:1:1.85:60:4:0.011:0:1
    380. 

  380. 1	179095628	179095628	T	C	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon3:c.A508G:p.I170V,ABL2:NM_001168236:exon3:c.A508G:p.I170V,ABL2:NM_001168238:exon3:c.A508G:p.I170V,ABL2:NM_001168239:exon3:c.A463G:p.I155V,ABL2:NM_001136000:exon4:c.A526G:p.I176V,ABL2:NM_001168237:exon4:c.A571G:p.I191V,ABL2:NM_005158:exon4:c.A526G:p.I176V,ABL2:NM_007314:exon4:c.A571G:p.I191V	.	.	.	.	.	.	.	.	.	.	.	0.038	0.427	D	0.793	0.428	P	0.896	0.618	P	0.000	0.537	D	1	0.810	D	0.365	0.121	N	-2.36	0.882	D	-0.94	0.251	N	0.266	0.451	0.394	0.890	D	0.668	0.885	D	0.045	0.621	D	4.746	0.636	24.7	0.996	0.764	0.943	0.605	D	c	0.180	0.338	1.000	0.747	0.731	0.878	0	5.6	0.849	7.941	0.871	1.011	0.635	1.000	0.715	0.985	0.512	14.950	0.706	SH2 domain|SH3 domain;SH3 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	289	1	179095628	.	T	C	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=703;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0071;SOR=0;LSEQ=CACCAGGAAGCTGCCATTGA;RSEQ=TAGACTGCTGAGCAGATACT;CSQ=C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136000.3|protein_coding|4/13||NM_001136000.3:c.526A>G|NP_001129472.1:p.Ile176Val|558|526|176|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|3/10||NM_001136001.2:c.508A>G|NP_001129473.1:p.Ile170Val|788|508|170|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|3/11||NM_001168236.2:c.508A>G|NP_001161708.1:p.Ile170Val|788|508|170|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|4/13||NM_001168237.2:c.571A>G|NP_001161709.1:p.Ile191Val|851|571|191|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|3/12||NM_001168238.2:c.508A>G|NP_001161710.1:p.Ile170Val|788|508|170|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168239.2|protein_coding|3/12||NM_001168239.2:c.463A>G|NP_001161711.1:p.Ile155Val|495|463|155|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_005158.5|protein_coding|4/12||NM_005158.5:c.526A>G|NP_005149.4:p.Ile176Val|558|526|176|I/V|Atc/Gtc|||-1||EntrezGene||||||1:g.179095628T>C||||||||||||||,C|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|4/12||NM_007314.4:c.571A>G|NP_009298.1:p.Ile191Val|851|571|191|I/V|Atc/Gtc|||-1||EntrezGene||YES||||1:g.179095628T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:703:0:0,0:367,335:702,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:289:4:2,2:145,140:285,4:0.0138:2,2:44.8:1:37:0:1:1.0356:60:8:0.0142:0:1
    381. 

  381. 1	179112037	179112037	C	T	intronic	ABL2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	207	1	179112037	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=140;VD=2;AF=0.0143;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.16208;SOR=inf;LSEQ=TGATTAATGTGGTTATCAAG;RSEQ=CTCCCTGAAACTATCAACTC;CSQ=T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136000.3|protein_coding||1/12|NM_001136000.3:c.112+31G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001136001.2|protein_coding||1/9|NM_001136001.2:c.158-11421G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168236.2|protein_coding||1/10|NM_001168236.2:c.158-11421G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168237.2|protein_coding||1/12|NM_001168237.2:c.158-9528G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168238.2|protein_coding||1/11|NM_001168238.2:c.158-11421G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_001168239.2|protein_coding||1/11|NM_001168239.2:c.112+31G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_005158.5|protein_coding||1/11|NM_005158.5:c.112+31G>A|||||||rs1436820087||-1||EntrezGene||||||1:g.179112037C>T||||||||||||||,T|intron_variant|MODIFIER|ABL2|27|Transcript|NM_007314.4|protein_coding||1/11|NM_007314.4:c.158-9528G>A|||||||rs1436820087||-1||EntrezGene||YES||||1:g.179112037C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:140:2:1,1:98,40:138,2:0.0143:2,2:28:1:37:0:0.50144:2.43227:60:4:0.0143:0:1	0/0:207:0:0,0:134,73:207,0:0:2,0:35.2:1:36.2:1:1:0:60:102.5:1:0:0
    382. 

  382. 1	179198425	179198425	G	T	exonic	ABL2	.	nonsynonymous SNV	ABL2:NM_001136001:exon1:c.C108A:p.D36E,ABL2:NM_001168236:exon1:c.C108A:p.D36E,ABL2:NM_001168237:exon1:c.C108A:p.D36E,ABL2:NM_001168238:exon1:c.C108A:p.D36E,ABL2:NM_007314:exon1:c.C108A:p.D36E	.	.	.	.	.	.	.	.	.	.	.	0.704	0.041	T	0.0	0.119	B	0.001	0.104	B	0.220	0.162	U	1.000	0.201	N	-0.345	0.033	N	-0.71	0.731	T	0.35	0.038	N	0.093	0.117	-0.986	0.337	T	0.078	0.310	T	0.673	0.973	D	0.704	0.161	8.852	0.992	0.539	0.128	0.173	N	c	-0.891	-0.676	1.000	0.747	0.524	0.211	1	1.96	0.251	0.533	0.226	0.878	0.384	1.000	0.715	1.000	0.888	2.839	0.051	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	11	1	179198425	.	G	T	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=73;VD=2;AF=0.0274;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.75387;SOR=inf;LSEQ=TCTGTGGTGCGCCCCGCCGG;RSEQ=TCCCGCCTGCGGCCGGAGGG;CSQ=T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001136001.2|protein_coding|1/10||NM_001136001.2:c.108C>A|NP_001129473.1:p.Asp36Glu|388|108|36|D/E|gaC/gaA|||-1||EntrezGene||||||1:g.179198425G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168236.2|protein_coding|1/11||NM_001168236.2:c.108C>A|NP_001161708.1:p.Asp36Glu|388|108|36|D/E|gaC/gaA|||-1||EntrezGene||||||1:g.179198425G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168237.2|protein_coding|1/13||NM_001168237.2:c.108C>A|NP_001161709.1:p.Asp36Glu|388|108|36|D/E|gaC/gaA|||-1||EntrezGene||||||1:g.179198425G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_001168238.2|protein_coding|1/12||NM_001168238.2:c.108C>A|NP_001161710.1:p.Asp36Glu|388|108|36|D/E|gaC/gaA|||-1||EntrezGene||||||1:g.179198425G>T||||||||||||||,T|missense_variant|MODERATE|ABL2|27|Transcript|NM_007314.4|protein_coding|1/12||NM_007314.4:c.108C>A|NP_009298.1:p.Asp36Glu|388|108|36|D/E|gaC/gaA|||-1||EntrezGene||YES||||1:g.179198425G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:73:2:1,1:44,27:71,2:0.0274:2,2:41:0:31:1:1:1.61829:60:4:0.0274:0:1	0/0:11:0:0,0:6,5:11,0:0:2,0:43.5:1:37:0:1:0:60:22:1:0:0
    383. 

  383. 1	193091319	193091319	-	G	UTR5	CDC73	NM_024529:c.-12_-11insG	.	.	0.022	0.0050	0.0016	0.0036	0	0	0.0052	0.0077	0.0031	rs545666726	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	270565	Parathyroid_carcinoma|Hyperparathyroidism_2|Hereditary_cancer-predisposing_syndrome|not_specified|Isolated_Hyperparathyroidism|not_provided	Human_Phenotype_Ontology:HP:0006780,MONDO:MONDO:0012004,MedGen:C0687150,OMIM:608266,Orphanet:ORPHA143,SNOMED_CT:255037004|MONDO:MONDO:0007768,MedGen:C1704981,OMIM:145001,Orphanet:ORPHA99880|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN239442|MedGen:CN517202	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	188	312	1	193091319	.	A	AG	188	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2405;VD=34;AF=0.0141;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.19967;SOR=2.22221;LSEQ=GCCCCGAGCCGGCGGAGGCG;RSEQ=GGGGGGGGAAGATGGCGGAC;CSQ=G|5_prime_UTR_variant|MODIFIER|CDC73|79577|Transcript|NM_024529.5|protein_coding|1/17||NM_024529.5:c.-4dup||159-160|||||rs545666726||1||EntrezGene||YES||||1:g.193091327dup|0.007289|0.002759|0.005453|0.001226|0.001109|0.002681|0.0102|0.004867|0.01049|0.01078|AA|uncertain_significance&benign&likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2405:34:19,14:1296,960:2256,34:0.0141:2,2:43.2:1:37.1:1:1:1.01:61:68:0.0155:0.0012:0.2	0/0:312:2:1,1:170,125:295,2:0.0064:2,2:20.9:0:38.7:0:1:1.35855:62.8:4:0.0069:0:0
    384. 

  384. 1	193094282	193094282	G	T	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon2:c.G172T:p.D58Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.938	0.506	P	0.547	0.473	P	0.000	0.843	D	1	0.810	D	1.935	0.520	L	-1.93	0.849	D	-3.09	0.634	D	0.908	0.898	0.212	0.861	D	0.586	0.852	D	0.178	0.854	D	6.302	0.870	29.1	0.994	0.628	0.995	0.968	D	c	0.666	0.730	1.0	0.983	0.732	0.924	0	5.88	0.945	8.092	0.893	0.930	0.439	1.000	0.715	1.000	0.888	20.242	0.984	Paf1 complex subunit Cdc73, N-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	209	1	193094282	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=61;VD=2;AF=0.0328;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05039;SOR=inf;LSEQ=CCAGAGAGTACTACACATTG;RSEQ=ATTCCATTTTATTTCTACTT;CSQ=T|missense_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|2/17||NM_024529.5:c.172G>T|NP_078805.3:p.Asp58Tyr|342|172|58|D/Y|Gat/Tat|||1||EntrezGene||YES||||1:g.193094282G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:61:2:1,1:32,27:59,2:0.0328:2,2:19:0:37:0:1:1.18187:60:4:0.0328:0:1	0/0:209:0:0,0:93,116:209,0:0:2,0:38.6:1:36.5:1:1:0:60:103.5:1:0:0.5
    385. 

  385. 1	193094302	193094302	T	C	exonic	CDC73	.	synonymous SNV	CDC73:NM_024529:exon2:c.T192C:p.L64L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	186	1	193094302	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.55723;SOR=0;LSEQ=GATTCCATTTTATTTCTACT;RSEQ=AATAACGTGCACCTTTCTCA;CSQ=C|synonymous_variant|LOW|CDC73|79577|Transcript|NM_024529.5|protein_coding|2/17||NM_024529.5:c.192T>C|NP_078805.3:p.Leu64%3D|362|192|64|L|ctT/ctC|||1||EntrezGene||YES||||1:g.193094302T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:63:0:0,0:32,31:63,0:0:2,0:42.2:1:36.8:1:1:0:60:126:1:0:0.5	0/1:186:2:1,1:81,101:182,2:0.0108:2,2:37.5:1:31:1:1:1.25:60:4:0.011:0:1
    386. 

  386. 1	193094346	193094346	C	A	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon2:c.C236A:p.A79D	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.992	0.629	D	0.871	0.601	P	0.000	0.843	D	1	0.810	D	2.77	0.812	M	-2.02	0.856	D	-3.39	0.669	D	0.915	0.906	0.324	0.879	D	0.724	0.905	D	0.233	0.884	D	7.224	0.946	34	0.997	0.777	0.996	0.980	D	c	0.800	0.808	1.0	0.983	0.732	0.924	0	5.88	0.945	7.881	0.856	0.831	0.339	1.000	0.715	0.998	0.697	20.242	0.984	Paf1 complex subunit Cdc73, N-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	142	1	193094346	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=49;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.40868;SOR=0;LSEQ=TGTTTATGTCCGACGTGCAG;RSEQ=TGTAAGTAGAATTCATTTTA;CSQ=A|missense_variant&splice_region_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|2/17||NM_024529.5:c.236C>A|NP_078805.3:p.Ala79Asp|406|236|79|A/D|gCt/gAt|||1||EntrezGene||YES||||1:g.193094346C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:49:0:0,0:22,27:49,0:0:2,0:36.3:1:36.8:1:1:0:60:98:1:0:0.7	0/1:142:3:1,2:54,84:138,3:0.0211:2,2:40.3:1:28.3:1:1:1.28349:60:2:0.0144:0:3.7
    387. 

  387. 1	193099337	193099337	C	T	exonic	CDC73	.	stopgain	CDC73:NM_024529:exon3:c.C271T:p.R91X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.378	0.967	36	0.997	0.771	0.968	0.709	D	c	0.549	0.371	0.988	0.313	0.732	0.924	0	0.715	0.173	3.530	0.530	0.935	0.490	1.000	0.715	0.998	0.697	15.930	0.793	Paf1 complex subunit Cdc73, N-terminal domain	.	.	ID=COSV66471502;OCCURENCE=1(stomach),1(upper_aerodigestive_tract)	823082	Parathyroid_carcinoma|Hyperparathyroidism_1|Familial_cancer_of_breast	Human_Phenotype_Ontology:HP:0006780,MONDO:MONDO:0012004,MedGen:C0687150,OMIM:608266,Orphanet:ORPHA143,SNOMED_CT:255037004|MONDO:MONDO:0007767,MedGen:C1840402,OMIM:145000|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_multiple_submitters,_no_conflicts	Pathogenic	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU121068386	GACA-JP|1|585|0.0017094	0.25	37	88	1	193099337	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.82216;SOR=0;LSEQ=CTGTGGTTAGAAGACCTGAT;RSEQ=GAAAAGATCTACTTGGATAT;CSQ=T|stop_gained|HIGH|CDC73|79577|Transcript|NM_024529.5|protein_coding|3/17||NM_024529.5:c.271C>T|NP_078805.3:p.Arg91Ter|441|271|91|R/*|Cga/Tga|CM121613&COSV66471502||1||EntrezGene||YES||||1:g.193099337C>T|||||||||||||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:5,4:9,0:0:2,0:37.7:1:37:0:1:0:60:18:1:0:0.8	0/1:88:2:1,1:45,41:86,2:0.0227:2,2:36.5:1:37:0:1:1.0964:60:4:0.0235:0:1
    388. 

  388. 1	193116993	193116993	T	G	intronic	CDC73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	128	1	193116993	.	T	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=48;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.52779;SOR=0;LSEQ=AATTAAAATCCATTTATATT;RSEQ=TAGAATTTTTCCAAGAACAT;CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CDC73|79577|Transcript|NM_024529.5|protein_coding||7/16|NM_024529.5:c.730-4T>G|||||||||1||EntrezGene||YES||||1:g.193116993T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:48:0:0,0:30,18:48,0:0:2,0:26:1:36.2:1:1:0:60:96:1:0:0	0/1:128:2:1,1:87,39:126,2:0.0156:2,2:11.5:1:31:1:0.52904:2.21537:60:4:0.0157:0:1
    389. 

  389. 1	193117035	193117035	A	-	exonic	CDC73	.	frameshift deletion	CDC73:NM_024529:exon8:c.768delA:p.A258Pfs*61	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	168	1	193117034	.	TA	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=103;VD=2;AF=0.0194;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.14358;SOR=inf;LSEQ=TTTTGCAATTCTTCAATCTG;RSEQ=AAAGCCAGAGAAGAAGGGCG;CSQ=-|frameshift_variant|HIGH|CDC73|79577|Transcript|NM_024529.5|protein_coding|8/17||NM_024529.5:c.771del|NP_078805.3:p.Ala258ProfsTer61|938|768|256|V/X|gtA/gt|||1||EntrezGene||YES|||3|1:g.193117038del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:103:2:1,1:57,44:101,2:0.0194:2,2:14:0:37:0:1:1.29216:60:4:0.0194:0:0	0/0:168:0:0,0:93,75:168,0:0:2,0:39:1:36.9:1:1:0:60:336:1:0:0.1
    390. 

  390. 1	193117051	193117051	G	T	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon8:c.G784T:p.G262W	.	.	.	.	.	.	.	.	.	.	.	0.075	0.344	T	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	1.96	0.533	M	-0.13	0.648	T	-5.16	0.834	D	0.753	0.748	-0.032	0.816	T	0.489	0.806	T	0.157	0.839	D	7.314	0.948	34	0.995	0.679	0.990	0.891	D	c	0.891	0.861	1.000	0.747	0.707	0.730	0	5.66	0.872	7.907	0.867	1.048	0.713	1.000	0.715	0.999	0.750	19.351	0.943	Paf1 complex subunit Cdc73, N-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	190	1	193117051	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=113;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.39243;SOR=0;LSEQ=CTGTAAAAGCCAGAGAAGAA;RSEQ=GGCGTGCACCTGAACAGCGA;CSQ=T|missense_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|8/17||NM_024529.5:c.784G>T|NP_078805.3:p.Gly262Trp|954|784|262|G/W|Ggg/Tgg|||1||EntrezGene||YES||||1:g.193117051G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:113:0:0,0:61,52:113,0:0:2,0:42.5:1:36.7:1:1:0:60:226:1:0:0	0/1:190:2:1,1:94,94:188,2:0.0105:2,2:33.5:1:37:0:1:1:60:4:0.0106:0:1
    391. 

  391. 1	193119417	193119417	A	T	intronic	CDC73	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	119	1	193119417	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=2;AF=0.0156;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.26754;SOR=inf;LSEQ=AATATTAACAAGTAACTCAT;RSEQ=ATTAATTTTTTTACAGGATC;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|CDC73|79577|Transcript|NM_024529.5|protein_coding||8/16|NM_024529.5:c.829-17A>T|||||||||1||EntrezGene||YES||||1:g.193119417A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:128:2:1,1:89,36:125,2:0.0156:2,2:16.5:1:37:0:0.49944:2.45226:60:4:0.0164:0:1	0/0:119:0:0,0:72,47:119,0:0:2,0:35.5:1:35.9:1:1:0:60:38.667:1:0:0.1
    392. 

  392. 1	193119434	193119434	G	A	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon9:c.G829A:p.D277N	.	.	.	.	.	.	.	.	.	.	.	0.504	0.076	T	0.125	0.253	B	0.049	0.237	B	0.000	0.843	D	1	0.810	D	0.69	0.170	N	-0.11	0.645	T	-0.13	0.090	N	0.104	0.109	-0.962	0.388	T	0.148	0.474	T	0.057	0.668	D	1.968	0.297	16.01	0.905	0.192	0.975	0.750	D	c	0.011	0.172	0.994	0.335	0.707	0.730	0	5.53	0.825	7.774	0.841	1.048	0.713	1.000	0.715	0.873	0.365	16.964	0.861	Paf1 complex subunit Cdc73, N-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	144	1	193119434	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=180;VD=2;AF=0.0111;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.30788;SOR=inf;LSEQ=CATAATTAATTTTTTTACAG;RSEQ=ATCCCACTTTGCGCACCAAA;CSQ=A|missense_variant&splice_region_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|9/17||NM_024529.5:c.829G>A|NP_078805.3:p.Asp277Asn|999|829|277|D/N|Gat/Aat|||1||EntrezGene||YES||||1:g.193119434G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:180:2:1,1:122,56:178,2:0.0111:2,2:12:1:37:0:0.53426:2.16825:60:4:0.0114:0:1	0/0:144:0:0,0:84,60:144,0:0:2,0:37.2:1:36.5:1:1:0:60:288:1:0:0.1
    393. 

  393. 1	193119467	193119467	G	A	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon9:c.G862A:p.A288T	.	.	.	.	.	.	.	.	.	.	.	0.185	0.215	T	0.002	0.090	B	0.006	0.112	B	0.000	0.629	D	1	0.810	D	0.71	0.187	N	-0.15	0.652	T	-0.64	0.187	N	0.3	0.360	-0.979	0.352	T	0.147	0.472	T	0.012	0.306	T	3.276	0.453	22.8	0.996	0.729	0.975	0.748	D	c	0.011	0.242	0.995	0.337	0.707	0.730	0	5.53	0.825	7.865	0.854	1.048	0.713	1.000	0.715	1.000	0.888	16.964	0.861	Paf1 complex subunit Cdc73, N-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	178	1	193119467	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=242;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.17903;SOR=0;LSEQ=GCACCAAACAGCCTATCCCA;RSEQ=CTGCCTATAACAGATACGAT;CSQ=A|missense_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|9/17||NM_024529.5:c.862G>A|NP_078805.3:p.Ala288Thr|1032|862|288|A/T|Gct/Act|||1||EntrezGene||YES||||1:g.193119467G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:242:0:0,0:139,103:242,0:0:2,0:39.8:1:36.4:1:1:0:60:79.667:1:0:0.1	0/1:178:2:1,1:97,79:176,2:0.0112:2,2:43.5:1:37:0:1:1.22642:60:4:0.0113:0:1
    394. 

  394. 1	193202298	193202299	TA	-	intronic	CDC73	.	.	.	0.0002	.	.	.	.	.	.	.	.	rs781134485	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	106	1	193202297	.	CTA	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=15;VD=0;AF=0;SHIFT3=9;MSI=5;MSILEN=2;SSF=0.76653;SOR=0;LSEQ=CAAGACTGGTAAGATAGTCT;RSEQ=TATATATATCTTTTCACAGG;CSQ=-|intron_variant|MODIFIER|CDC73|79577|Transcript|NM_024529.5|protein_coding||14/16|NM_024529.5:c.1316+23_1316+24del|||||||rs747940099||1||EntrezGene||YES||||1:g.193202307_193202308del|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:6,9:15,0:0:2,0:23.2:1:37:0:1:0:60:30:1:0:0.1	0/1:106:2:1,1:33,71:104,2:0.0189:2,2:48:1:37:0:0.5407:2.13:60:4:0.019:0:0
    395. 

  395. 1	193205475	193205475	T	C	exonic	CDC73	.	nonsynonymous SNV	CDC73:NM_024529:exon15:c.T1406C:p.I469T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.993	0.797	D	0.000	0.843	D	1	0.810	D	1.785	0.466	L	-0.57	0.713	T	-4.57	0.787	D	0.962	0.961	0.278	0.872	D	0.570	0.844	D	0.149	0.831	D	6.134	0.846	28.4	0.998	0.885	0.993	0.946	D	c	0.835	0.789	1.000	0.747	0.732	0.924	0	5.45	0.796	7.574	0.816	1.061	0.807	1.000	0.715	1.000	0.888	15.530	0.756	Cell division control protein 73, C-terminal	.	.	ID=COSV99054740;OCCURENCE=1(breast),1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	113	1	193205475	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=140;VD=2;AF=0.0143;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.30523;SOR=inf;LSEQ=TGATGGATCACCAGTTGATA;RSEQ=ATTTGCTAAAAGTAAGATTC;CSQ=C|missense_variant|MODERATE|CDC73|79577|Transcript|NM_024529.5|protein_coding|15/17||NM_024529.5:c.1406T>C|NP_078805.3:p.Ile469Thr|1576|1406|469|I/T|aTa/aCa|COSV99054740||1||EntrezGene||YES||||1:g.193205475T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:140:2:1,1:51,87:138,2:0.0143:2,2:25.5:1:37:0:1:1.7:60:4:0.0144:0:1.5	0/0:113:0:0,0:39,74:113,0:0:2,0:35.1:1:35.8:1:1:0:60:36.667:1:0:0.2
    396. 

  396. 1	201981862	201981862	T	C	exonic	ELF3	.	synonymous SNV	ELF3:NM_001114309:exon5:c.T573C:p.P191P,ELF3:NM_004433:exon5:c.T573C:p.P191P	0.85	0.6257	0.7838	0.6002	0.5933	0.7574	0.5828	0.5337	0.5939	rs2819362	rs2819362	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62839434;OCCURENCE=1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4555319	COCA-CN|5|321|0.0155763	0.5	73	0	1	201981862	.	T	C	73	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGCAGGAGCCCCCTCCCC;RSEQ=GGCAGCTCTGACGTCTCCAC;CSQ=C|synonymous_variant|LOW|ELF3|1999|Transcript|NM_001114309.2|protein_coding|5/9||NM_001114309.2:c.573T>C|NP_001107781.1:p.Pro191%3D|815|573|191|P|ccT/ccC|rs2819362&COSV62839434&COSV62840506||1||EntrezGene||YES||||1:g.201981862T>C|0.6011|0.7948|0.6229|0.5604|0.7746|0.591|0.5188|0.5646|0.6895|0.8464|AFR||0&1&1|0&1&1,C|synonymous_variant|LOW|ELF3|1999|Transcript|NM_004433.5|protein_coding|5/9||NM_004433.5:c.573T>C|NP_004424.3:p.Pro191%3D|701|573|191|P|ccT/ccC|rs2819362&COSV62839434&COSV62840506||1||EntrezGene||||||1:g.201981862T>C|0.6011|0.7948|0.6229|0.5604|0.7746|0.591|0.5188|0.5646|0.6895|0.8464|AFR||0&1&1|0&1&1,C|upstream_gene_variant|MODIFIER|ELF3-AS1|102723465|Transcript|NR_146472.1|lncRNA||||||||||rs2819362&COSV62839434&COSV62840506|2381|-1||EntrezGene||YES||||1:g.201981862T>C|0.6011|0.7948|0.6229|0.5604|0.7746|0.591|0.5188|0.5646|0.6895|0.8464|AFR||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:1,4:0,0:0,5:1:0,2:45:1:31.8:1:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    397. 

  397. 1	204397250	204397250	C	T	intronic	PIK3C2B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	198	1	204397250	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=789;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.04008;SOR=0;LSEQ=AGGAGTTGGCAGTAAGGTCT;RSEQ=AGAGAAGATACTGTACCTGA;CSQ=T|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||30/32|NM_001377334.1:c.4480+17G>A|||||||||-1||EntrezGene||||||1:g.204397250C>T||||||||||||||,T|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||33/35|NM_001377335.1:c.4396+17G>A|||||||||-1||EntrezGene||||||1:g.204397250C>T||||||||||||||,T|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||32/34|NM_002646.4:c.4480+17G>A|||||||||-1||EntrezGene||YES||||1:g.204397250C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:789:0:0,0:386,402:788,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:198:2:1,1:108,88:196,2:0.0101:2,2:46.5:1:37:0:1:1.22599:60:4:0.0102:0:1
    398. 

  398. 1	204400783	204400783	A	G	intronic	PIK3C2B	.	.	.	0.46	0.1021	0.0370	0.0990	0.0795	0.4553	0.1082	0.0995	0.1286	rs2271421	rs2271421	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65808800;OCCURENCE=1(liver),18(meninges),1(haematopoietic_and_lymphoid_tissue),4(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11367805	ESAD-UK|1|409|0.00244499,LICA-CN|2|402|0.00497512,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.25	261	248	1	204400783	.	A	G	261	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2713;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCCCTCTGTGCAGATAGTA;RSEQ=AGGGGGCAGCTACCTGGGCA;CSQ=G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||28/32|NM_001377334.1:c.4280+14T>C|||||||rs2271421&COSV65808800||-1||EntrezGene||||||1:g.204400783A>G|0.1418|0.03063|0.1043|0.1076|0.467|0.1177|0.09647|0.1232|0.2486|0.467|gnomAD_EAS||0&1|0&1,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||31/35|NM_001377335.1:c.4196+14T>C|||||||rs2271421&COSV65808800||-1||EntrezGene||||||1:g.204400783A>G|0.1418|0.03063|0.1043|0.1076|0.467|0.1177|0.09647|0.1232|0.2486|0.467|gnomAD_EAS||0&1|0&1,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||30/34|NM_002646.4:c.4280+14T>C|||||||rs2271421&COSV65808800||-1||EntrezGene||YES||||1:g.204400783A>G|0.1418|0.03063|0.1043|0.1076|0.467|0.1177|0.09647|0.1232|0.2486|0.467|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2713:0:0,0:1523,1187:2710,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:248:136:84,52:65,47:112,136:0.5484:2,2:38.6:1:36.9:1:0.60291:1.17:60:272:0.5667:0:1.1
    399. 

  399. 1	204403659	204403659	A	G	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon25:c.T3594C:p.N1198N	0.53	0.3431	0.4997	0.2685	0.1854	0.5248	0.3210	0.2464	0.3208	rs3747636	rs3747636	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65811498;OCCURENCE=1(breast),1(large_intestine),1(stomach),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU145541	ESAD-UK|1|409|0.00244499,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611,BRCA-KR|1|50|0.02	0.25	268	314	1	204403659	.	A	G	268	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2543;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTTCAGCATGATGTTGTC;RSEQ=TTATGTCGGTCACAGATGCC;CSQ=G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|24/33||NM_001377334.1:c.3594T>C|NP_001364263.1:p.Asn1198%3D|4128|3594|1198|N|aaT/aaC|rs3747636&COSV65811498||-1||EntrezGene||||||1:g.204403659A>G|0.2962|0.4892|0.2773|0.2071|0.5263|0.3265|0.2254|0.2686|0.3531|0.5263|gnomAD_EAS||0&1|1&1,G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|27/36||NM_001377335.1:c.3510T>C|NP_001364264.1:p.Asn1170%3D|4843|3510|1170|N|aaT/aaC|rs3747636&COSV65811498||-1||EntrezGene||||||1:g.204403659A>G|0.2962|0.4892|0.2773|0.2071|0.5263|0.3265|0.2254|0.2686|0.3531|0.5263|gnomAD_EAS||0&1|1&1,G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|26/35||NM_002646.4:c.3594T>C|NP_002637.3:p.Asn1198%3D|4927|3594|1198|N|aaT/aaC|rs3747636&COSV65811498||-1||EntrezGene||YES||||1:g.204403659A>G|0.2962|0.4892|0.2773|0.2071|0.5263|0.3265|0.2254|0.2686|0.3531|0.5263|gnomAD_EAS||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2543:0:0,0:1233,1309:2542,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:314:158:84,74:77,78:155,158:0.5032:2,2:36.8:1:36.7:1:0.57253:1.15:60:157:0.5032:0:1.1
    400. 

  400. 1	204408022	204408023	CA	-	intronic	PIK3C2B	.	.	.	0.023	.	.	.	.	.	.	.	.	rs759538786	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	136	100	1	204408021	.	GCA	G	136	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=724;VD=13;AF=0.018;SHIFT3=11;MSI=6;MSILEN=2;SSF=0.18357;SOR=inf;LSEQ=GAGCTGTGTGCCGGCATCAG;RSEQ=CACACACACACCAGACGCAC;CSQ=-|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||23/32|NM_001377334.1:c.3516+40_3516+41del|||||||rs548441991||-1||EntrezGene||||||1:g.204408033_204408034del|0.0002396|0|0.0001816|0.0005362|6.705e-05|0.001142|0.0001647|0|0.0002629|0.02302|EA|||,-|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||26/35|NM_001377335.1:c.3432+40_3432+41del|||||||rs548441991||-1||EntrezGene||||||1:g.204408033_204408034del|0.0002396|0|0.0001816|0.0005362|6.705e-05|0.001142|0.0001647|0|0.0002629|0.02302|EA|||,-|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||25/34|NM_002646.4:c.3516+40_3516+41del|||||||rs548441991||-1||EntrezGene||YES||||1:g.204408033_204408034del|0.0002396|0|0.0001816|0.0005362|6.705e-05|0.001142|0.0001647|0|0.0002629|0.02302|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:724:13:9,4:446,265:711,13:0.018:2,2:49.7:1:37:0:0.77624:1.34:60:26:0.018:0:0	0/0:100:0:0,0:72,28:100,0:0:2,0:39.1:1:36.6:1:1:0:60:200:1:0:0.1
    401. 

  401. 1	204408119	204408119	G	A	exonic	PIK3C2B	.	nonsynonymous SNV	PIK3C2B:NM_002646:exon24:c.C3460T:p.R1154W	0.0001	6.459e-05	0	0	0	0	0	0.0001	0	rs776639121	.	0.0	0.912	D	1.0	0.899	D	0.988	0.764	D	0.000	0.513	D	0.898	0.361	D	2.365	0.684	M	-1.46	0.810	T	-6.02	0.900	D	0.653	0.667	0.596	0.919	D	0.673	0.887	D	0.156	0.837	D	7.460	0.951	34	0.999	0.992	0.831	0.420	D	c	0.589	0.532	1.000	0.747	0.732	0.924	0	4.58	0.559	2.287	0.429	0.097	0.197	1.000	0.715	0.999	0.750	13.043	0.581	Phosphatidylinositol 3-/4-kinase, catalytic domain|Protein kinase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	175	1	204408119	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1244;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.01513;SOR=0;LSEQ=CAGCCAGTCTGCCAGGGGCC;RSEQ=GTCCTTGAACGAGCCGGTCA;CSQ=A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|23/33||NM_001377334.1:c.3460C>T|NP_001364263.1:p.Arg1154Trp|3994|3460|1154|R/W|Cgg/Tgg|rs776639121||-1||EntrezGene||||||1:g.204408119G>A|2.786e-05|0|2.892e-05|0|0|4.642e-05|3.518e-05|0|3.267e-05|4.642e-05|gnomAD_FIN|||,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|26/36||NM_001377335.1:c.3376C>T|NP_001364264.1:p.Arg1126Trp|4709|3376|1126|R/W|Cgg/Tgg|rs776639121||-1||EntrezGene||||||1:g.204408119G>A|2.786e-05|0|2.892e-05|0|0|4.642e-05|3.518e-05|0|3.267e-05|4.642e-05|gnomAD_FIN|||,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|25/35||NM_002646.4:c.3460C>T|NP_002637.3:p.Arg1154Trp|4793|3460|1154|R/W|Cgg/Tgg|rs776639121||-1||EntrezGene||YES||||1:g.204408119G>A|2.786e-05|0|2.892e-05|0|0|4.642e-05|3.518e-05|0|3.267e-05|4.642e-05|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1244:0:0,0:654,590:1244,0:0:2,0:37.6:1:36.7:1:1:0:60:621:1:0:0.1	0/1:175:2:1,1:101,72:173,2:0.0114:2,2:34.5:1:37:0:1:1.39999:60:4:0.0115:0:1.5
    402. 

  402. 1	204409281	204409281	C	G	intronic	PIK3C2B	.	.	.	1.	0.9298	0.7547	0.9809	1	1	1	0.999	0.9898	rs3014631	rs3014631	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81719045	COCA-CN|5|321|0.0155763	1	345	78	1	204409281	.	C	G	345	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=745;VD=740;AF=0.9933;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.60705;SOR=0;LSEQ=CAGAAGGACAATAAGCAAAG;RSEQ=GGTCCCCTCCTCCACCCTCA;CSQ=G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||22/32|NM_001377334.1:c.3379+39G>C|||||||rs3014631||-1||EntrezGene||||||1:g.204409281C>G|0.9807|0.7358|0.9882|0.9994|1|1|0.999|0.9918|0.9994|1|EAS&SAS&gnomAD_EAS&gnomAD_FIN|||,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||25/35|NM_001377335.1:c.3295+39G>C|||||||rs3014631||-1||EntrezGene||||||1:g.204409281C>G|0.9807|0.7358|0.9882|0.9994|1|1|0.999|0.9918|0.9994|1|EAS&SAS&gnomAD_EAS&gnomAD_FIN|||,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||24/34|NM_002646.4:c.3379+39G>C|||||||rs3014631||-1||EntrezGene||YES||||1:g.204409281C>G|0.9807|0.7358|0.9882|0.9994|1|1|0.999|0.9918|0.9994|1|EAS&SAS&gnomAD_EAS&gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:745:740:506,234:0,0:0,740:0.9933:0,2:35.5:1:36.2:1:1:0:60:73:0.9946:0:1.1	1/1:78:78:57,21:0,0:0,78:1:0,2:37:1:36.2:1:1:0:60:38:1:0:1.1
    403. 

  403. 1	204411665	204411665	T	G	exonic	PIK3C2B	.	nonsynonymous SNV	PIK3C2B:NM_002646:exon21:c.A3145C:p.I1049L	.	.	.	.	.	.	.	.	.	.	.	0.452	0.090	T	0.001	0.254	B	0.011	0.247	B	0.000	0.843	D	0.635	0.328	D	1.715	0.445	L	-1.5	0.813	D	-0.5	0.158	N	0.374	0.435	-0.494	0.689	T	0.305	0.676	T	0.060	0.681	D	2.875	0.406	21.7	0.975	0.340	0.780	0.381	D	c	-0.218	-0.007	1.000	0.747	0.732	0.924	0	5.57	0.840	2.126	0.414	1.009	0.627	0.995	0.385	0.964	0.448	13.959	0.635	Protein kinase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	65	295	1	204411665	.	T	G	65	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3261;VD=21;AF=0.0064;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.32052;SOR=0.63097;LSEQ=GTCACTCACCCTGGGCACAA;RSEQ=TCCCTTAACCAGCAGACTGG;CSQ=G|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|20/33||NM_001377334.1:c.3145A>C|NP_001364263.1:p.Ile1049Leu|3679|3145|1049|I/L|Att/Ctt|||-1||EntrezGene||||||1:g.204411665T>G||||||||||||||,G|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|23/36||NM_001377335.1:c.3061A>C|NP_001364264.1:p.Ile1021Leu|4394|3061|1021|I/L|Att/Ctt|||-1||EntrezGene||||||1:g.204411665T>G||||||||||||||,G|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|22/35||NM_002646.4:c.3145A>C|NP_002637.3:p.Ile1049Leu|4478|3145|1049|I/L|Att/Ctt|||-1||EntrezGene||YES||||1:g.204411665T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3261:21:2,19:1760,1480:3240,21:0.0064:2,2:37.7:1:15:1:3e-05:11.2909:60:0.4:0.0021:0:1.5	0/1:295:3:0,3:180,112:292,3:0.0102:2,0:18:1:24.3:1:0.0583:0:60:2:0.0081:0:1.3
    404. 

  404. 1	204412605	204412605	A	G	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon20:c.T2988C:p.L996L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	141	1	204412605	.	A	G	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1910;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00469;SOR=0;LSEQ=AGTTTGGCCAGGGCATTGAC;RSEQ=AGCCAGCACTGGCGGTTAAA;CSQ=G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|19/33||NM_001377334.1:c.2988T>C|NP_001364263.1:p.Leu996%3D|3522|2988|996|L|ctT/ctC|||-1||EntrezGene||||||1:g.204412605A>G||||||||||||||,G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|22/36||NM_001377335.1:c.2904T>C|NP_001364264.1:p.Leu968%3D|4237|2904|968|L|ctT/ctC|||-1||EntrezGene||||||1:g.204412605A>G||||||||||||||,G|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|21/35||NM_002646.4:c.2988T>C|NP_002637.3:p.Leu996%3D|4321|2988|996|L|ctT/ctC|||-1||EntrezGene||YES||||1:g.204412605A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1910:0:0,0:1127,781:1908,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:141:2:1,1:85,54:139,2:0.0142:2,2:40:0:31:1:1:1.56879:60:4:0.0142:0:1
    405. 

  405. 1	204412671	204412671	C	T	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon20:c.G2922A:p.L974L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100915991;OCCURENCE=1(stomach)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU130908754	STAD-US|1|439|0.0022779	0.25	58	200	1	204412671	.	C	T	58	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2540;VD=3;AF=0.0012;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04577;SOR=0.11727;LSEQ=CAGCACAGTAAGGCTGCCAG;RSEQ=AGATACTGGTAGCGGATGCT;CSQ=T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|19/33||NM_001377334.1:c.2922G>A|NP_001364263.1:p.Leu974%3D|3456|2922|974|L|ctG/ctA|COSV100915991||-1||EntrezGene||||||1:g.204412671C>T|||||||||||||1|1,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|22/36||NM_001377335.1:c.2838G>A|NP_001364264.1:p.Leu946%3D|4171|2838|946|L|ctG/ctA|COSV100915991||-1||EntrezGene||||||1:g.204412671C>T|||||||||||||1|1,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|21/35||NM_002646.4:c.2922G>A|NP_002637.3:p.Leu974%3D|4255|2922|974|L|ctG/ctA|COSV100915991||-1||EntrezGene||YES||||1:g.204412671C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2540:3:2,1:1282,1255:2537,3:0.0012:2,2:27:1:37:0:1:1.96:60:6:0.0012:0:1	0/1:200:2:1,1:109,89:198,2:0.01:2,2:36.5:1:37:0:1:1.22347:60:4:0.0102:0:1
    406. 

  406. 1	204412727	204412727	T	C	splicing	PIK3C2B	NM_002646:exon20:c.2868-2A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.748	0.637	24.7	0.995	0.692	0.979	0.777	D	c	1.120	0.973	1.0	0.983	0.099	0.020	0	5.98	0.971	7.959	0.873	0.998	0.613	1.000	0.715	0.795	0.335	16.134	0.812	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	178	1	204412727	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2447;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00457;SOR=0;LSEQ=GAGGCCGTCCTTCAGTAACC;RSEQ=GCAAGGCAGAGGGAGTCAGG;CSQ=C|splice_acceptor_variant|HIGH|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||18/32|NM_001377334.1:c.2868-2A>G|||||||||-1||EntrezGene||||||1:g.204412727T>C||||||||||||||,C|splice_acceptor_variant|HIGH|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||21/35|NM_001377335.1:c.2784-2A>G|||||||||-1||EntrezGene||||||1:g.204412727T>C||||||||||||||,C|splice_acceptor_variant|HIGH|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||20/34|NM_002646.4:c.2868-2A>G|||||||||-1||EntrezGene||YES||||1:g.204412727T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2447:0:0,0:1079,1364:2443,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:178:2:1,1:74,102:176,2:0.0112:2,2:43:1:37:0:1:1.38:60:4:0.0113:0:1
    407. 

  407. 1	204413297	204413297	C	T	intronic	PIK3C2B	.	.	.	0.81	0.6782	0.4977	0.7578	0.8433	0.4751	0.7230	0.7839	0.7270	rs2292459	rs2292459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65809619;OCCURENCE=1(liver),1(haematopoietic_and_lymphoid_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU813473	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	350	264	1	204413297	.	C	T	350	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1934;VD=1071;AF=0.5538;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=80.5122;LSEQ=TCATACTTCAGGGCCTGTTT;RSEQ=GGAGAAAGGGAGAAAGAGAA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||17/32|NM_001377334.1:c.2773-7G>A|||||||rs2292459&COSV65809619||-1||EntrezGene||||||1:g.204413297C>T|0.7333|0.4985|0.7528|0.8349|0.4748|0.7153|0.8041|0.7668|0.7009|0.8349|gnomAD_ASJ||0&1|0&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||20/35|NM_001377335.1:c.2689-7G>A|||||||rs2292459&COSV65809619||-1||EntrezGene||||||1:g.204413297C>T|0.7333|0.4985|0.7528|0.8349|0.4748|0.7153|0.8041|0.7668|0.7009|0.8349|gnomAD_ASJ||0&1|0&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||19/34|NM_002646.4:c.2773-7G>A|||||||rs2292459&COSV65809619||-1||EntrezGene||YES||||1:g.204413297C>T|0.7333|0.4985|0.7528|0.8349|0.4748|0.7153|0.8041|0.7668|0.7009|0.8349|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:1934:1071:419,652:0,0:0,1071:0.5538:0,2:34.4:1:34.8:1:1:0:60:23.907:0.5451:0:1.2	0/1:264:4:1,3:76,73:149,4:0.0152:2,2:30.2:1:24:1:0.36675:3.10205:60:1:0.0076:0:1.5
    408. 

  408. 1	204416640	204416640	G	A	exonic	PIK3C2B	.	nonsynonymous SNV	PIK3C2B:NM_002646:exon16:c.C2413T:p.R805C	0.0003	6.478e-05	0.0002	0	0	0	0	0	0	rs749588530	.	0.128	0.269	T	0.006	0.126	B	0.003	0.080	B	0.089	0.205	N	0.893	0.360	D	0.895	0.225	L	-0.08	0.639	T	-1.17	0.314	N	0.181	0.274	-1.028	0.211	T	0.114	0.405	T	0.017	0.388	T	3.594	0.489	23.2	0.987	0.445	0.706	0.344	D	c	-0.463	-0.327	1.000	0.458	0.706	0.609	0	0.809	0.178	0.565	0.231	1.048	0.713	1.000	0.715	0.997	0.653	4.863	0.129	Armadillo-type fold|Phosphoinositide 3-kinase, accessory (PIK) domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	58	213	1	204416640	.	G	A	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3204;VD=2;AF=0.0006;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.00218;SOR=0.04384;LSEQ=GAGGCTGCCAAACTCATAGC;RSEQ=GGGGCTGAACTTGTCTCCAG;CSQ=A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|15/33||NM_001377334.1:c.2413C>T|NP_001364263.1:p.Arg805Cys|2947|2413|805|R/C|Cgc/Tgc|rs749588530&COSV65814770||-1||EntrezGene||||||1:g.204416640G>A|2.388e-05|0.0002462|2.892e-05|0|0|0|8.795e-06|0|0|0.0002462|gnomAD_AFR||0&1|0&1,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|17/36||NM_001377335.1:c.2413C>T|NP_001364264.1:p.Arg805Cys|3746|2413|805|R/C|Cgc/Tgc|rs749588530&COSV65814770||-1||EntrezGene||||||1:g.204416640G>A|2.388e-05|0.0002462|2.892e-05|0|0|0|8.795e-06|0|0|0.0002462|gnomAD_AFR||0&1|0&1,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|17/35||NM_002646.4:c.2413C>T|NP_002637.3:p.Arg805Cys|3746|2413|805|R/C|Cgc/Tgc|rs749588530&COSV65814770||-1||EntrezGene||YES||||1:g.204416640G>A|2.388e-05|0.0002462|2.892e-05|0|0|0|8.795e-06|0|0|0.0002462|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3204:2:1,1:1791,1408:3199,2:0.0006:2,2:40:1:37:0:1:1.27191:60:4:0.0006:0:1	0/1:213:3:2,1:116,94:210,3:0.0141:2,2:43.7:1:37:0:1:1.62:60:6:0.0145:0:1.3
    409. 

  409. 1	204418364	204418364	G	A	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon15:c.C2295T:p.S765S	0.14	0.0160	0.0250	0.0072	0.0033	0.1475	0.0003	0.0017	0.0041	rs17847754	rs17847754	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65809406;OCCURENCE=1(soft_tissue),1(lung)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	MU22235963	LICA-CN|1|402|0.00248756,LUSC-KR|2|170|0.0117647,COCA-CN|2|321|0.00623053	0.25	399	463	1	204418364	.	G	A	399	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=5471;VD=2645;AF=0.4835;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=TTAGGTGCACTCCAACGGGC;RSEQ=CTGGGATTTTCCTGTGTTGC;CSQ=A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|14/33||NM_001377334.1:c.2295C>T|NP_001364263.1:p.Ser765%3D|2829|2295|765|S|agC/agT|rs17847754&COSV65809406||-1||EntrezGene||||||1:g.204418364G>A|0.01702|0.02209|0.005027|0.005384|0.129|0.0009342|0.001364|0.008025|0.03597|0.129|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|16/36||NM_001377335.1:c.2295C>T|NP_001364264.1:p.Ser765%3D|3628|2295|765|S|agC/agT|rs17847754&COSV65809406||-1||EntrezGene||||||1:g.204418364G>A|0.01702|0.02209|0.005027|0.005384|0.129|0.0009342|0.001364|0.008025|0.03597|0.129|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|16/35||NM_002646.4:c.2295C>T|NP_002637.3:p.Ser765%3D|3628|2295|765|S|agC/agT|rs17847754&COSV65809406||-1||EntrezGene||YES||||1:g.204418364G>A|0.01702|0.02209|0.005027|0.005384|0.129|0.0009342|0.001364|0.008025|0.03597|0.129|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:5471:2645:1232,1413:1339,1479:2818,2645:0.4835:2,2:38.3:1:35.1:1:0.49781:1.03836:60:26.842:0.4777:0:1.1	0/0:463:0:0,0:223,240:463,0:0:2,0:40.2:1:36.4:1:1:0:60:114.75:1:0:0
    410. 

  410. 1	204419139	204419139	G	C	exonic	PIK3C2B	.	nonsynonymous SNV	PIK3C2B:NM_002646:exon14:c.C2073G:p.C691W	0.015	0.0002	0	0	0	0.0043	0	0	0	rs17847749	rs17847749	0.039	0.424	D	0.993	0.689	D	0.97	0.706	D	0.000	0.523	D	1.000	0.530	D	1.7	0.440	L	-1.02	0.763	T	-2.89	0.606	D	0.759	0.753	-0.221	0.771	T	0.367	0.728	T	.	.	.	5.678	0.774	26.7	0.994	0.624	0.901	0.507	D	c	0.384	0.371	1.000	0.747	0.615	0.372	0	4.83	0.617	1.317	0.330	0.902	0.416	1.000	0.715	0.998	0.697	7.344	0.257	C2 domain|Phosphatidylinositol 3-kinase, C2 domain	.	.	ID=COSV65809434;OCCURENCE=1(testis)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	MU82069386	COCA-CN|1|321|0.00311526	0.25	244	263	1	204419139	.	G	C	244	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2775;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGTTCACCTGCACTGGGAA;RSEQ=CAGATCCTATGGAGGACAGG;CSQ=C|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|13/33||NM_001377334.1:c.2073C>G|NP_001364263.1:p.Cys691Trp|2607|2073|691|C/W|tgC/tgG|rs17847749&COSV65809434||-1||EntrezGene||||||1:g.204419139G>C|0.0005988|0|0|0|0.007834|0|0|0.000215|4.212e-05|0.007834|gnomAD_EAS||0&1|0&1,C|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|15/36||NM_001377335.1:c.2073C>G|NP_001364264.1:p.Cys691Trp|3406|2073|691|C/W|tgC/tgG|rs17847749&COSV65809434||-1||EntrezGene||||||1:g.204419139G>C|0.0005988|0|0|0|0.007834|0|0|0.000215|4.212e-05|0.007834|gnomAD_EAS||0&1|0&1,C|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|15/35||NM_002646.4:c.2073C>G|NP_002637.3:p.Cys691Trp|3406|2073|691|C/W|tgC/tgG|rs17847749&COSV65809434||-1||EntrezGene||YES||||1:g.204419139G>C|0.0005988|0|0|0|0.007834|0|0|0.000215|4.212e-05|0.007834|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2775:0:0,0:1277,1497:2774,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:263:106:46,60:69,88:157,106:0.403:2,2:37.7:1:36.3:1:1:1.02265:60:34.333:0.4008:0:1.2
    411. 

  411. 1	204425028	204425028	G	A	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon12:c.C1899T:p.F633F	0.41	0.1695	0.0746	0.0668	0.1457	0.4098	0.1970	0.1963	0.2065	rs3765156	rs3765156	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65808813;OCCURENCE=1(breast),1(liver),1(large_intestine),1(stomach),1(haematopoietic_and_lymphoid_tissue),7(soft_tissue),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU145551	ESAD-UK|2|409|0.00488998,LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.5	248	122	1	204425028	.	G	A	248	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1017;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGTGGGTGGCATAGACAGT;RSEQ=AAGGCCAGGGACCTGGCGAA;CSQ=A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|11/33||NM_001377334.1:c.1899C>T|NP_001364263.1:p.Phe633%3D|2433|1899|633|F|ttC/ttT|rs3765156&COSV65808813||-1||EntrezGene||||||1:g.204425028G>A|0.1875|0.06537|0.06849|0.1474|0.4149|0.2049|0.1807|0.1803|0.2777|0.4149|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|13/36||NM_001377335.1:c.1899C>T|NP_001364264.1:p.Phe633%3D|3232|1899|633|F|ttC/ttT|rs3765156&COSV65808813||-1||EntrezGene||||||1:g.204425028G>A|0.1875|0.06537|0.06849|0.1474|0.4149|0.2049|0.1807|0.1803|0.2777|0.4149|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|13/35||NM_002646.4:c.1899C>T|NP_002637.3:p.Phe633%3D|3232|1899|633|F|ttC/ttT|rs3765156&COSV65808813||-1||EntrezGene||YES||||1:g.204425028G>A|0.1875|0.06537|0.06849|0.1474|0.4149|0.2049|0.1807|0.1803|0.2777|0.4149|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1017:0:0,0:618,399:1017,0:0:2,0:35.5:1:36.6:1:1:0:60:168.5:1:0:0.1	1/1:122:122:70,52:0,0:0,122:1:0,2:36.5:1:35.9:1:1:0:60:29.5:1:0:1
    412. 

  412. 1	204426853	204426853	T	G	intronic	PIK3C2B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	65	172	1	204426853	.	T	G	65	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1379;VD=22;AF=0.016;SHIFT3=4;MSI=1;MSILEN=1;SSF=0.32433;SOR=0.68111;LSEQ=GCTAGCACCCTGGGCCCCTT;RSEQ=ACCTTCTGAATTTTAGGCTG;CSQ=G|splice_donor_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||9/32|NM_001377334.1:c.1713+3A>C|||||||||-1||EntrezGene||||||1:g.204426853T>G||||||||||||||,G|splice_donor_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||11/35|NM_001377335.1:c.1713+3A>C|||||||||-1||EntrezGene||||||1:g.204426853T>G||||||||||||||,G|splice_donor_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||11/34|NM_002646.4:c.1713+3A>C|||||||||-1||EntrezGene||YES||||1:g.204426853T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1379:22:0,22:795,561:1356,22:0.016:2,1:33.1:1:14.7:1:0:0:60:0.294:0.0043:0:2.3	0/1:172:4:0,4:106,62:168,4:0.0233:2,0:32.2:1:24.5:1:0.02047:0:60:3:0.0207:0:1.2
    413. 

  413. 1	204428998	204428998	G	C	intronic	PIK3C2B	.	.	.	0.13	0.0156	0.0238	0.0119	0.0033	0.1456	0.0003	0.0015	0.0071	rs17847745	rs17847745	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65803404;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),1(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18049663	LICA-CN|1|402|0.00248756,LAML-KR|3|205|0.0146341,LUSC-KR|2|170|0.0117647,COCA-CN|2|321|0.00623053	0.25	367	295	1	204428998	.	G	C	367	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2384;VD=1116;AF=0.4681;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CAGGGCCAGCCCCTGGATTC;RSEQ=TACTCACATCAGCCAGCAGG;CSQ=C|splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||8/32|NM_001377334.1:c.1566+8C>G|||||||rs17847745&COSV65803404||-1||EntrezGene||||||1:g.204428998G>C|0.01782|0.02525|0.00932|0.005367|0.129|0.0009255|0.001286|0.008317|0.03608|0.129|gnomAD_EAS||0&1|0&1,C|splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||10/35|NM_001377335.1:c.1566+8C>G|||||||rs17847745&COSV65803404||-1||EntrezGene||||||1:g.204428998G>C|0.01782|0.02525|0.00932|0.005367|0.129|0.0009255|0.001286|0.008317|0.03608|0.129|gnomAD_EAS||0&1|0&1,C|splice_region_variant&intron_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||10/34|NM_002646.4:c.1566+8C>G|||||||rs17847745&COSV65803404||-1||EntrezGene||YES||||1:g.204428998G>C|0.01782|0.02525|0.00932|0.005367|0.129|0.0009255|0.001286|0.008317|0.03608|0.129|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2384:1116:573,543:641,627:1268,1116:0.4681:2,2:38.2:1:36.3:1:0.71187:1.03:60:84.846:0.4672:0:1.1	0/0:295:0:0,0:170,125:295,0:0:2,0:36.8:1:36.3:1:1:0:60:48.167:1:0:0.1
    414. 

  414. 1	204433093	204433093	A	C	intronic	PIK3C2B	.	.	.	0.82	0.6419	0.3453	0.7864	0.8179	0.3517	0.7838	0.7945	0.7388	rs2271415	rs2271415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65804266;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU14420293	LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235	0.25	360	172	1	204433093	.	A	C	360	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1839;VD=905;AF=0.4921;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TCCCATGAAGCCCCCTCACA;RSEQ=TCTTACTACCAGGAAGGCAG;CSQ=C|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||5/32|NM_001377334.1:c.1310+47T>G|||||||rs2271415&COSV65804266||-1||EntrezGene||||||1:g.204433093A>C|0.7225|0.3401|0.7984|0.8192|0.3799|0.7781|0.8084|0.7673|0.661|0.8192|gnomAD_ASJ||0&1|0&1,C|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||7/35|NM_001377335.1:c.1310+47T>G|||||||rs2271415&COSV65804266||-1||EntrezGene||||||1:g.204433093A>C|0.7225|0.3401|0.7984|0.8192|0.3799|0.7781|0.8084|0.7673|0.661|0.8192|gnomAD_ASJ||0&1|0&1,C|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||7/34|NM_002646.4:c.1310+47T>G|||||||rs2271415&COSV65804266||-1||EntrezGene||YES||||1:g.204433093A>C|0.7225|0.3401|0.7984|0.8192|0.3799|0.7781|0.8084|0.7673|0.661|0.8192|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1839:905:619,286:616,315:931,905:0.4921:2,2:33.6:1:36.7:1:0.31999:1.11:60:225.25:0.5011:0:1.1	0/0:172:0:0,0:124,48:172,0:0:2,0:33.8:1:34.7:1:1:0:60:20.5:1:0:0.1
    415. 

  415. 1	204433283	204433283	A	G	intronic	PIK3C2B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	283	1	204433283	.	A	G	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3366;VD=3;AF=0.0009;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00774;SOR=0.08339;LSEQ=GTGAAGGGTAAGGTAGGGGG;RSEQ=GCAATCATGATGGATGTCAA;CSQ=G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding||4/32|NM_001377334.1:c.1190-23T>C|||||||||-1||EntrezGene||||||1:g.204433283A>G||||||||||||||,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding||6/35|NM_001377335.1:c.1190-23T>C|||||||||-1||EntrezGene||||||1:g.204433283A>G||||||||||||||,G|intron_variant|MODIFIER|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding||6/34|NM_002646.4:c.1190-23T>C|||||||||-1||EntrezGene||YES||||1:g.204433283A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3366:3:1,2:1410,1951:3361,3:0.0009:2,2:23:1:37:0:1:1.44526:60:6:0.0009:0:1	0/1:283:3:1,2:113,167:280,3:0.0106:2,2:42.7:1:37:0:1:1.3519:60:6:0.0107:0:1
    416. 

  416. 1	204438334	204438334	C	T	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon3:c.G597A:p.P199P	0.98	0.7878	0.3585	0.8413	0.9636	0.7540	0.9648	0.9841	0.9265	rs1124777	rs1124777	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU17996773	COCA-CN|5|321|0.0155763	0.5	379	292	1	204438334	.	C	T	379	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3543;VD=1674;AF=0.4725;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.35019;SOR=1.05609;LSEQ=CGATGCTCTAGCAGTTTGCC;RSEQ=GGCAATTGTTCGACCAAAGA;CSQ=T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|2/33||NM_001377334.1:c.597G>A|NP_001364263.1:p.Pro199%3D|1131|597|199|P|ccG/ccA|rs1124777||-1||EntrezGene||||||1:g.204438334C>T|0.8984|0.3421|0.8596|0.9613|0.7845|0.9653|0.9842|0.9382|0.9153|0.9842|gnomAD_NFE|||,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|4/36||NM_001377335.1:c.597G>A|NP_001364264.1:p.Pro199%3D|1930|597|199|P|ccG/ccA|rs1124777||-1||EntrezGene||||||1:g.204438334C>T|0.8984|0.3421|0.8596|0.9613|0.7845|0.9653|0.9842|0.9382|0.9153|0.9842|gnomAD_NFE|||,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|4/35||NM_002646.4:c.597G>A|NP_002637.3:p.Pro199%3D|1930|597|199|P|ccG/ccA|rs1124777||-1||EntrezGene||YES||||1:g.204438334C>T|0.8984|0.3421|0.8596|0.9613|0.7845|0.9653|0.9842|0.9382|0.9153|0.9842|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3543:1674:873,801:946,915:1861,1674:0.4725:2,2:38.4:1:35.4:1:0.43844:1.05:60:27.373:0.4665:0:1.1	0/1:292:134:72,62:87,69:156,134:0.4589:2,2:39.1:1:36.1:1:0.81297:1.08544:60:43.667:0.458:0:1.1
    417. 

  417. 1	204438643	204438643	G	T	exonic	PIK3C2B	.	synonymous SNV	PIK3C2B:NM_002646:exon3:c.C288A:p.L96L	0.98	0.7869	0.3551	0.8405	0.9636	0.7531	0.9645	0.9840	0.9264	rs1553921	rs1553921	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU17996820	COCA-CN|5|321|0.0155763	0.5	364	460	1	204438643	.	G	T	364	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3673;VD=1769;AF=0.4816;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.33069;SOR=1.04954;LSEQ=GGCGGCCCTTCCTGTGGGGA;RSEQ=AGTGAGTTGTAGTTAAGGGT;CSQ=T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|2/33||NM_001377334.1:c.288C>A|NP_001364263.1:p.Leu96%3D|822|288|96|L|ctC/ctA|rs1553921||-1||EntrezGene||||||1:g.204438643G>T|0.8967|0.3405|0.8588|0.9606|0.7844|0.9652|0.9838|0.9378|0.9139|0.9841|EUR|||,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|4/36||NM_001377335.1:c.288C>A|NP_001364264.1:p.Leu96%3D|1621|288|96|L|ctC/ctA|rs1553921||-1||EntrezGene||||||1:g.204438643G>T|0.8967|0.3405|0.8588|0.9606|0.7844|0.9652|0.9838|0.9378|0.9139|0.9841|EUR|||,T|synonymous_variant|LOW|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|4/35||NM_002646.4:c.288C>A|NP_002637.3:p.Leu96%3D|1621|288|96|L|ctC/ctA|rs1553921||-1||EntrezGene||YES||||1:g.204438643G>T|0.8967|0.3405|0.8588|0.9606|0.7844|0.9652|0.9838|0.9378|0.9139|0.9841|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3673:1769:829,940:892,1006:1898,1769:0.4816:2,2:37.5:1:33.8:1:0.94721:1.0054:60:12.504:0.4651:0:1.1	0/1:460:216:88,128:105,138:243,216:0.4696:2,2:39.7:1:34.2:1:0.63604:1.10647:60:15.615:0.4552:0:1.1
    418. 

  418. 1	204438916	204438916	C	A	exonic	PIK3C2B	.	nonsynonymous SNV	PIK3C2B:NM_002646:exon3:c.G15T:p.Q5H	.	.	.	.	.	.	.	.	.	.	.	0.005	0.632	D	0.828	0.441	P	0.471	0.450	P	0.051	0.230	N	0.914	0.274	N	0.695	0.181	N	0.07	0.617	T	-1.17	0.765	N	0.277	0.358	-1.014	0.256	T	0.110	0.397	T	0.021	0.443	T	3.037	0.425	22.3	0.853	0.153	0.937	0.586	D	c	-0.025	0.058	0.998	0.361	0.707	0.730	0	3.3	0.368	0.731	0.255	0.852	0.362	1.000	0.715	1.000	0.888	5.502	0.160	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	62	1	204438916	.	C	A	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=489;VD=1;AF=0.002;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03471;SOR=0.06211;LSEQ=TTCCAGTGTTCCCCATTGCC;RSEQ=TGAGTCGAAGACATGGTGAG;CSQ=A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377334.1|protein_coding|2/33||NM_001377334.1:c.15G>T|NP_001364263.1:p.Gln5His|549|15|5|Q/H|caG/caT|||-1||EntrezGene||||||1:g.204438916C>A||||||||||||||,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_001377335.1|protein_coding|4/36||NM_001377335.1:c.15G>T|NP_001364264.1:p.Gln5His|1348|15|5|Q/H|caG/caT|||-1||EntrezGene||||||1:g.204438916C>A||||||||||||||,A|missense_variant|MODERATE|PIK3C2B|5287|Transcript|NM_002646.4|protein_coding|4/35||NM_002646.4:c.15G>T|NP_002637.3:p.Gln5His|1348|15|5|Q/H|caG/caT|||-1||EntrezGene||YES||||1:g.204438916C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:489:1:1,0:147,341:488,1:0.002:2,0:56:0:11:0:0.30266:0:60:0:0:0:3	0/1:62:2:1,1:21,39:60,2:0.0323:2,2:49.5:1:37:0:1:1.84:60:4:0.0323:0:1
    419. 

  419. 1	204494635	204494635	T	C	UTR5	MDM4	NM_002393:c.-12T>C;NM_001278516:c.-12T>C;NM_001278517:c.-12T>C;NM_001278518:c.-12T>C;NM_001204172:c.-12T>C;NM_001204171:c.-12T>C;NM_001278519:c.-12T>C	.	.	0.0002	.	.	.	.	.	.	.	.	rs373702394	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	95	1	204494635	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=2;AF=0.0256;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.20184;SOR=inf;LSEQ=TACCAACAGACTGCAGTTTC;RSEQ=TCACTACCAAAATGACATCA;CSQ=C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding|2/10||NM_001204171.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding|2/3||NM_001204172.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding|2/10||NM_001278516.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding|2/8||NM_001278517.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding|2/7||NM_001278518.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding|2/5||NM_001278519.2:c.-12T>C||128|||||rs373702394||1||EntrezGene||||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||,C|5_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding|2/11||NM_002393.5:c.-12T>C||128|||||rs373702394||1||EntrezGene||YES||||1:g.204494635T>C|4.304e-06|6.285e-05|0|0|0|0|0|0|0|0.000227|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:78:2:1,1:44,32:76,2:0.0256:2,2:54:0:37:0:1:1.36929:60:4:0.027:0:1.5	0/0:95:0:0,0:55,40:95,0:0:2,0:40.3:1:35.3:1:1:0:60:30.667:1:0:0.2
    420. 

  420. 1	204495508	204495508	T	C	exonic	MDM4	.	synonymous SNV	MDM4:NM_001204171:exon3:c.T99C:p.L33L,MDM4:NM_001278516:exon3:c.T99C:p.L33L,MDM4:NM_001278518:exon3:c.T99C:p.L33L,MDM4:NM_001278519:exon3:c.T99C:p.L33L,MDM4:NM_002393:exon3:c.T99C:p.L33L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	148	1	204495508	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=295;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=GTACGACCAAAACTGCCGCT;RSEQ=TTGAAGATTTTGCATGCAGC;CSQ=C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001204171.2|protein_coding|3/10||NM_001204171.2:c.99T>C|NP_001191100.1:p.Leu33%3D|238|99|33|L|ctT/ctC|||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.78+784T>C|||||||||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278516.2|protein_coding|3/10||NM_001278516.2:c.99T>C|NP_001265445.1:p.Leu33%3D|238|99|33|L|ctT/ctC|||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.78+784T>C|||||||||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278518.2|protein_coding|3/7||NM_001278518.2:c.99T>C|NP_001265447.1:p.Leu33%3D|238|99|33|L|ctT/ctC|||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278519.2|protein_coding|3/5||NM_001278519.2:c.99T>C|NP_001265448.1:p.Leu33%3D|238|99|33|L|ctT/ctC|||1||EntrezGene||||||1:g.204495508T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_002393.5|protein_coding|3/11||NM_002393.5:c.99T>C|NP_002384.2:p.Leu33%3D|238|99|33|L|ctT/ctC|||1||EntrezGene||YES||||1:g.204495508T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:295:0:0,0:137,158:295,0:0:2,0:42.9:1:34.5:1:1:0:60:17.438:1:0:0.3	0/1:148:2:1,1:75,71:146,2:0.0135:2,2:53.5:1:31:1:1:1.05597:60:4:0.0143:0:1
    421. 

  421. 1	204499762	204499762	T	-	intronic	MDM4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	152	1	204499761	.	GT	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=154;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.24592;SOR=0;LSEQ=ACCTCCTCTAATGAATTTGT;RSEQ=TTTTGGTAGCAGCTGGACAG;CSQ=-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||3/9|NM_001204171.2:c.154-46del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.78+5042del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||3/9|NM_001278516.2:c.154-46del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.78+5042del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||3/6|NM_001278518.2:c.154-46del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.153+4204del|||||||||1||EntrezGene||||||1:g.204499766del||||||||||||||,-|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding||3/10|NM_002393.5:c.154-46del|||||||||1||EntrezGene||YES||||1:g.204499766del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:154:0:0,0:112,42:154,0:0:2,0:33.1:1:36.1:1:1:0:60:76:1:0:0.1	0/1:152:2:1,1:124,26:150,2:0.0132:2,2:37:0:37:0:0.32468:4.69895:60:4:0.0132:0:0
    422. 

  422. 1	204501287	204501287	G	A	intronic	MDM4	.	.	.	0.0099	0.0005	0.0001	0	0	0.0099	0	0	0	rs137991330	rs137991330	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	175	53	1	204501287	.	G	A	175	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02011;SOR=0;LSEQ=TCTTCATAGTGGCATTTGGG;RSEQ=TTGTTAATTTTTTATCTTCT;CSQ=A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||4/9|NM_001204171.2:c.288-32G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.78+6563G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||4/9|NM_001278516.2:c.288-32G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.79-5300G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||4/6|NM_001278518.2:c.288-32G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.153+5725G>A|||||||rs137991330||1||EntrezGene||||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding||4/10|NM_002393.5:c.288-32G>A|||||||rs137991330||1||EntrezGene||YES||||1:g.204501287G>A|0.0006491|0|0.0003045|0|0.007943|0|1.787e-05|0.0003358|6.875e-05|0.0099|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:4,2:6,0:0:2,0:34.3:1:37:0:1:0:60:12:1:0:0.2	1/0:53:27:21,6:21,5:26,27:0.5094:2,2:36.8:1:37:0:1:1.19588:60:54:0.5294:0:1.6
    423. 

  423. 1	204501383	204501383	C	T	intronic	MDM4	.	.	.	0.4	0.1771	0.0792	0.0859	0.1987	0.3660	0.2064	0.2104	0.1986	rs4252697	rs4252697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65797201;OCCURENCE=1(breast),8(meninges),2(haematopoietic_and_lymphoid_tissue),4(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11368138	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.25	207	104	1	204501383	.	C	T	207	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.00711;SOR=0;LSEQ=CTGCTACTACAGGTATGTCA;RSEQ=ATCATATTTCTTCAGTCTGT;CSQ=T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||5/9|NM_001204171.2:c.343+9C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.78+6659C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||5/9|NM_001278516.2:c.343+9C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.79-5204C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.343+9C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.153+5821C>T|||||||rs4252697&COSV65797201||1||EntrezGene||||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding||5/10|NM_002393.5:c.343+9C>T|||||||rs4252697&COSV65797201||1||EntrezGene||YES||||1:g.204501383C>T|0.1871|0.07445|0.07147|0.1736|0.389|0.2183|0.1936|0.178|0.2154|0.4018|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:38.8:1:37:0:1:0:60:16:1:0:0.1	0/1:104:50:23,27:31,23:54,50:0.4808:2,2:41.4:1:36.8:1:0.32618:1.57516:60:100:0.5102:0:1.3
    424. 

  424. 1	204506538	204506538	T	C	intronic	MDM4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	175	1	204506538	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=828;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.0303;SOR=0;LSEQ=TACCAGGGAAGGTTTTCCTT;RSEQ=TGTTTTACTTGCTATCCAGA;CSQ=C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||5/9|NM_001204171.2:c.344-20T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.78+11814T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||5/9|NM_001278516.2:c.344-799T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.79-49T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.343+5164T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-9387T>C|||||||||1||EntrezGene||||||1:g.204506538T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding||5/10|NM_002393.5:c.344-20T>C|||||||||1||EntrezGene||YES||||1:g.204506538T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:828:0:0,0:487,341:828,0:0:2,0:38.9:1:35.2:1:1:0:60:24.091:1:0:0.1	0/1:175:2:1,1:103,70:173,2:0.0114:2,2:18.5:1:37:0:1:1.46807:60:4:0.0116:0:1
    425. 

  425. 1	204506581	204506581	G	A	exonic	MDM4	.	nonsynonymous SNV	MDM4:NM_001204171:exon6:c.G367A:p.A123T,MDM4:NM_002393:exon6:c.G367A:p.A123T	0.0001	3.231e-05	0	0	0	0	0.0003	0	0	rs145156544	rs145156544	0.302	0.302	T	0.865	0.456	P	0.129	0.312	B	0.000	0.629	D	1.000	0.810	D	1.74	0.453	L	1.48	0.320	T	-0.21	0.103	N	0.422	0.546	-1.084	0.067	T	0.055	0.232	T	0.009	0.234	T	3.192	0.443	22.7	0.996	0.759	0.954	0.641	D	c	0.263	0.371	1.000	0.747	0.707	0.730	0	5.27	0.737	5.121	0.643	1.048	0.713	1.000	0.715	1.000	0.888	16.702	0.851	.	.	.	ID=COSV65796819;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),2(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU1921166	UCEC-US|2|531|0.00376648,LAML-US|1|139|0.00719424	0.25	58	211	1	204506581	.	G	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1009;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=6;SSF=0.00511;SOR=0;LSEQ=CTGCTCAGACTCTCGCTCTC;RSEQ=CACAGGATCACAGTATGGAT;CSQ=A|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001204171.2|protein_coding|6/10||NM_001204171.2:c.367G>A|NP_001191100.1:p.Ala123Thr|506|367|123|A/T|Gca/Aca|rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-11813G>A|||||||rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||5/9|NM_001278516.2:c.344-756G>A|||||||rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MDM4|4194|Transcript|NM_001278517.2|protein_coding||2/7|NM_001278517.2:c.79-6G>A|||||||rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.343+5207G>A|||||||rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-9344G>A|||||||rs145156544&COSV65796819||1||EntrezGene||||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1,A|missense_variant|MODERATE|MDM4|4194|Transcript|NM_002393.5|protein_coding|6/11||NM_002393.5:c.367G>A|NP_002384.2:p.Ala123Thr|506|367|123|A/T|Gca/Aca|rs145156544&COSV65796819||1||EntrezGene||YES||||1:g.204506581G>A|7.957e-06|0|0|0|0|0|1.759e-05|0|0|0.0001163|EA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1009:0:0,0:517,491:1008,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:211:3:1,2:108,100:208,3:0.0142:2,2:28.3:1:37:0:0.61102:2.15239:60:6:0.0145:0:1
    426. 

  426. 1	204507394	204507394	A	G	exonic	MDM4	.	nonsynonymous SNV	MDM4:NM_001278517:exon4:c.A175G:p.T59A,MDM4:NM_001278516:exon6:c.A401G:p.H134R,MDM4:NM_001204171:exon7:c.A469G:p.T157A,MDM4:NM_002393:exon7:c.A469G:p.T157A	.	.	.	.	.	.	.	.	.	rs555716350	.	0.807	0.143	T	0.0	0.026	B	0.0	0.013	B	0.424	0.128	N	1	0.090	N	1.185	0.302	L	1.57	0.421	T	-0.64	0.197	N	0.026	0.074	-1.008	0.275	T	0.061	0.255	T	0.007	0.187	T	-1.792	0.011	0.002	0.345	0.021	0.027	0.072	N	c	-0.976	-0.948	0.936	0.272	0.707	0.730	0	-0.854	0.101	0.213	0.172	0.195	0.250	0.000	0.063	0.252	0.228	10.327	0.428	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	146	1	204507394	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=330;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.09363;SOR=0;LSEQ=CTACAGAAGACGATATCCCC;RSEQ=CACTGCCTACCTCAGAGCAT;CSQ=G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001204171.2|protein_coding|7/10||NM_001204171.2:c.469A>G|NP_001191100.1:p.Thr157Ala|608|469|157|T/A|Aca/Gca|rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-11000A>G|||||||rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001278516.2|protein_coding|6/10||NM_001278516.2:c.401A>G|NP_001265445.1:p.His134Arg|540|401|134|H/R|cAc/cGc|rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001278517.2|protein_coding|4/8||NM_001278517.2:c.175A>G|NP_001265446.1:p.Thr59Ala|314|175|59|T/A|Aca/Gca|rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.343+6020A>G|||||||rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-8531A>G|||||||rs555716350||1||EntrezGene||||||1:g.204507394A>G||||||||||||||,G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_002393.5|protein_coding|7/11||NM_002393.5:c.469A>G|NP_002384.2:p.Thr157Ala|608|469|157|T/A|Aca/Gca|rs555716350||1||EntrezGene||YES||||1:g.204507394A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:330:0:0,0:110,220:330,0:0:2,0:33.7:1:35.5:1:1:0:60:29:1:0:0.1	0/1:146:2:1,1:63,81:144,2:0.0137:2,2:9:0:31:1:1:1.28:60:4:0.0139:0:1
    427. 

  427. 1	204507426	204507426	T	C	exonic	MDM4	.	synonymous SNV	MDM4:NM_001278517:exon4:c.T207C:p.H69H,MDM4:NM_001204171:exon7:c.T501C:p.H167H,MDM4:NM_002393:exon7:c.T501C:p.H167H	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	74	127	1	204507426	.	T	C	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=194;VD=4;AF=0.0206;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13177;SOR=inf;LSEQ=TCAGAGCATAAATGCATACA;RSEQ=TCTAGAGAAGGTATGTTTTG;CSQ=C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001204171.2|protein_coding|7/10||NM_001204171.2:c.501T>C|NP_001191100.1:p.His167%3D|640|501|167|H|caT/caC|||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-10968T>C|||||||||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|3_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding|6/10||NM_001278516.2:c.*10T>C||572|||||||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278517.2|protein_coding|4/8||NM_001278517.2:c.207T>C|NP_001265446.1:p.His69%3D|346|207|69|H|caT/caC|||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.343+6052T>C|||||||||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-8499T>C|||||||||1||EntrezGene||||||1:g.204507426T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_002393.5|protein_coding|7/11||NM_002393.5:c.501T>C|NP_002384.2:p.His167%3D|640|501|167|H|caT/caC|||1||EntrezGene||YES||||1:g.204507426T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:194:4:2,2:42,148:190,4:0.0206:2,2:35.5:1:37:0:0.22188:3.49:60:8:0.0214:0:1	0/0:127:0:0,0:53,73:126,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    428. 

  428. 1	204512062	204512062	A	G	exonic	MDM4	.	nonsynonymous SNV	MDM4:NM_001278517:exon5:c.A368G:p.Q123R,MDM4:NM_001204171:exon8:c.A662G:p.Q221R,MDM4:NM_002393:exon8:c.A662G:p.Q221R	.	.	.	.	.	.	.	.	.	.	.	0.033	0.599	D	0.995	0.657	D	0.844	0.586	P	0.000	0.629	D	0.980	0.810	D	2.48	0.723	M	2.97	0.095	T	-1.51	0.412	N	0.095	0.143	-1.134	0.016	T	0.048	0.207	T	0.013	0.330	T	2.574	0.371	19.94	0.994	0.625	0.982	0.807	D	c	0.363	0.346	1.000	0.489	0.707	0.730	0	4.91	0.638	5.541	0.667	1.199	0.960	1.000	0.715	1.000	0.888	10.607	0.444	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	233	1	204512062	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=2;AF=0.0476;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02285;SOR=inf;LSEQ=TAATGGCTCAACTGATTTAC;RSEQ=GACAAATCAGGTAAATTTCA;CSQ=G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001204171.2|protein_coding|8/10||NM_001204171.2:c.662A>G|NP_001191100.1:p.Gln221Arg|801|662|221|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-6332A>G|||||||||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|3_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding|7/10||NM_001278516.2:c.*171A>G||733|||||||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_001278517.2|protein_coding|5/8||NM_001278517.2:c.368A>G|NP_001265446.1:p.Gln123Arg|507|368|123|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.344-3863A>G|||||||||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-3863A>G|||||||||1||EntrezGene||||||1:g.204512062A>G||||||||||||||,G|missense_variant|MODERATE|MDM4|4194|Transcript|NM_002393.5|protein_coding|8/11||NM_002393.5:c.662A>G|NP_002384.2:p.Gln221Arg|801|662|221|Q/R|cAg/cGg|||1||EntrezGene||YES||||1:g.204512062A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:42:2:1,1:18,22:40,2:0.0476:2,2:16.5:1:37:0:1:1.22:60:4:0.0476:0:1	0/0:233:0:0,0:78,155:233,0:0:2,0:36.6:1:36.9:1:1:0:60:466:1:0:0.5
    429. 

  429. 1	204512100	204512100	T	C	intronic	MDM4	.	.	.	0.79	0.5961	0.2859	0.5957	0.6225	0.6482	0.7934	0.7178	0.6888	rs4252717	rs4252717	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65794912;OCCURENCE=17(soft_tissue),2(lung),1(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU23413008	LUSC-KR|2|170|0.0117647,COCA-CN|4|321|0.0124611	0.5	220	148	1	204512100	.	T	C	220	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=11;AF=0.6111;SHIFT3=0;MSI=8;MSILEN=1;SSF=0.21127;SOR=1.69878;LSEQ=TCACATTTGAAGGGAAGTGG;RSEQ=TTTTTTTCTTTTGAAAGGGT;CSQ=C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||8/9|NM_001204171.2:c.672+28T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-6294T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding||7/9|NM_001278516.2:c.*181+28T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278517.2|protein_coding||5/7|NM_001278517.2:c.378+28T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.344-3825T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-3825T>C|||||||rs4252717&COSV65794912||1||EntrezGene||||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_002393.5|protein_coding||8/10|NM_002393.5:c.672+28T>C|||||||rs4252717&COSV65794912||1||EntrezGene||YES||||1:g.204512100T>C|0.6491|0.2726|0.6248|0.6259|0.6896|0.7989|0.6903|0.6461|0.5971|0.7989|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:18:11:5,6:2,5:7,11:0.6111:2,2:28:1:37:0:0.63707:2:60:22:0.6111:0:1	0/1:148:71:18,53:16,60:76,71:0.4797:2,2:39.8:1:35.8:1:0.56261:1.27:60:34.5:0.4859:0:1.2
    430. 

  430. 1	204513767	204513767	T	C	exonic	MDM4	.	synonymous SNV	MDM4:NM_001278517:exon6:c.T483C:p.D161D,MDM4:NM_002393:exon9:c.T777C:p.D259D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	194	1	204513767	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.93139;SOR=0;LSEQ=ATAAAAGTTGAAGCTGCTGA;RSEQ=ACTGAACAAACAAGTGAAGA;CSQ=C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204171.2|protein_coding||8/9|NM_001204171.2:c.672+1695T>C|||||||||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-4627T>C|||||||||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|3_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding|8/10||NM_001278516.2:c.*286T>C||848|||||||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278517.2|protein_coding|6/8||NM_001278517.2:c.483T>C|NP_001265446.1:p.Asp161%3D|622|483|161|D|gaT/gaC|||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding||5/6|NM_001278518.2:c.344-2158T>C|||||||||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001278519.2|protein_coding||3/4|NM_001278519.2:c.154-2158T>C|||||||||1||EntrezGene||||||1:g.204513767T>C||||||||||||||,C|synonymous_variant|LOW|MDM4|4194|Transcript|NM_002393.5|protein_coding|9/11||NM_002393.5:c.777T>C|NP_002384.2:p.Asp259%3D|916|777|259|D|gaT/gaC|||1||EntrezGene||YES||||1:g.204513767T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:5,2:7,0:0:2,0:34:1:37:0:1:0:60:14:1:0:0	0/1:194:2:1,1:99,93:192,2:0.0103:2,2:37:1:37:0:1:1.06421:60:4:0.0103:0:1
    431. 

  431. 1	204515960	204515960	C	T	exonic	MDM4	.	synonymous SNV	MDM4:NM_001278519:exon4:c.C189T:p.D63D,MDM4:NM_001278517:exon7:c.C564T:p.D188D,MDM4:NM_001204171:exon9:c.C708T:p.D236D,MDM4:NM_002393:exon10:c.C858T:p.D286D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	189	1	204515960	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=83;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.48204;SOR=0;LSEQ=AAAAATGATGACCTGGAGGA;RSEQ=TCTAAGTCCTTAAGTGATGA;CSQ=T|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001204171.2|protein_coding|9/10||NM_001204171.2:c.708C>T|NP_001191100.1:p.Asp236%3D|847|708|236|D|gaC/gaT|||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|intron_variant|MODIFIER|MDM4|4194|Transcript|NM_001204172.2|protein_coding||2/2|NM_001204172.2:c.79-2434C>T|||||||||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|3_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278516.2|protein_coding|9/10||NM_001278516.2:c.*367C>T||929|||||||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278517.2|protein_coding|7/8||NM_001278517.2:c.564C>T|NP_001265446.1:p.Asp188%3D|703|564|188|D|gaC/gaT|||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|3_prime_UTR_variant|MODIFIER|MDM4|4194|Transcript|NM_001278518.2|protein_coding|6/7||NM_001278518.2:c.*28C>T||518|||||||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|synonymous_variant|LOW|MDM4|4194|Transcript|NM_001278519.2|protein_coding|4/5||NM_001278519.2:c.189C>T|NP_001265448.1:p.Asp63%3D|328|189|63|D|gaC/gaT|||1||EntrezGene||||||1:g.204515960C>T||||||||||||||,T|synonymous_variant|LOW|MDM4|4194|Transcript|NM_002393.5|protein_coding|10/11||NM_002393.5:c.858C>T|NP_002384.2:p.Asp286%3D|997|858|286|D|gaC/gaT|||1||EntrezGene||YES||||1:g.204515960C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:83:0:0,0:53,30:83,0:0:2,0:40:1:36.9:1:1:0:60:166:1:0:0.5	0/1:189:2:1,1:99,88:187,2:0.0106:2,2:37.5:1:37:0:1:1.1243:60:4:0.0106:0:2
    432. 

  432. 1	206646651	206646651	C	T	exonic	IKBKE	.	synonymous SNV	IKBKE:NM_001193322:exon3:c.C81T:p.R27R,IKBKE:NM_014002:exon3:c.C81T:p.R27R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	184	1	206646651	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2434;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00491;SOR=0;LSEQ=GCCAGTGTGTACAAGGCCCG;RSEQ=AACAAGGTAGGAAGCAACCC;CSQ=T|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding||2/20|NM_001193321.2:c.-168-1023C>T|||||||||1||EntrezGene||||||1:g.206646651C>T||||||||||||||,T|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_001193322.2|protein_coding|3/21||NM_001193322.2:c.81C>T|NP_001180251.1:p.Arg27%3D|426|81|27|R|cgC/cgT|||1||EntrezGene||||||1:g.206646651C>T||||||||||||||,T|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_014002.4|protein_coding|3/22||NM_014002.4:c.81C>T|NP_054721.1:p.Arg27%3D|426|81|27|R|cgC/cgT|||1||EntrezGene||YES||||1:g.206646651C>T||||||||||||||,T|upstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA|||||||||||1495|1||EntrezGene||YES||||1:g.206646651C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2434:0:0,0:1048,1385:2433,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:184:2:1,1:79,103:182,2:0.0109:2,2:62:1:37:0:1:1.3:60:4:0.0109:0:1
    433. 

  433. 1	206647742	206647742	A	G	exonic	IKBKE	.	synonymous SNV	IKBKE:NM_001193322:exon4:c.A156G:p.Q52Q,IKBKE:NM_014002:exon4:c.A156G:p.Q52Q	1.	0.9985	0.9998	0.9988	1	1	0.9991	0.9974	0.9980	rs1539242	rs1539242	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65626479;OCCURENCE=1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4564045	COCA-CN|5|321|0.0155763	1	447	343	1	206647742	.	A	G	447	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4698;VD=4687;AF=0.9977;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.46027;SOR=0;LSEQ=CTGCGGCCCCGCGAGGTGCA;RSEQ=GTGAGGGAGTTTGAGGTCCT;CSQ=G|5_prime_UTR_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding|3/21||NM_001193321.2:c.-100A>G||382|||||rs1539242&COSV65626479||1||EntrezGene||||||1:g.206647742A>G|0.9985|0.9997|0.9988|0.9999|1|0.9994|0.9975|0.9985|0.9992|1|AFR&AMR&EAS&SAS&AA&gnomAD_EAS||0&1|0&1,G|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_001193322.2|protein_coding|4/21||NM_001193322.2:c.156A>G|NP_001180251.1:p.Gln52%3D|501|156|52|Q|caA/caG|rs1539242&COSV65626479||1||EntrezGene||||||1:g.206647742A>G|0.9985|0.9997|0.9988|0.9999|1|0.9994|0.9975|0.9985|0.9992|1|AFR&AMR&EAS&SAS&AA&gnomAD_EAS||0&1|0&1,G|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_014002.4|protein_coding|4/22||NM_014002.4:c.156A>G|NP_054721.1:p.Gln52%3D|501|156|52|Q|caA/caG|rs1539242&COSV65626479||1||EntrezGene||YES||||1:g.206647742A>G|0.9985|0.9997|0.9988|0.9999|1|0.9994|0.9975|0.9985|0.9992|1|AFR&AMR&EAS&SAS&AA&gnomAD_EAS||0&1|0&1,G|upstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA||||||||||rs1539242&COSV65626479|404|1||EntrezGene||YES||||1:g.206647742A>G|0.9985|0.9997|0.9988|0.9999|1|0.9994|0.9975|0.9985|0.9992|1|AFR&AMR&EAS&SAS&AA&gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4698:4687:2452,2235:0,0:0,4687:0.9977:0,2:39.7:1:36.7:1:1:0:60:186.48:0.9987:0:1.8	1/1:343:343:182,161:0,0:0,343:1:0,2:39.8:1:36.7:1:1:0:60:170.5:1:0:1.8
    434. 

  434. 1	206647787	206647787	T	C	exonic	IKBKE	.	synonymous SNV	IKBKE:NM_001193322:exon4:c.T201C:p.I67I,IKBKE:NM_014002:exon4:c.T201C:p.I67I	0.98	0.8525	0.8711	0.9129	0.7947	0.9846	0.8333	0.8311	0.8299	rs1539243	rs1539243	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU81719582	COCA-CN|5|321|0.0155763	1	445	333	1	206647787	.	T	C	445	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4656;VD=4646;AF=0.9979;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.50086;SOR=0;LSEQ=AAGCTGAACCACCAGAACAT;RSEQ=GTCAAGCTCTTTGCGGTGGA;CSQ=C|5_prime_UTR_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding|3/21||NM_001193321.2:c.-55T>C||427|||||rs1539243||1||EntrezGene||||||1:g.206647787T>C|0.8613|0.8701|0.9298|0.7767|0.9774|0.8298|0.8327|0.8434|0.8695|0.9774|gnomAD_EAS|||,C|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_001193322.2|protein_coding|4/21||NM_001193322.2:c.201T>C|NP_001180251.1:p.Ile67%3D|546|201|67|I|atT/atC|rs1539243||1||EntrezGene||||||1:g.206647787T>C|0.8613|0.8701|0.9298|0.7767|0.9774|0.8298|0.8327|0.8434|0.8695|0.9774|gnomAD_EAS|||,C|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_014002.4|protein_coding|4/22||NM_014002.4:c.201T>C|NP_054721.1:p.Ile67%3D|546|201|67|I|atT/atC|rs1539243||1||EntrezGene||YES||||1:g.206647787T>C|0.8613|0.8701|0.9298|0.7767|0.9774|0.8298|0.8327|0.8434|0.8695|0.9774|gnomAD_EAS|||,C|upstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA||||||||||rs1539243|359|1||EntrezGene||YES||||1:g.206647787T>C|0.8613|0.8701|0.9298|0.7767|0.9774|0.8298|0.8327|0.8434|0.8695|0.9774|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4656:4646:2125,2521:1,0:1,4646:0.9979:0,2:39.1:1:36.6:1:0.4575:0:60:148.871:0.9983:0:1.8	1/1:333:333:142,191:0,0:0,333:1:0,2:39:1:36.1:1:1:0:60:32.3:1:0:1.9
    435. 

  435. 1	206647861	206647861	T	C	intronic	IKBKE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	180	1	206647861	.	T	C	25	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2429;VD=0;AF=0;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.00474;SOR=0;LSEQ=GGTCTTGTCCTTGACCCTTA;RSEQ=GGTCTGGGGAGAATCAGGCC;CSQ=C|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding||3/20|NM_001193321.2:c.-28+47T>C|||||||rs1214242152||1||EntrezGene||||||1:g.206647861T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193322.2|protein_coding||4/20|NM_001193322.2:c.228+47T>C|||||||rs1214242152||1||EntrezGene||||||1:g.206647861T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_014002.4|protein_coding||4/21|NM_014002.4:c.228+47T>C|||||||rs1214242152||1||EntrezGene||YES||||1:g.206647861T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,C|upstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA||||||||||rs1214242152|285|1||EntrezGene||YES||||1:g.206647861T>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2429:0:0,0:866,1562:2428,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:180:2:1,1:59,119:178,2:0.0111:2,2:50:1:25:0:1:2.01:60:4:0.0116:0:2.5
    436. 

  436. 1	206648378	206648378	G	A	intronic	IKBKE	.	.	.	0.69	0.5826	0.4100	0.6563	0.6026	0.3383	0.6396	0.6883	0.6258	rs1059704	rs1059704	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65624186;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),20(soft_tissue),2(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU675344	LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|1|321|0.00311526	0.25	246	216	1	206648378	.	G	A	246	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1556;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTCCACCCTCAGACCAGC;RSEQ=GCAGGCCTGGGACAGATGCT;CSQ=A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding||4/20|NM_001193321.2:c.103+41G>A|||||||rs1059704&COSV65624186||1||EntrezGene||||||1:g.206648378G>A|0.6222|0.4025|0.6403|0.627|0.334|0.6362|0.6813|0.6306|0.6611|0.6881|EA||0&1|0&1,A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193322.2|protein_coding||5/20|NM_001193322.2:c.358+41G>A|||||||rs1059704&COSV65624186||1||EntrezGene||||||1:g.206648378G>A|0.6222|0.4025|0.6403|0.627|0.334|0.6362|0.6813|0.6306|0.6611|0.6881|EA||0&1|0&1,A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_014002.4|protein_coding||5/21|NM_014002.4:c.358+41G>A|||||||rs1059704&COSV65624186||1||EntrezGene||YES||||1:g.206648378G>A|0.6222|0.4025|0.6403|0.627|0.334|0.6362|0.6813|0.6306|0.6611|0.6881|EA||0&1|0&1,A|downstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA||||||||||rs1059704&COSV65624186|171|1||EntrezGene||YES||||1:g.206648378G>A|0.6222|0.4025|0.6403|0.627|0.334|0.6362|0.6813|0.6306|0.6611|0.6881|EA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1556:0:0,0:496,1060:1556,0:0:2,0:34.2:1:36.7:1:1:0:60:193.5:1:0:0.1	0/1:216:102:35,67:38,76:114,102:0.4722:2,2:38.6:1:36.9:1:0.88652:1.04:60:204:0.4722:0:1
    437. 

  437. 1	206651107	206651107	G	A	exonic	IKBKE	.	synonymous SNV	IKBKE:NM_001193321:exon7:c.G462A:p.T154T,IKBKE:NM_001193322:exon8:c.G717A:p.T239T,IKBKE:NM_014002:exon8:c.G717A:p.T239T	0.68	0.2324	0.1714	0.3493	0.2252	0.6378	0.2370	0.2155	0.2480	rs2297545	rs2297545	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV65624190;OCCURENCE=9(soft_tissue),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4564039	ESAD-UK|1|409|0.00244499,COCA-CN|5|321|0.0155763	0.5	376	162	1	206651107	.	G	A	376	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1553;VD=1550;AF=0.9981;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=CGCAGGTACCGGATCACCAC;RSEQ=GAGAAGCCGGCTGGGGCCAT;CSQ=A|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_001193321.2|protein_coding|7/21||NM_001193321.2:c.462G>A|NP_001180250.1:p.Thr154%3D|943|462|154|T|acG/acA|rs2297545&COSV65624190||1||EntrezGene||||||1:g.206651107G>A|0.2684|0.1639|0.3648|0.2094|0.6421|0.2308|0.2123|0.2649|0.2205|0.6421|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_001193322.2|protein_coding|8/21||NM_001193322.2:c.717G>A|NP_001180251.1:p.Thr239%3D|1062|717|239|T|acG/acA|rs2297545&COSV65624190||1||EntrezGene||||||1:g.206651107G>A|0.2684|0.1639|0.3648|0.2094|0.6421|0.2308|0.2123|0.2649|0.2205|0.6421|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|IKBKE|9641|Transcript|NM_014002.4|protein_coding|8/22||NM_014002.4:c.717G>A|NP_054721.1:p.Thr239%3D|1062|717|239|T|acG/acA|rs2297545&COSV65624190||1||EntrezGene||YES||||1:g.206651107G>A|0.2684|0.1639|0.3648|0.2094|0.6421|0.2308|0.2123|0.2649|0.2205|0.6421|gnomAD_EAS||0&1|0&1,A|downstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA||||||||||rs2297545&COSV65624190|2900|1||EntrezGene||YES||||1:g.206651107G>A|0.2684|0.1639|0.3648|0.2094|0.6421|0.2308|0.2123|0.2649|0.2205|0.6421|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1553:1550:818,732:1,1:2,1550:0.9981:2,2:36.6:1:35.5:1:1:1.12:60:31.979:0.9987:0:1.1	0/0:162:0:0,0:91,71:162,0:0:2,0:35.4:1:36.8:1:1:0:60:161:1:0:0.1
    438. 

  438. 1	206651485	206651485	C	A	intronic	IKBKE	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	77	1	206651485	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=787;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00785;SOR=0;LSEQ=CCCCCACCCCTGACAGTCTC;RSEQ=ATGTCCTGGGAGGGCAGGGG;CSQ=A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193321.2|protein_coding||7/20|NM_001193321.2:c.558-18C>A|||||||||1||EntrezGene||||||1:g.206651485C>A||||||||||||||,A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193322.2|protein_coding||8/20|NM_001193322.2:c.813-18C>A|||||||||1||EntrezGene||||||1:g.206651485C>A||||||||||||||,A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_014002.4|protein_coding||8/21|NM_014002.4:c.813-18C>A|||||||||1||EntrezGene||YES||||1:g.206651485C>A||||||||||||||,A|downstream_gene_variant|MODIFIER|MIR6769B|102466202|Transcript|NR_106919.1|miRNA|||||||||||3278|1||EntrezGene||YES||||1:g.206651485C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:787:0:0,0:519,268:787,0:0:2,0:34.7:1:36.6:1:1:0:60:156.4:1:0:0.1	0/1:77:2:1,1:55,20:75,2:0.026:2,2:35:1:37:0:0.47368:2.70801:60:4:0.026:0:1
    439. 

  439. 1	206661280	206661280	A	T	exonic	IKBKE	.	nonsynonymous SNV	IKBKE:NM_001193321:exon15:c.A1391T:p.K464M,IKBKE:NM_001193322:exon16:c.A1646T:p.K549M,IKBKE:NM_014002:exon16:c.A1646T:p.K549M	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.998	0.715	D	0.879	0.606	P	0.000	0.629	D	0.875	0.281	N	2.79	0.817	M	1.99	0.217	T	.	.	.	0.426	0.718	-0.960	0.393	T	0.110	0.398	T	0.015	0.352	T	6.232	0.860	28.8	0.995	0.700	0.964	0.687	D	c	0.609	0.615	1.000	0.500	0.707	0.730	0	5.83	0.930	3.061	0.494	1.140	0.893	1.000	0.715	1.000	0.888	13.577	0.612	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	121	1	206661280	.	A	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1691;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00442;SOR=0;LSEQ=GATTCAGTGCTGTTTGGACA;RSEQ=GATGAACTTCATCTACAAAC;CSQ=T|missense_variant|MODERATE|IKBKE|9641|Transcript|NM_001193321.2|protein_coding|15/21||NM_001193321.2:c.1391A>T|NP_001180250.1:p.Lys464Met|1872|1391|464|K/M|aAg/aTg|||1||EntrezGene||||||1:g.206661280A>T||||||||||||||,T|missense_variant|MODERATE|IKBKE|9641|Transcript|NM_001193322.2|protein_coding|16/21||NM_001193322.2:c.1646A>T|NP_001180251.1:p.Lys549Met|1991|1646|549|K/M|aAg/aTg|||1||EntrezGene||||||1:g.206661280A>T||||||||||||||,T|missense_variant|MODERATE|IKBKE|9641|Transcript|NM_014002.4|protein_coding|16/22||NM_014002.4:c.1646A>T|NP_054721.1:p.Lys549Met|1991|1646|549|K/M|aAg/aTg|||1||EntrezGene||YES||||1:g.206661280A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1691:0:0,0:840,850:1690,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:121:2:1,1:68,51:119,2:0.0165:2,2:37.5:1:37:0:1:1.33011:60:4:0.0167:0:1
    440. 

  440. 1	206666656	206666656	T	A	exonic	IKBKE	.	nonsynonymous SNV	IKBKE:NM_001193321:exon19:c.T1735A:p.S579T,IKBKE:NM_014002:exon20:c.T1990A:p.S664T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.651	0.388	P	0.212	0.357	B	0.952	0.077	N	1.000	0.282	N	1.885	0.502	L	2.38	0.158	T	.	.	.	0.134	0.342	-1.040	0.174	T	0.038	0.162	T	0.005	0.131	T	0.345	0.127	6.122	0.789	0.121	0.149	0.184	N	c	-0.454	-0.517	1.000	0.747	0.706	0.609	0	3.68	0.412	0.625	0.240	0.964	0.580	0.003	0.159	0.010	0.111	7.264	0.252	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	166	1	206666656	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1802;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00708;SOR=0;LSEQ=GAGCAAAGGGGGCTCAGGCC;RSEQ=CGCCGCCTCCCATAGCTCCT;CSQ=A|missense_variant|MODERATE|IKBKE|9641|Transcript|NM_001193321.2|protein_coding|19/21||NM_001193321.2:c.1735T>A|NP_001180250.1:p.Ser579Thr|2216|1735|579|S/T|Tcg/Acg|||1||EntrezGene||||||1:g.206666656T>A||||||||||||||,A|intron_variant|MODIFIER|IKBKE|9641|Transcript|NM_001193322.2|protein_coding||19/20|NM_001193322.2:c.1932+204T>A|||||||||1||EntrezGene||||||1:g.206666656T>A||||||||||||||,A|missense_variant|MODERATE|IKBKE|9641|Transcript|NM_014002.4|protein_coding|20/22||NM_014002.4:c.1990T>A|NP_054721.1:p.Ser664Thr|2335|1990|664|S/T|Tcg/Acg|||1||EntrezGene||YES||||1:g.206666656T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1802:0:0,0:870,932:1802,0:0:2,0:38.6:1:36.4:1:1:0:60:119.133:1:0:0.3	0/1:166:2:1,1:77,87:164,2:0.012:2,2:37:1:37:0:1:1.13:60:4:0.012:0:1
    441. 

  441. 1	226019613	226019613	A	G	exonic	EPHX1	.	nonsynonymous SNV	EPHX1:NM_000120:exon3:c.A317G:p.Q106R,EPHX1:NM_001136018:exon3:c.A317G:p.Q106R,EPHX1:NM_001291163:exon3:c.A317G:p.Q106R	.	.	.	.	.	.	.	.	.	.	.	0.526	0.109	T	0.94	0.508	P	0.897	0.619	P	0.000	0.843	D	1	0.810	D	1.255	0.319	L	3.78	0.039	T	-2.27	0.506	N	0.931	0.929	-1.013	0.259	T	0.022	0.093	T	0.011	0.284	T	4.360	0.584	24.1	0.997	0.813	0.986	0.846	D	c	0.383	0.467	1.000	0.747	0.707	0.730	0	5.71	0.890	7.039	0.761	1.115	0.880	1.000	0.715	1.000	0.888	16.004	0.801	Alpha/Beta hydrolase fold|Epoxide hydrolase, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	192	1	226019613	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1408;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01433;SOR=0;LSEQ=TGAATTTGACTGGAAGAAGC;RSEQ=GGTGGAGATTCTCAACAGAT;CSQ=G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_000120.4|protein_coding|3/9||NM_000120.4:c.317A>G|NP_000111.1:p.Gln106Arg|513|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001136018.4|protein_coding|3/9||NM_001136018.4:c.317A>G|NP_001129490.1:p.Gln106Arg|368|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001291163.2|protein_coding|3/9||NM_001291163.2:c.317A>G|NP_001278092.1:p.Gln106Arg|814|317|106|Q/R|cAg/cGg|||1||EntrezGene||YES||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378426.1|protein_coding|4/10||NM_001378426.1:c.317A>G|NP_001365355.1:p.Gln106Arg|572|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378427.1|protein_coding|3/9||NM_001378427.1:c.317A>G|NP_001365356.1:p.Gln106Arg|415|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378428.1|protein_coding|3/9||NM_001378428.1:c.290A>G|NP_001365357.1:p.Gln97Arg|486|290|97|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378429.1|protein_coding|3/9||NM_001378429.1:c.317A>G|NP_001365358.1:p.Gln106Arg|368|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378430.1|protein_coding|3/9||NM_001378430.1:c.317A>G|NP_001365359.1:p.Gln106Arg|513|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378431.1|protein_coding|3/8||NM_001378431.1:c.317A>G|NP_001365360.1:p.Gln106Arg|368|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378432.1|protein_coding|3/6||NM_001378432.1:c.317A>G|NP_001365361.1:p.Gln106Arg|368|317|106|Q/R|cAg/cGg|||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|splice_region_variant&non_coding_transcript_exon_variant|LOW|EPHX1|2052|Transcript|NR_165624.1|misc_RNA|3/6||NR_165624.1:n.368A>G||368|||||||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165625.1|misc_RNA|3/9||NR_165625.1:n.368A>G||368|||||||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165626.1|misc_RNA|3/8||NR_165626.1:n.814A>G||814|||||||1||EntrezGene||||||1:g.226019613A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165627.1|misc_RNA|3/9||NR_165627.1:n.513A>G||513|||||||1||EntrezGene||||||1:g.226019613A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1408:0:0,0:562,846:1408,0:0:2,0:36.9:1:36:1:1:0:60:55.32:1:0:0.4	0/1:192:2:1,1:85,105:190,2:0.0104:2,2:22:0:31:1:1:1.23:60:4:0.0106:0:2
    442. 

  442. 1	226019633	226019633	T	C	exonic	EPHX1	.	nonsynonymous SNV	EPHX1:NM_000120:exon3:c.T337C:p.Y113H,EPHX1:NM_001136018:exon3:c.T337C:p.Y113H,EPHX1:NM_001291163:exon3:c.T337C:p.Y113H	0.48	0.2784	0.1876	0.3544	0.2748	0.4615	0.3038	0.2992	0.3129	rs1051740	rs1051740	0.012	0.912	D	0.998	0.715	D	0.986	0.754	D	0.000	0.629	D	0.000	0.588	P	1.92	0.515	L	3.7	0.041	T	-4.32	0.766	D	0.668	0.686	-0.886	0.493	T	0.000	0.000	T	.	.	.	6.403	0.884	29.6	0.999	0.952	0.997	0.991	D	c	0.774	0.753	1.000	0.747	0.707	0.730	0	5.58	0.843	7.789	0.843	0.989	0.601	1.000	0.715	0.997	0.653	15.758	0.777	Alpha/Beta hydrolase fold|Epoxide hydrolase, N-terminal	.	.	ID=COSV55298811;OCCURENCE=4(haematopoietic_and_lymphoid_tissue),2(lung)	31643	EPOXIDE_HYDROLASE_1_POLYMORPHISM|Cystic_fibrosis|carbamazepine_response_-_Dosage	.|MONDO:MONDO:0009061,MedGen:C0010674,OMIM:219700,Orphanet:ORPHA586,SNOMED_CT:190905008|MedGen:CN236494	reviewed_by_expert_panel	drug_response	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU11399563	LAML-KR|3|205|0.0146341,LUSC-KR|3|170|0.0176471,COCA-CN|2|321|0.00623053	0.25	242	187	1	226019633	.	T	C	242	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1146;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTGGAGATTCTCAACAGA;RSEQ=ACCCTCACTTCAAGACTAAG;CSQ=C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_000120.4|protein_coding|3/9||NM_000120.4:c.337T>C|NP_000111.1:p.Tyr113His|533|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001136018.4|protein_coding|3/9||NM_001136018.4:c.337T>C|NP_001129490.1:p.Tyr113His|388|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001291163.2|protein_coding|3/9||NM_001291163.2:c.337T>C|NP_001278092.1:p.Tyr113His|834|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||YES||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378426.1|protein_coding|4/10||NM_001378426.1:c.337T>C|NP_001365355.1:p.Tyr113His|592|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378427.1|protein_coding|3/9||NM_001378427.1:c.337T>C|NP_001365356.1:p.Tyr113His|435|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378428.1|protein_coding|3/9||NM_001378428.1:c.310T>C|NP_001365357.1:p.Tyr104His|506|310|104|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378429.1|protein_coding|3/9||NM_001378429.1:c.337T>C|NP_001365358.1:p.Tyr113His|388|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378430.1|protein_coding|3/9||NM_001378430.1:c.337T>C|NP_001365359.1:p.Tyr113His|533|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378431.1|protein_coding|3/8||NM_001378431.1:c.337T>C|NP_001365360.1:p.Tyr113His|388|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|missense_variant|MODERATE|EPHX1|2052|Transcript|NM_001378432.1|protein_coding|3/6||NM_001378432.1:c.337T>C|NP_001365361.1:p.Tyr113His|388|337|113|Y/H|Tac/Cac|rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|intron_variant&non_coding_transcript_variant|MODIFIER|EPHX1|2052|Transcript|NR_165624.1|misc_RNA||3/5|NR_165624.1:n.369+19T>C|||||||rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165625.1|misc_RNA|3/9||NR_165625.1:n.388T>C||388|||||rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165626.1|misc_RNA|3/8||NR_165626.1:n.834T>C||834|||||rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1,C|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165627.1|misc_RNA|3/9||NR_165627.1:n.533T>C||533|||||rs1051740&CM940369&COSV55298811||1||EntrezGene||||||1:g.226019633T>C|0.3213|0.1782|0.3932|0.2833|0.4613|0.3011|0.2968|0.3074|0.3524|0.4821|EAS|drug_response&risk_factor&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1146:0:0,0:433,712:1145,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:187:98:43,55:41,48:89,98:0.5241:2,2:38:1:36.6:1:0.77077:1.09202:60:97:0.533:0:1.1
    443. 

  443. 1	226019653	226019653	G	A	exonic	EPHX1	.	synonymous SNV	EPHX1:NM_000120:exon3:c.G357A:p.K119K,EPHX1:NM_001136018:exon3:c.G357A:p.K119K,EPHX1:NM_001291163:exon3:c.G357A:p.K119K	0.31	0.1388	0.1312	0.1253	0.1954	0.3069	0.1085	0.1332	0.1184	rs1131873	rs1131873	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55300861;OCCURENCE=1(cervix),1(large_intestine),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU150991	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	303	168	1	226019653	.	G	A	303	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=897;VD=426;AF=0.4749;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.37833;SOR=1.06887;LSEQ=TACCCTCACTTCAAGACTAA;RSEQ=ATTGAAGGTATGTTTGCAAA;CSQ=A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_000120.4|protein_coding|3/9||NM_000120.4:c.357G>A|NP_000111.1:p.Lys119%3D|553|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001136018.4|protein_coding|3/9||NM_001136018.4:c.357G>A|NP_001129490.1:p.Lys119%3D|408|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001291163.2|protein_coding|3/9||NM_001291163.2:c.357G>A|NP_001278092.1:p.Lys119%3D|854|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||YES||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378426.1|protein_coding|4/10||NM_001378426.1:c.357G>A|NP_001365355.1:p.Lys119%3D|612|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378427.1|protein_coding|3/9||NM_001378427.1:c.357G>A|NP_001365356.1:p.Lys119%3D|455|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378428.1|protein_coding|3/9||NM_001378428.1:c.330G>A|NP_001365357.1:p.Lys110%3D|526|330|110|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378429.1|protein_coding|3/9||NM_001378429.1:c.357G>A|NP_001365358.1:p.Lys119%3D|408|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378430.1|protein_coding|3/9||NM_001378430.1:c.357G>A|NP_001365359.1:p.Lys119%3D|553|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378431.1|protein_coding|3/8||NM_001378431.1:c.357G>A|NP_001365360.1:p.Lys119%3D|408|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|synonymous_variant|LOW|EPHX1|2052|Transcript|NM_001378432.1|protein_coding|3/6||NM_001378432.1:c.357G>A|NP_001365361.1:p.Lys119%3D|408|357|119|K|aaG/aaA|rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|EPHX1|2052|Transcript|NR_165624.1|misc_RNA||3/5|NR_165624.1:n.369+39G>A|||||||rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165625.1|misc_RNA|3/9||NR_165625.1:n.408G>A||408|||||rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165626.1|misc_RNA|3/8||NR_165626.1:n.854G>A||854|||||rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1,A|non_coding_transcript_exon_variant|MODIFIER|EPHX1|2052|Transcript|NR_165627.1|misc_RNA|3/9||NR_165627.1:n.553G>A||553|||||rs1131873&COSV55300861||1||EntrezGene||||||1:g.226019653G>A|0.1581|0.1294|0.1085|0.1924|0.3062|0.1128|0.1415|0.1427|0.2256|0.3062|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:897:426:135,291:136,334:470,426:0.4749:2,2:36.5:1:34.8:1:0.3828:1.14:60:24.059:0.4701:0:1.2	0/1:168:77:33,44:34,56:90,77:0.4583:2,2:38:1:35.6:1:0.52967:1.23:60:76:0.4606:0:1.1
    444. 

  444. 1	226252141	226252141	C	T	exonic	H3F3A	.	nonsynonymous SNV	H3F3A:NM_002107:exon2:c.C89T:p.A30V	.	.	.	.	.	.	.	.	.	.	.	0.009	0.574	D	1.0	0.899	D	0.986	0.754	D	0.000	0.843	D	1.000	0.588	D	2.355	0.679	M	0.89	0.456	T	-3.6	0.701	D	0.571	0.611	-0.437	0.709	T	0.273	0.644	T	0.039	0.585	D	3.808	0.515	23.4	0.968	0.307	0.963	0.680	D	c	0.395	0.448	1.0	0.983	0.543	0.218	0	4.32	0.507	7.899	0.859	0.935	0.490	1.000	0.715	1.000	0.888	16.760	0.853	Histone H2A/H2B/H3|Histone-fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	204	1	226252141	.	C	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=594;VD=2;AF=0.0034;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.10888;SOR=0.22688;LSEQ=AAAAGCCGCTCGCAAGAGTG;RSEQ=GCCCTCTACTGGAGGGGTGA;CSQ=T|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379043.1|protein_coding|3/5||NM_001379043.1:c.89C>T|NP_001365972.1:p.Ala30Val|448|89|30|A/V|gCg/gTg|||1||EntrezGene||YES||||1:g.226252141C>T||||||||||||||,T|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379045.1|protein_coding|3/5||NM_001379045.1:c.89C>T|NP_001365974.1:p.Ala30Val|299|89|30|A/V|gCg/gTg|||1||EntrezGene||||||1:g.226252141C>T||||||||||||||,T|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379046.1|protein_coding|3/5||NM_001379046.1:c.89C>T|NP_001365975.1:p.Ala30Val|304|89|30|A/V|gCg/gTg|||1||EntrezGene||||||1:g.226252141C>T||||||||||||||,T|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379047.1|protein_coding|3/5||NM_001379047.1:c.89C>T|NP_001365976.1:p.Ala30Val|232|89|30|A/V|gCg/gTg|||1||EntrezGene||||||1:g.226252141C>T||||||||||||||,T|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_002107.7|protein_coding|2/4||NM_002107.7:c.89C>T|NP_002098.1:p.Ala30Val|208|89|30|A/V|gCg/gTg|||1||EntrezGene||||||1:g.226252141C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:594:2:1,1:215,377:592,2:0.0034:2,2:21:1:37:0:1:1.75:50:4:0.0034:0:1.5	0/1:204:3:1,2:79,121:200,3:0.0147:2,2:11.3:1:37:0:1:1.30412:60:6:0.0151:0:1.7
    445. 

  445. 1	226252232	226252232	C	T	ncRNA_intronic	H3F3AP4	.	.	.	1.	0.9846	0.9464	0.9976	1	1	1	0.9997	0.9969	rs2036870	rs2036870	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100831216;OCCURENCE=18(meninges)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	229	86	1	226252232	.	C	T	229	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=51;VD=51;AF=1;SHIFT3=0;MSI=2;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTCTCTTGTATGTATCCA;RSEQ=ATAATTTAACAAAAAGATGG;CSQ=T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379043.1|protein_coding||3/4|NM_001379043.1:c.128+52C>T|||||||rs2036870&COSV100831216||1||EntrezGene||YES||||1:g.226252232C>T|0.9957|0.9439|0.9973|1|1|1|0.9998|0.9977|0.9997|1|EAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379045.1|protein_coding||3/4|NM_001379045.1:c.128+52C>T|||||||rs2036870&COSV100831216||1||EntrezGene||||||1:g.226252232C>T|0.9957|0.9439|0.9973|1|1|1|0.9998|0.9977|0.9997|1|EAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379046.1|protein_coding||3/4|NM_001379046.1:c.128+52C>T|||||||rs2036870&COSV100831216||1||EntrezGene||||||1:g.226252232C>T|0.9957|0.9439|0.9973|1|1|1|0.9998|0.9977|0.9997|1|EAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379047.1|protein_coding||3/4|NM_001379047.1:c.128+52C>T|||||||rs2036870&COSV100831216||1||EntrezGene||||||1:g.226252232C>T|0.9957|0.9439|0.9973|1|1|1|0.9998|0.9977|0.9997|1|EAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_002107.7|protein_coding||2/3|NM_002107.7:c.128+52C>T|||||||rs2036870&COSV100831216||1||EntrezGene||||||1:g.226252232C>T|0.9957|0.9439|0.9973|1|1|1|0.9998|0.9977|0.9997|1|EAS&EA&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:51:51:7,44:0,0:0,51:1:0,2:29.5:1:35.5:1:1:0:60:50:1:0:1.2	1/1:86:86:15,71:0,0:0,86:1:0,2:37.6:1:35.7:1:1:0:60:42:1:0:1.3
    446. 

  446. 1	226253316	226253316	G	T	ncRNA_intronic	H3F3AP4	.	.	.	1.	0.9846	0.9464	0.9976	1	1	1	0.9997	0.9969	rs1849032	rs1849032	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100831217;OCCURENCE=18(meninges)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81722091	COCA-CN|5|321|0.0155763	1	210	66	1	226253316	.	G	T	210	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=47;AF=1;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTTACCTTTTTGTGCTA;RSEQ=TTATGTTTTTGGTAACAGTT;CSQ=T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379043.1|protein_coding||3/4|NM_001379043.1:c.129-41G>T|||||||rs1849032&COSV100831217||1||EntrezGene||YES||||1:g.226253316G>T|0.9953|0.9433|0.9973|1|1|1|0.9999|0.9978|0.9998|1|EAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379045.1|protein_coding||3/4|NM_001379045.1:c.129-41G>T|||||||rs1849032&COSV100831217||1||EntrezGene||||||1:g.226253316G>T|0.9953|0.9433|0.9973|1|1|1|0.9999|0.9978|0.9998|1|EAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379046.1|protein_coding||3/4|NM_001379046.1:c.129-41G>T|||||||rs1849032&COSV100831217||1||EntrezGene||||||1:g.226253316G>T|0.9953|0.9433|0.9973|1|1|1|0.9999|0.9978|0.9998|1|EAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379047.1|protein_coding||3/4|NM_001379047.1:c.129-41G>T|||||||rs1849032&COSV100831217||1||EntrezGene||||||1:g.226253316G>T|0.9953|0.9433|0.9973|1|1|1|0.9999|0.9978|0.9998|1|EAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_002107.7|protein_coding||2/3|NM_002107.7:c.129-41G>T|||||||rs1849032&COSV100831217||1||EntrezGene||||||1:g.226253316G>T|0.9953|0.9433|0.9973|1|1|1|0.9999|0.9978|0.9998|1|EAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:47:47:39,8:0,0:0,47:1:0,2:23.7:1:35.2:1:1:0:60:46:1:0:1.3	1/1:66:66:52,14:0,0:0,66:1:0,2:33.1:1:34.9:1:1:0:60:15.5:1:0:1.1
    447. 

  447. 1	226259031	226259031	T	C	ncRNA_intronic	H3F3AP4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	48	1	226259031	.	T	C	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=83;VD=2;AF=0.0241;SHIFT3=1;MSI=6;MSILEN=1;SSF=0.39965;SOR=inf;LSEQ=AAATAACATCATCAGTAATT;RSEQ=TTTCTTCATTCCTTTTGCAG;CSQ=C|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379043.1|protein_coding||4/4|NM_001379043.1:c.283-21T>C|||||||||1||EntrezGene||YES||||1:g.226259031T>C||||||||||||||,C|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379045.1|protein_coding||4/4|NM_001379045.1:c.283-21T>C|||||||||1||EntrezGene||||||1:g.226259031T>C||||||||||||||,C|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379046.1|protein_coding||4/4|NM_001379046.1:c.283-21T>C|||||||||1||EntrezGene||||||1:g.226259031T>C||||||||||||||,C|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379047.1|protein_coding||4/4|NM_001379047.1:c.283-21T>C|||||||||1||EntrezGene||||||1:g.226259031T>C||||||||||||||,C|intron_variant|MODIFIER|H3F3A|3020|Transcript|NM_002107.7|protein_coding||3/3|NM_002107.7:c.283-21T>C|||||||||1||EntrezGene||||||1:g.226259031T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:83:2:1,1:53,28:81,2:0.0241:2,2:33:0:31:1:1:1.87747:60:4:0.0241:0:1	0/0:48:0:0,0:36,12:48,0:0:2,0:35.7:1:36.2:1:1:0:60:47:1:0:0.1
    448. 

  448. 1	226259049	226259049	C	T	ncRNA_intronic	H3F3AP4	.	.	.	0.0002	3.233e-05	0	0	0	0	0	6.668e-05	0	rs374324778	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	57	1	226259049	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08704;SOR=0;LSEQ=TTTTTTCTTCATTCCTTTTG;RSEQ=AGGAGGCAAGTGAGGCCTAT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|H3F3A|3020|Transcript|NM_001379043.1|protein_coding||4/4|NM_001379043.1:c.283-3C>T|||||||rs374324778||1||EntrezGene||YES||||1:g.226259049C>T|1.61e-05|0.0001235|0|0|0|0|1.782e-05|0|0|0.000227|AA|||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|H3F3A|3020|Transcript|NM_001379045.1|protein_coding||4/4|NM_001379045.1:c.283-3C>T|||||||rs374324778||1||EntrezGene||||||1:g.226259049C>T|1.61e-05|0.0001235|0|0|0|0|1.782e-05|0|0|0.000227|AA|||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|H3F3A|3020|Transcript|NM_001379046.1|protein_coding||4/4|NM_001379046.1:c.283-3C>T|||||||rs374324778||1||EntrezGene||||||1:g.226259049C>T|1.61e-05|0.0001235|0|0|0|0|1.782e-05|0|0|0.000227|AA|||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|H3F3A|3020|Transcript|NM_001379047.1|protein_coding||4/4|NM_001379047.1:c.283-3C>T|||||||rs374324778||1||EntrezGene||||||1:g.226259049C>T|1.61e-05|0.0001235|0|0|0|0|1.782e-05|0|0|0.000227|AA|||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|H3F3A|3020|Transcript|NM_002107.7|protein_coding||3/3|NM_002107.7:c.283-3C>T|||||||rs374324778||1||EntrezGene||||||1:g.226259049C>T|1.61e-05|0.0001235|0|0|0|0|1.782e-05|0|0|0.000227|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:135:0:0,0:79,56:135,0:0:2,0:24.5:1:36.3:1:1:0:48.8:134:1:0:0.1	0/1:57:2:1,1:38,17:55,2:0.0351:2,2:50:1:37:0:0.53571:2.20075:60:4:0.0351:0:1
    449. 

  449. 1	226259071	226259071	T	A	exonic	H3F3A	.	nonsynonymous SNV	H3F3A:NM_002107:exon4:c.T302A:p.L101Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.999	0.764	D	0.978	0.725	D	0.000	0.629	D	1	0.810	D	3.83	0.957	H	0.49	0.558	T	-5.19	0.836	D	0.98	0.986	-0.285	0.754	T	0.360	0.722	T	0.288	0.905	D	6.121	0.844	28.3	0.980	0.371	0.991	0.917	D	c	0.769	0.787	1.000	0.747	0.707	0.730	0	5.87	0.942	8.004	0.880	1.061	0.807	1.000	0.715	1.000	0.888	16.576	0.845	Histone H2A/H2B/H3|Histone-fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	71	1	226259071	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=201;VD=2;AF=0.01;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.54537;SOR=inf;LSEQ=GGAGGCAAGTGAGGCCTATC;RSEQ=GGTTGGCCTTTTTGAAGACA;CSQ=A|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379043.1|protein_coding|5/5||NM_001379043.1:c.302T>A|NP_001365972.1:p.Leu101Gln|661|302|101|L/Q|cTg/cAg|||1||EntrezGene||YES||||1:g.226259071T>A||||||||||||||,A|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379045.1|protein_coding|5/5||NM_001379045.1:c.302T>A|NP_001365974.1:p.Leu101Gln|512|302|101|L/Q|cTg/cAg|||1||EntrezGene||||||1:g.226259071T>A||||||||||||||,A|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379046.1|protein_coding|5/5||NM_001379046.1:c.302T>A|NP_001365975.1:p.Leu101Gln|517|302|101|L/Q|cTg/cAg|||1||EntrezGene||||||1:g.226259071T>A||||||||||||||,A|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379047.1|protein_coding|5/5||NM_001379047.1:c.302T>A|NP_001365976.1:p.Leu101Gln|445|302|101|L/Q|cTg/cAg|||1||EntrezGene||||||1:g.226259071T>A||||||||||||||,A|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_002107.7|protein_coding|4/4||NM_002107.7:c.302T>A|NP_002098.1:p.Leu101Gln|421|302|101|L/Q|cTg/cAg|||1||EntrezGene||||||1:g.226259071T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:201:2:1,1:110,89:199,2:0.01:2,2:59.5:1:37:0:1:1.23464:60:4:0.01:0:1	0/0:71:0:0,0:41,30:71,0:0:2,0:35.6:1:36.5:1:1:0:44.2:142:1:0:0.1
    450. 

  450. 1	226259113	226259113	C	G	exonic	H3F3A	.	nonsynonymous SNV	H3F3A:NM_002107:exon4:c.C344G:p.A115G	0.025	0.0002	0.0004	0	0	0.0020	0	6.909e-05	0	rs749423281	.	.	.	.	0.015	0.158	B	0.006	0.112	B	0.000	0.843	D	1	0.810	D	2.9	0.842	M	0.64	0.529	T	-3.19	0.646	D	0.782	0.773	-0.983	0.343	T	0.141	0.461	T	.	.	.	6.237	0.861	28.8	0.979	0.359	0.984	0.821	D	c	0.253	0.443	1.000	0.747	0.707	0.730	0	5.83	0.930	7.887	0.857	0.929	0.438	1.000	0.715	1.000	0.888	20.563	0.993	Histone H2A/H2B/H3|Histone-fold	.	.	ID=COSV64731809;OCCURENCE=2(liver),2(central_nervous_system),1(stomach),2(haematopoietic_and_lymphoid_tissue),1(urinary_tract),1(skin),5(upper_aerodigestive_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	MU4603415	LICA-CN|1|402|0.00248756,GACA-CN|1|123|0.00813008,BLCA-CN|1|103|0.00970874	0.5	147	80	1	226259113	.	C	G	147	PASS	STATUS=AFDiff;SAMPLE=LibM078FTT;TYPE=SNV;DP=228;VD=29;AF=0.1272;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.23072;SOR=1.51784;LSEQ=CAACCTGTGTGCTATCCATG;RSEQ=CAAACGTGTAACAATTATGC;CSQ=G|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379043.1|protein_coding|5/5||NM_001379043.1:c.344C>G|NP_001365972.1:p.Ala115Gly|703|344|115|A/G|gCc/gGc|rs749423281&COSV64731809||1||EntrezGene||YES||||1:g.226259113C>G|0.004557|0.0004108|0.009746|0.001236|0.007597|0.001702|0.004326|0.004326|0.003488|0.009746|gnomAD_AMR||0&1|0&1,G|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379045.1|protein_coding|5/5||NM_001379045.1:c.344C>G|NP_001365974.1:p.Ala115Gly|554|344|115|A/G|gCc/gGc|rs749423281&COSV64731809||1||EntrezGene||||||1:g.226259113C>G|0.004557|0.0004108|0.009746|0.001236|0.007597|0.001702|0.004326|0.004326|0.003488|0.009746|gnomAD_AMR||0&1|0&1,G|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379046.1|protein_coding|5/5||NM_001379046.1:c.344C>G|NP_001365975.1:p.Ala115Gly|559|344|115|A/G|gCc/gGc|rs749423281&COSV64731809||1||EntrezGene||||||1:g.226259113C>G|0.004557|0.0004108|0.009746|0.001236|0.007597|0.001702|0.004326|0.004326|0.003488|0.009746|gnomAD_AMR||0&1|0&1,G|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_001379047.1|protein_coding|5/5||NM_001379047.1:c.344C>G|NP_001365976.1:p.Ala115Gly|487|344|115|A/G|gCc/gGc|rs749423281&COSV64731809||1||EntrezGene||||||1:g.226259113C>G|0.004557|0.0004108|0.009746|0.001236|0.007597|0.001702|0.004326|0.004326|0.003488|0.009746|gnomAD_AMR||0&1|0&1,G|missense_variant|MODERATE|H3F3A|3020|Transcript|NM_002107.7|protein_coding|4/4||NM_002107.7:c.344C>G|NP_002098.1:p.Ala115Gly|463|344|115|A/G|gCc/gGc|rs749423281&COSV64731809||1||EntrezGene||||||1:g.226259113C>G|0.004557|0.0004108|0.009746|0.001236|0.007597|0.001702|0.004326|0.004326|0.003488|0.009746|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:228:29:16,13:99,100:199,29:0.1272:2,2:42.1:1:30.4:1:0.69193:1.24:7.4:4.8:0.1096:0:1.2	0/1:80:7:5,2:35,38:73,7:0.0875:2,2:49.1:1:35.3:1:0.43153:2.68:4.6:14:0.0886:0:1
    451. 

  451. 1	226259212	226259212	-	A	ncRNA_exonic	H3F3AP4	.	.	.	0.27	0.0291	0.0058	0.0440	0.0563	0.0352	0.0444	0.0435	0.0259	rs377545570	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	124	40	1	226259212	.	C	CA	124	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=34;VD=5;AF=0.1471;SHIFT3=17;MSI=18;MSILEN=1;SSF=0.14701;SOR=0.45931;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAAAAATTT;CSQ=A|3_prime_UTR_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379043.1|protein_coding|5/5||NM_001379043.1:c.*49dup||802-803|||||rs34523945||1||EntrezGene||YES||||1:g.226259229dup|0.3921|0.4038|0.4364|0.3605|0.4331|0.216|0.3676|0.4084|0.4242|0.4364|gnomAD_AMR|||,A|3_prime_UTR_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379045.1|protein_coding|5/5||NM_001379045.1:c.*49dup||653-654|||||rs34523945||1||EntrezGene||||||1:g.226259229dup|0.3921|0.4038|0.4364|0.3605|0.4331|0.216|0.3676|0.4084|0.4242|0.4364|gnomAD_AMR|||,A|3_prime_UTR_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379046.1|protein_coding|5/5||NM_001379046.1:c.*49dup||658-659|||||rs34523945||1||EntrezGene||||||1:g.226259229dup|0.3921|0.4038|0.4364|0.3605|0.4331|0.216|0.3676|0.4084|0.4242|0.4364|gnomAD_AMR|||,A|3_prime_UTR_variant|MODIFIER|H3F3A|3020|Transcript|NM_001379047.1|protein_coding|5/5||NM_001379047.1:c.*49dup||586-587|||||rs34523945||1||EntrezGene||||||1:g.226259229dup|0.3921|0.4038|0.4364|0.3605|0.4331|0.216|0.3676|0.4084|0.4242|0.4364|gnomAD_AMR|||,A|3_prime_UTR_variant|MODIFIER|H3F3A|3020|Transcript|NM_002107.7|protein_coding|4/4||NM_002107.7:c.*49dup||562-563|||||rs34523945||1||EntrezGene||||||1:g.226259229dup|0.3921|0.4038|0.4364|0.3605|0.4331|0.216|0.3676|0.4084|0.4242|0.4364|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:5:1,4:7,20:27,5:0.1471:2,2:50.7:1:40.9:0:1:1.38625:29.4:10:0.1923:0:1.3	0/1:40:11:2,8:9,18:27,11:0.275:2,2:45.4:1:35.9:1:0.68841:1.96531:24.1:22:0.3235:0.025:0.9
    452. 

  452. 1	226550829	226550829	T	C	exonic	PARP1	.	nonsynonymous SNV	PARP1:NM_001618:exon21:c.A2819G:p.K940R	0.09	0.0026	0.0022	0.0012	0.0066	0.0278	0	0.0003	0.0092	rs3219145	rs3219145	0.006	0.614	D	0.884	0.466	P	0.783	0.556	P	0.000	0.843	D	1	0.810	D	2.68	0.787	M	2.46	0.149	T	-2.87	0.603	D	0.566	0.599	-1.190	0.002	T	0.015	0.061	T	.	.	.	4.703	0.630	24.6	0.999	0.969	0.973	0.739	D	c	0.735	0.746	1.000	0.747	0.707	0.730	0	5.77	0.910	7.986	0.877	1.061	0.807	1.000	0.715	1.000	0.888	16.088	0.808	Poly(ADP-ribose) polymerase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	MU81722129	COCA-CN|2|321|0.00623053	0.25	256	271	1	226550829	.	T	C	256	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2817;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGCTTGCCCTTGGGTAAC;RSEQ=TGCTGATATGTGAAGCGTGC;CSQ=C|missense_variant|MODERATE|PARP1|142|Transcript|NM_001618.4|protein_coding|21/23||NM_001618.4:c.2819A>G|NP_001609.2:p.Lys940Arg|2983|2819|940|K/R|aAg/aGg|rs3219145&CM077831||-1||EntrezGene||YES||||1:g.226550829T>C|0.01239|0.002092|0.0004625|0.009226|0.02854|0|0.0004571|0.006026|0.07706|0.09|SAS|||0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2817:0:0,0:1249,1567:2816,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:271:126:61,65:71,74:145,126:0.4649:2,2:38.6:1:36.7:1:1:1.0223:60:252:0.4737:0:1.1
    453. 

  453. 1	226555302	226555302	A	G	exonic	PARP1	.	nonsynonymous SNV	PARP1:NM_001618:exon17:c.T2285C:p.V762A	0.45	0.1620	0.0490	0.3600	0.1589	0.4412	0.2358	0.1662	0.2112	rs1136410	rs1136410	0.176	0.223	T	0.728	0.406	P	0.731	0.535	P	0.000	0.843	D	0.000	0.588	P	2.22	0.631	M	2.69	0.123	T	-1.33	0.332	N	0.428	0.484	-0.836	0.529	T	0.000	0.000	T	.	.	.	6.781	0.923	32	0.997	0.809	0.976	0.754	D	c	0.616	0.655	1.000	0.747	0.707	0.730	0	5.56	0.836	8.942	0.924	1.199	0.960	1.000	0.715	0.998	0.697	15.709	0.773	Poly(ADP-ribose) polymerase, regulatory domain	.	.	ID=COSV64689246;OCCURENCE=1(breast),1(liver),5(haematopoietic_and_lymphoid_tissue),1(skin),2(prostate),2(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU4559871	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.5	365	247	1	226555302	.	A	G	365	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2235;VD=1037;AF=0.464;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.45895;SOR=0.97754;LSEQ=GCAGGTTGTCAAGCATTTCC;RSEQ=CCTTGGCCTGGAGGAGCAAA;CSQ=G|missense_variant|MODERATE|PARP1|142|Transcript|NM_001618.4|protein_coding|17/23||NM_001618.4:c.2285T>C|NP_001609.2:p.Val762Ala|2449|2285|762|V/A|gTg/gCg|rs1136410&CM042761&COSV64689246||-1||EntrezGene||YES||||1:g.226555302A>G|0.2131|0.04866|0.4231|0.1596|0.4477|0.2342|0.1664|0.1921|0.1026|0.4477|gnomAD_EAS||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2235:1037:478,559:566,627:1193,1037:0.464:2,2:39.1:1:36.5:1:0.55145:1.05563:60:85.417:0.4655:0:1.1	0/1:247:116:51,65:50,81:131,116:0.4696:2,2:35.4:1:36.7:1:0.36707:1.27:60:115:0.4675:0:1.1
    454. 

  454. 1	226555348	226555348	G	A	intronic	PARP1	.	.	.	0.067	0.0394	0.0093	0.0310	0.0960	0	0.0341	0.0617	0.0389	rs3219123	rs3219123	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	169	1	226555348	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1639;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00869;SOR=0;LSEQ=GCCCCCGACTTAGGTATCAT;RSEQ=GTGAATGAGACAGACTCACC;CSQ=A|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||16/22|NM_001618.4:c.2278-39C>T|||||||rs3219123||-1||EntrezGene||YES||||1:g.226555348G>A|0.04449|0.008616|0.02368|0.09003|0.0003808|0.03541|0.06013|0.05122|0.04518|0.09003|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1639:0:0,0:682,956:1638,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:169:2:1,1:59,108:167,2:0.0118:2,2:51:1:37:0:1:1.82:60:4:0.012:0:2
    455. 

  455. 1	226564836	226564836	G	A	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon13:c.C1914T:p.F638F	0.033	0.0013	0.0002	0	0.0066	0.0204	0	0.0002	0	rs13306137	rs13306137	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	718697	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	.	.	0.25	231	184	1	226564836	.	G	A	231	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=609;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGTCAATCTCCAGGGGGTA;RSEQ=AACTTTTTGGGATACTTCGT;CSQ=A|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|13/23||NM_001618.4:c.1914C>T|NP_001609.2:p.Phe638%3D|2078|1914|638|F|ttC/ttT|rs13306137||-1||EntrezGene||YES||||1:g.226564836G>A|0.0021|6.152e-05|0.0001156|0.008829|0.02066|0|0.0001934|0.00114|0.0008166|0.0327|EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:609:0:0,0:337,272:609,0:0:2,0:38.8:1:36.2:1:1:0:60:100.5:1:0:0.1	0/1:184:90:46,44:51,43:94,90:0.4891:2,2:37.9:1:35.6:1:0.76782:1.1337:60:29:0.4833:0:1
    456. 

  456. 1	226566798	226566798	C	T	intronic	PARP1	.	.	.	0.001	.	.	.	.	.	.	.	.	rs539088651	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	172	1	226566798	.	C	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2164;VD=1;AF=0.0005;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.00149;SOR=0.02616;LSEQ=CAGCACTAACCAATGCAGGA;RSEQ=GGGCCCATGTCTCTGCACAA;CSQ=T|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||12/22|NM_001618.4:c.1745+45G>A|||||||rs539088651||-1||EntrezGene||YES||||1:g.226566798C>T||||||||||0.001|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2164:1:1,0:1399,764:2163,1:0.0005:2,0:37:0:37:0:1:0:60:2:0.0005:0:1	0/1:172:3:2,1:116,53:169,3:0.0174:2,2:24:1:37:0:1:1.09375:60:6:0.0175:0:1
    457. 

  457. 1	226567299	226567299	T	A	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon11:c.A1587T:p.G529G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	44	37	1	226567299	.	T	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=160;VD=3;AF=0.0187;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.53385;SOR=inf;LSEQ=TCAGGATCCACAGCTGCTCC;RSEQ=CCTTTAAGAGTTAATTTCAT;CSQ=A|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|11/23||NM_001618.4:c.1587A>T|NP_001609.2:p.Gly529%3D|1751|1587|529|G|ggA/ggT|||-1||EntrezGene||YES||||1:g.226567299T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:160:3:1,2:52,105:157,3:0.0187:2,2:49.7:1:28.3:1:1:1.01:60:2:0.0128:0:1	0/0:37:0:0,0:12,25:37,0:0:2,0:43.2:1:35.6:1:1:0:60:36:1:0:0.1
    458. 

  458. 1	226567563	226567563	C	G	intronic	PARP1	.	.	.	0.39	0.2328	0.3811	0.1364	0.1523	0.3734	0.1588	0.162	0.1398	rs2271343	rs2271343	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64691546;OCCURENCE=1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU16391178	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.25	162	36	1	226567563	.	C	G	162	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGAGAGGTTCCGTGGACAA;RSEQ=AACCTGGCCACCAATGTCCC;CSQ=G|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||10/22|NM_001618.4:c.1543+60G>C|||||||rs2271343&COSV64691546||-1||EntrezGene||YES||||1:g.226567563C>G||||||||||0.3949|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:187:0:0,0:152,35:187,0:0:2,0:31.2:1:36.7:1:1:0:60:186:1:0:0.1	1/0:36:21:17,4:12,3:15,21:0.5833:2,2:41.8:1:37:0:1:1.06:60:42:0.5833:0:1
    459. 

  459. 1	226567594	226567594	C	T	intronic	PARP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	57	1	226567594	.	C	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=295;VD=3;AF=0.0102;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.58765;SOR=inf;LSEQ=CCAATGTCCCTGGCTTTTGG;RSEQ=CCTGGAGGGGGCAGCTTGGG;CSQ=T|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||10/22|NM_001618.4:c.1543+29G>A|||||||||-1||EntrezGene||YES||||1:g.226567594C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:295:3:3,0:227,65:292,3:0.0102:2,0:39:1:37:0:1:0:60:6:0.0102:0:1.3	0/0:57:0:0,0:44,13:57,0:0:2,0:35.9:1:36.8:1:1:0:60:114:1:0:0.4
    460. 

  460. 1	226567789	226567789	G	T	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon10:c.C1377A:p.L459L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	165	1	226567789	.	G	T	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=796;VD=1;AF=0.0013;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.07802;SOR=0.10289;LSEQ=GTGGAGGCGGAGACGTCCTG;RSEQ=AGGAAGTCCTCAGACACAAC;CSQ=T|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|10/23||NM_001618.4:c.1377C>A|NP_001609.2:p.Leu459%3D|1541|1377|459|L|ctC/ctA|||-1||EntrezGene||YES||||1:g.226567789G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:796:1:0,1:290,505:795,1:0.0013:2,0:38:0:11:0:1:0:60:0:0:0:1	0/1:165:2:1,1:72,91:163,2:0.0121:2,2:24:1:37:0:1:1.26:60:4:0.0124:0:1
    461. 

  461. 1	226568826	226568826	G	T	exonic	PARP1	.	nonsynonymous SNV	PARP1:NM_001618:exon9:c.C1243A:p.L415I	.	.	.	.	.	.	.	.	.	.	.	0.009	0.574	D	0.985	0.592	D	0.954	0.677	D	0.000	0.629	D	1	0.810	D	3.475	0.927	M	-1.5	0.813	D	-1.69	0.402	N	0.348	0.409	0.455	0.899	D	0.716	0.903	D	0.096	0.767	D	3.663	0.497	23.2	0.996	0.751	0.975	0.750	D	c	0.625	0.528	1.000	0.747	0.707	0.730	0	5.66	0.872	4.399	0.592	1.048	0.713	1.000	0.715	0.039	0.156	19.746	0.962	BRCT domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	130	1	226568826	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1652;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.00528;SOR=0;LSEQ=CCCCGTCAACTTCCCCCCGA;RSEQ=TTTCTCAATCATGGCCTTCA;CSQ=T|missense_variant|MODERATE|PARP1|142|Transcript|NM_001618.4|protein_coding|9/23||NM_001618.4:c.1243C>A|NP_001609.2:p.Leu415Ile|1407|1243|415|L/I|Ctc/Atc|||-1||EntrezGene||YES||||1:g.226568826G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1652:0:0,0:838,814:1652,0:0:2,0:40.5:1:36.4:1:1:0:60:109.133:1:0:0.1	0/1:130:2:1,1:75,53:128,2:0.0154:2,2:41.5:1:31:1:1:1.41122:60:4:0.0154:0:1.5
    462. 

  462. 1	226568935	226568935	A	G	intronic	PARP1	.	.	.	0.	.	.	.	.	.	.	.	.	rs748688114	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	92	1	226568935	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=837;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00971;SOR=0;LSEQ=ATGAAAGGAGAGAATCATTC;RSEQ=GCAAGGCCAGCTCTGGTGCT;CSQ=G|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||8/22|NM_001618.4:c.1160-26T>C|||||||rs748688114||-1||EntrezGene||YES||||1:g.226568935A>G|3.978e-06|0|0|0|0|0|8.795e-06|0|0|8.795e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:837:0:0,0:302,535:837,0:0:2,0:36.8:1:36.2:1:1:0:60:92:1:0:0.2	0/1:92:2:1,1:30,60:90,2:0.0217:2,2:60:1:37:0:1:1.98:60:4:0.022:0:1
    463. 

  463. 1	226570690	226570690	A	G	intronic	PARP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	177	1	226570690	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=895;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.02713;SOR=0;LSEQ=CACCAGCAAGTAGTGGGCAA;RSEQ=CAATTCCTGCAAAGCAGCTC;CSQ=G|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||8/22|NM_001618.4:c.1159+47T>C|||||||||-1||EntrezGene||YES||||1:g.226570690A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:895:0:0,0:530,365:895,0:0:2,0:36.1:1:35.9:1:1:0:60:62.929:1:0:0.1	0/1:177:2:1,1:119,56:175,2:0.0113:2,2:10.5:1:37:0:0.5416:2.11516:60:4:0.0114:0:1
    464. 

  464. 1	226570840	226570840	T	C	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon8:c.A1056G:p.K352K	0.91	0.8228	0.8962	0.6388	0.8411	0.5603	0.7643	0.8339	0.7895	rs1805415	rs1805415	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64689254;OCCURENCE=1(liver),2(haematopoietic_and_lymphoid_tissue),2(prostate),5(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4559844	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,COCA-CN|5|321|0.0155763	0.5	294	241	1	226570840	.	T	C	294	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=569;VD=301;AF=0.529;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.04419;SOR=1.31492;LSEQ=GGGGGGAATATACGGTCCTG;RSEQ=TTTTTAACCTTCAATTTCTT;CSQ=C|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|8/23||NM_001618.4:c.1056A>G|NP_001609.2:p.Lys352%3D|1220|1056|352|K|aaA/aaG|rs1805415&COSV64689254||-1||EntrezGene||YES||||1:g.226570840T>C|0.7834|0.9002|0.5748|0.84|0.5531|0.7657|0.8337|0.8065|0.8974|0.9123|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:569:301:94,207:81,186:267,301:0.529:2,2:31.1:1:35.8:1:0.8557:1.04:60:36.625:0.526:0:1.1	0/1:241:111:41,70:53,77:130,111:0.4606:2,2:40.9:1:36.5:1:0.59688:1.17438:60:54.5:0.4599:0:1.1
    465. 

  465. 1	226570897	226570897	A	G	intronic	PARP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	142	1	226570897	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=154;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.22929;SOR=0;LSEQ=CGGAATTCCTAAAAAATATT;RSEQ=AGTTTTAGTTAAGAAGCCAG;CSQ=G|splice_polypyrimidine_tract_variant&intron_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding||7/22|NM_001618.4:c.1012-13T>C|||||||||-1||EntrezGene||YES||||1:g.226570897A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:154:0:0,0:29,125:154,0:0:2,0:28.2:1:36.1:1:1:0:60:50.333:1:0:0.6	0/1:142:2:1,1:35,104:139,2:0.0141:2,2:63:1:37:0:0.44681:2.94:60:4:0.0146:0:2
    466. 

  466. 1	226573217	226573217	C	T	exonic	PARP1	.	stopgain	PARP1:NM_001618:exon7:c.G999A:p.W333X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.561	0.997	46	0.997	0.781	0.954	0.643	D	c	0.916	0.801	1.0	0.983	0.707	0.730	0	5.45	0.796	5.887	0.693	0.935	0.490	1.000	0.715	0.998	0.697	19.298	0.941	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	183	1	226573217	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1875;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00787;SOR=0;LSEQ=CCCCTTACCTTTGGGGTTAC;RSEQ=CACTCCTTCCGGTTGGGTGT;CSQ=T|stop_gained|HIGH|PARP1|142|Transcript|NM_001618.4|protein_coding|7/23||NM_001618.4:c.999G>A|NP_001609.2:p.Trp333Ter|1163|999|333|W/*|tgG/tgA|||-1||EntrezGene||YES||||1:g.226573217C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1875:0:0,0:1201,674:1875,0:0:2,0:35.4:1:36.4:1:1:0:60:84.227:1:0:0.1	0/1:183:2:1,1:125,56:181,2:0.0109:2,2:38:1:37:0:0.52711:2.22134:60:4:0.0111:0:1.5
    467. 

  467. 1	226573364	226573364	A	G	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon7:c.T852C:p.A284A	0.81	0.4306	0.5477	0.5060	0.33	0.8154	0.3971	0.3312	0.3605	rs1805414	rs1805414	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64689261;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),2(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4559841	ESAD-UK|1|409|0.00244499,COCA-CN|5|321|0.0155763	0.75	387	291	1	226573364	.	A	G	387	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3184;VD=1564;AF=0.4912;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00335;LSEQ=GCACCGAACACCATGCCATC;RSEQ=GCTACTCGGTCCAAGATCTG;CSQ=G|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|7/23||NM_001618.4:c.852T>C|NP_001609.2:p.Ala284%3D|1016|852|284|A|gcT/gcC|rs1805414&CM071915&COSV64689261||-1||EntrezGene||YES||||1:g.226573364A>G|0.4262|0.5525|0.5538|0.3339|0.8133|0.408|0.3377|0.3759|0.3647|0.8133|gnomAD_EAS||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3184:1564:723,841:766,851:1617,1564:0.4912:2,2:39.8:1:36.5:1:0.52256:1.04704:60:110.714:0.4922:0:1.1	1/1:291:290:115,175:0,0:0,290:0.9966:0,2:39.2:1:36.4:1:1:0:60:71.5:1:0:1.1
    468. 

  468. 1	226578099	226578099	T	C	intronic	PARP1	.	.	.	0.97	0.8477	0.9384	0.8246	0.6933	0.9481	0.8815	0.7819	0.8255	rs1805403	rs1805403	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18520760	COCA-CN|5|321|0.0155763	0.75	333	82	1	226578099	.	T	C	333	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1188;VD=541;AF=0.4554;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCCAGGGCAACCCCGCAG;RSEQ=GCTCCACCCACCCTTCACTC;CSQ=C|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||4/22|NM_001618.4:c.617+12A>G|||||||rs1805403||-1||EntrezGene||YES||||1:g.226578099T>C|0.8099|0.9411|0.8703|0.7187|0.9388|0.8797|0.7678|0.7752|0.7385|0.9713|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1188:541:395,146:453,193:646,541:0.4554:2,2:34:1:36.7:1:0.30199:1.15:60:1082:0.4644:0:1.5	1/1:82:82:61,21:0,0:0,82:1:0,2:41.6:1:36.6:1:1:0:60:164:1:0:1.3
    469. 

  469. 1	226589958	226589958	G	A	exonic	PARP1	.	synonymous SNV	PARP1:NM_001618:exon2:c.C243T:p.D81D	0.45	0.1842	0.1274	0.3652	0.1533	0.4411	0.2358	0.1661	0.2138	rs1805404	rs1805404	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64687027;OCCURENCE=5(haematopoietic_and_lymphoid_tissue),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU11400278	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.5	385	329	1	226589958	.	G	A	385	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3107;VD=1516;AF=0.4879;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.30099;SOR=1.06967;LSEQ=GTCTTCTTGACTTTCTGCTG;RSEQ=TCATCCCACCGAAGCTCAGA;CSQ=A|synonymous_variant|LOW|PARP1|142|Transcript|NM_001618.4|protein_coding|2/23||NM_001618.4:c.243C>T|NP_001609.2:p.Asp81%3D|407|243|81|D|gaC/gaT|rs1805404&COSV64687027||-1||EntrezGene||YES||||1:g.226589958G>A|0.2184|0.123|0.4261|0.1595|0.4479|0.2342|0.1663|0.1938|0.103|0.4479|gnomAD_EAS||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3107:1516:784,732:819,767:1586,1516:0.4879:2,2:36.7:1:36.5:1:0.97134:1:60:378:0.4892:0:1.1	0/1:329:155:79,76:77,93:170,155:0.4711:2,2:37.8:1:36.6:1:0.31906:1.25:60:154:0.4738:0:1
    470. 

  470. 1	226595495	226595495	G	A	intronic	PARP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	67	1	226595495	.	G	A	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=633;VD=2;AF=0.0032;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.0073;SOR=0.06823;LSEQ=GCGTCCCCGCCCCGCCGCCC;RSEQ=CACAGCGGCCCGCACCTGCA;CSQ=A|intron_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding||1/22|NM_001618.4:c.120+16C>T|||||||||-1||EntrezGene||YES||||1:g.226595495G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:633:2:1,1:314,316:630,2:0.0032:2,2:59:1:24:1:1:1.01:60:1:0.0016:0:1	0/1:67:3:2,1:30,33:63,3:0.0448:2,2:25.7:1:37:0:0.60769:2.17:60:6:0.0476:0:1
    471. 

  471. 1	226595647	226595647	C	G	UTR5	PARP1	NM_001618:c.-17G>C	.	.	0.44	0.1680	0.0486	0.3592	0.1656	0.4409	0.2681	0.1705	0.2263	rs907187	rs907187	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV64687065;OCCURENCE=1(breast),1(liver),1(central_nervous_system),2(haematopoietic_and_lymphoid_tissue),1(urinary_tract),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU1698315	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579,PBCA-DE|1|499|0.00200401,BRCA-KR|1|50|0.02,BLCA-CN|1|103|0.00970874	0.5	327	106	1	226595647	.	C	G	327	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=975;VD=493;AF=0.5056;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.49668;SOR=1.0228;LSEQ=CCATCCTCCCCTAGCTGCCG;RSEQ=CAAAGCTCCGGAAGCCCGAC;CSQ=G|5_prime_UTR_variant|MODIFIER|PARP1|142|Transcript|NM_001618.4|protein_coding|1/23||NM_001618.4:c.-17G>C||148|||||rs907187&COSV64687065||-1||EntrezGene||YES||||1:g.226595647C>G|0.2135|0.04649|0.4177|0.16|0.4433|0.2609|0.1652|0.1942|0.102|0.4433|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:975:493:237,256:215,267:482,493:0.5056:2,2:36.8:1:36.6:1:0.30414:1.15:60:122.25:0.5052:0:1.1	1/0:106:53:24,29:21,32:53,53:0.5:2,2:36.2:1:36.3:1:0.69454:1.26:60:52:0.5:0:1.2
    472. 

  472. 1	237048500	237048500	A	G	exonic	MTR	.	nonsynonymous SNV	MTR:NM_001291939:exon25:c.A2603G:p.D868G,MTR:NM_001291940:exon25:c.A1535G:p.D512G,MTR:NM_000254:exon26:c.A2756G:p.D919G	0.32	0.2113	0.2670	0.1878	0.1623	0.1068	0.1976	0.1944	0.2332	rs1805087	rs1805087	0.189	0.212	T	0.159	0.370	B	0.161	0.356	B	0.000	0.629	D	0.000	0.513	P	1.495	0.376	L	-0.62	0.719	T	-3.95	0.742	D	0.271	0.589	-1.079	0.075	T	0.000	0.000	T	.	.	.	3.904	0.526	23.5	0.985	0.411	0.991	0.905	D	c	0.264	0.443	1.000	0.747	0.707	0.730	0	5.99	0.973	8.536	0.904	1.088	0.866	1.000	0.715	1.000	0.888	16.494	0.840	Cobalamin (vitamin B12)-binding domain	.	.	ID=COSV63964936;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue),1(lung)	141992	Neural_tube_defects,_folate-sensitive,_susceptibility_to|Gastrointestinal_stromal_tumor|Disorders_of_Intracellular_Cobalamin_Metabolism|not_specified|none_provided	.|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MedGen:CN043592|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	MU113712	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,COCA-CN|2|321|0.00623053	0.25	235	187	1	237048500	.	A	G	235	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATGAAGATATTAGACAGG;RSEQ=CCATTATGAGTCTCTCAAGG;CSQ=G|missense_variant|MODERATE|MTR|4548|Transcript|NM_000254.3|protein_coding|26/33||NM_000254.3:c.2756A>G|NP_000245.2:p.Asp919Gly|3168|2756|919|D/G|gAc/gGc|rs1805087&CM983303&COSV63964936||1||EntrezGene||YES||||1:g.237048500A>G|0.203|0.2656|0.1842|0.168|0.1109|0.1921|0.1912|0.1966|0.311|0.3211|SAS|risk_factor&uncertain_significance&benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MTR|4548|Transcript|NM_001291939.1|protein_coding|25/32||NM_001291939.1:c.2603A>G|NP_001278868.1:p.Asp868Gly|3026|2603|868|D/G|gAc/gGc|rs1805087&CM983303&COSV63964936||1||EntrezGene||||||1:g.237048500A>G|0.203|0.2656|0.1842|0.168|0.1109|0.1921|0.1912|0.1966|0.311|0.3211|SAS|risk_factor&uncertain_significance&benign|0&0&1|1&1&1,G|missense_variant|MODERATE|MTR|4548|Transcript|NM_001291940.2|protein_coding|25/32||NM_001291940.2:c.1535A>G|NP_001278869.1:p.Asp512Gly|3055|1535|512|D/G|gAc/gGc|rs1805087&CM983303&COSV63964936||1||EntrezGene||||||1:g.237048500A>G|0.203|0.2656|0.1842|0.168|0.1109|0.1921|0.1912|0.1966|0.311|0.3211|SAS|risk_factor&uncertain_significance&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:11,19:30,0:0:2,0:28.6:1:35.7:1:1:0:60:29:1:0:0.4	0/1:187:83:37,46:50,54:104,83:0.4439:2,2:40.4:1:37:0:0.66026:1.15028:60:166:0.4439:0:1.7
    473. 

  473. 1	237048562	237048562	G	A	intronic	MTR	.	.	.	0.93	0.7243	0.8963	0.6635	0.5364	0.8224	0.6656	0.6359	0.7025	rs2275566	rs2275566	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU24513657	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,COCA-CN|5|321|0.0155763	1	252	127	1	237048562	.	G	A	252	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=6;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTGTTTTTAATGTGACT;RSEQ=TTTTTTATGATCCTAGTTTT;CSQ=A|intron_variant|MODIFIER|MTR|4548|Transcript|NM_000254.3|protein_coding||26/32|NM_000254.3:c.2775+43G>A|||||||rs2275566||1||EntrezGene||YES||||1:g.237048562G>A|0.6731|0.9063|0.6827|0.5118|0.8081|0.6517|0.6227|0.651|0.7187|0.9334|AFR|||,A|intron_variant|MODIFIER|MTR|4548|Transcript|NM_001291939.1|protein_coding||25/31|NM_001291939.1:c.2622+43G>A|||||||rs2275566||1||EntrezGene||||||1:g.237048562G>A|0.6731|0.9063|0.6827|0.5118|0.8081|0.6517|0.6227|0.651|0.7187|0.9334|AFR|||,A|intron_variant|MODIFIER|MTR|4548|Transcript|NM_001291940.2|protein_coding||25/31|NM_001291940.2:c.1554+43G>A|||||||rs2275566||1||EntrezGene||||||1:g.237048562G>A|0.6731|0.9063|0.6827|0.5118|0.8081|0.6517|0.6227|0.651|0.7187|0.9334|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:1,4:0,0:0,5:1:0,2:36:1:37:0:1:0:60:10:1:0:1.2	1/1:127:127:44,83:0,0:0,127:1:0,2:38.2:1:36.2:1:1:0:60:62.5:1:0:1.5
    474. 

  474. 1	241661084	241661084	T	C	UTR3	FH	NM_000143:c.*44A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	48	1	241661084	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=19;VD=0;AF=0;SHIFT3=0;MSI=7;MSILEN=1;SSF=0.51018;SOR=0;LSEQ=AAGAAATGGGAGTCTGTTTT;RSEQ=TTAAATTTTATACATGTTTA;CSQ=C|3_prime_UTR_variant|MODIFIER|FH|2271|Transcript|NM_000143.4|protein_coding|10/10||NM_000143.4:c.*44A>G||1610|||||||-1||EntrezGene||YES||||1:g.241661084T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:19:0:0,0:15,4:19,0:0:2,0:20.2:1:35:1:1:0:60:18:1:0:0.3	0/1:48:2:1,1:37,9:46,2:0.0417:2,2:36.5:1:37:0:0.37677:3.9525:60:4:0.0417:0:1
    475. 

  475. 1	241663903	241663904	GA	-	intronic	FH	.	.	.	.	.	.	.	.	.	.	.	.	rs879069854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	280521	Hereditary_leiomyomatosis_and_renal_cell_cancer|Fumarase_deficiency|Multiple_Cutaneous_and_Uterine_Leiomyomas	Human_Phenotype_Ontology:HP:0007437,MONDO:MONDO:0007888,MedGen:C1708350,OMIM:150800,Orphanet:ORPHA523|MONDO:MONDO:0011730,MedGen:C0342770,OMIM:606812,Orphanet:ORPHA24,SNOMED_CT:237983002|MedGen:CN239164	criteria_provided,_single_submitter	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	78	1	241663902	.	TGA	T	58	MSI12;MSI12	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=22;VD=3;AF=0.1364;SHIFT3=36;MSI=19;MSILEN=2;SSF=0.00952;SOR=inf;LSEQ=ATTTTTAATCTTTGAGTGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|FH|2271|Transcript|NM_000143.4|protein_coding||8/9|NM_000143.4:c.1237-14_1237-13del|||||||rs144131869||-1||EntrezGene||YES||||1:g.241663939_241663940del||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:22:3:1,2:8,11:19,3:0.1364:2,2:44:1:37:0:1:1.43071:60:6:0.1364:0:1.3	0/0:78:0:0,0:26,52:78,0:0:2,0:34.6:1:35.1:1:1:0:58.9:25:1:0:0.9
    476. 

  476. 1	241663906	241663906	A	T	intronic	FH	.	.	.	.	3.326e-05	0.0001	0	0	0	0	0	0	rs201040163	rs201040163	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63818425;OCCURENCE=1(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU50963483	COCA-CN|1|321|0.00311526	0.25	37	74	1	241663906	.	A	T	37	v3;pSTD;MSI12	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=2;AF=0.1111;SHIFT3=0;MSI=18;MSILEN=2;SSF=0.03655;SOR=inf;LSEQ=TTAATCTTTGAGTGAGTGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FH|2271|Transcript|NM_000143.4|protein_coding||8/9|NM_000143.4:c.1237-16T>A|||||||rs201040163&COSV63818425||-1||EntrezGene||YES||||1:g.241663906A>T|4.505e-05|0.000275|3.547e-05|0|0.0001444|0.0001341|1.076e-05|0|0|0.000275|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:18:2:1,1:6,10:16,2:0.1111:2,2:37:0:37:0:1:1.62:60:4:0.1176:0:1	0/0:74:0:0,0:23,50:73,0:0:2,0:35.3:1:35.4:1:1:0:58.8:23.333:1:0:1
    477. 

  477. 1	241665751	241665751	G	A	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon8:c.C1228T:p.P410S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.998	0.715	D	0.934	0.652	D	0.000	0.843	D	1	0.810	D	4.535	0.991	H	-5.33	0.990	D	-7.61	0.954	D	0.793	0.783	1.053	0.982	D	0.982	0.995	D	0.661	0.972	D	6.755	0.921	32	0.999	0.976	0.993	0.941	D	c	1.057	0.989	1.000	0.747	0.732	0.924	0	5.61	0.853	9.352	0.965	1.048	0.713	1.000	0.715	0.998	0.697	17.137	0.866	L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	163	1	241665751	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=93;VD=2;AF=0.0215;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13107;SOR=inf;LSEQ=TTTAAAGCTTACCATCATTG;RSEQ=CTTGAAAACATTCAACTCAA;CSQ=A|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|8/10||NM_000143.4:c.1228C>T|NP_000134.2:p.Pro410Ser|1261|1228|410|P/S|Cca/Tca|||-1||EntrezGene||YES||||1:g.241665751G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:93:2:1,1:55,36:91,2:0.0215:2,2:32.5:1:37:0:1:1.52059:60:4:0.0222:0:1	0/0:163:0:0,0:115,48:163,0:0:2,0:35.2:1:36.6:1:1:0:60:326:1:0:0.1
    478. 

  478. 1	241665786	241665786	C	T	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon8:c.G1193A:p.G398D	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	0.998	0.715	D	0.957	0.682	D	0.000	0.843	D	1	0.810	D	3.665	0.944	H	-5.34	0.990	D	-6.67	0.923	D	0.951	0.947	1.056	0.982	D	0.982	0.995	D	0.602	0.965	D	7.099	0.942	33	0.999	0.930	0.988	0.867	D	c	1.000	0.928	1.000	0.747	0.732	0.924	0	5.61	0.853	7.378	0.788	0.935	0.490	1.000	0.715	0.991	0.552	17.137	0.866	L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	230	1	241665786	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=161;VD=2;AF=0.0124;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.16893;SOR=inf;LSEQ=ACTCAAAATGTCCATTGCTG;RSEQ=CTCCGACAGTGACAGCAACA;CSQ=T|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|8/10||NM_000143.4:c.1193G>A|NP_000134.2:p.Gly398Asp|1226|1193|398|G/D|gGc/gAc|||-1||EntrezGene||YES||||1:g.241665786C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:161:2:1,1:86,73:159,2:0.0124:2,2:22:0:37:0:1:1.17688:60:4:0.0126:0:1	0/0:230:0:0,0:136,94:230,0:0:2,0:35.4:1:36.3:1:1:0:60:75.667:1:0:0
    479. 

  479. 1	241667422	241667422	C	A	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon7:c.G1028T:p.R343L	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.715	0.995	H	-6.45	0.997	D	-6.98	0.936	D	0.961	0.959	0.949	0.964	D	0.994	0.999	D	0.881	0.991	D	7.877	0.956	35	0.999	0.959	0.987	0.858	D	c	1.061	0.961	1.000	0.747	0.707	0.730	0	5.73	0.897	7.373	0.787	0.935	0.490	1.000	0.715	0.994	0.587	17.394	0.873	Fumarate lyase, N-terminal|L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	226	1	241667422	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=998;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00623;SOR=0;LSEQ=GAGGACCAGAACCCAAAAAT;RSEQ=GAATATCATTTGCTATCTTC;CSQ=A|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|7/10||NM_000143.4:c.1028G>T|NP_000134.2:p.Arg343Leu|1061|1028|343|R/L|cGa/cTa|COSV100845069||-1||EntrezGene||YES||||1:g.241667422C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:998:0:0,0:465,533:998,0:0:2,0:38.2:1:36.1:1:1:0:60:61.375:1:0:0.2	0/1:226:3:2,1:118,105:223,3:0.0133:2,2:42.3:1:28.3:1:1:1.78:60:2:0.009:0:3.3
    480. 

  480. 1	241667523	241667523	C	T	exonic	FH	.	synonymous SNV	FH:NM_000143:exon7:c.G927A:p.P309P	0.09	0.0265	0.0203	0.0239	0.0629	0.0482	0.0281	0.0266	0.0316	rs61737760	rs61737760	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63817570;OCCURENCE=2(soft_tissue)	141073	Hereditary_leiomyomatosis_and_renal_cell_cancer|Fumarase_deficiency|Hereditary_cancer-predisposing_syndrome|not_specified|none_provided|Multiple_Cutaneous_and_Uterine_Leiomyomas|not_provided	Human_Phenotype_Ontology:HP:0007437,MONDO:MONDO:0007888,MedGen:C1708350,OMIM:150800,Orphanet:ORPHA523|MONDO:MONDO:0011730,MedGen:C0342770,OMIM:606812,Orphanet:ORPHA24,SNOMED_CT:237983002|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN235283|MedGen:CN239164|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	1	1	MU113546617	COCA-CN|1|321|0.00311526	0.25	276	173	1	241667523	.	C	T	276	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=421;VD=189;AF=0.4489;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=GCCAGAGCTTCAAATTTATT;RSEQ=GGAGCAGTGACAAAAGGCAA;CSQ=T|synonymous_variant|LOW|FH|2271|Transcript|NM_000143.4|protein_coding|7/10||NM_000143.4:c.927G>A|NP_000134.2:p.Pro309%3D|960|927|309|P|ccG/ccA|rs61737760&COSV63817570||-1||EntrezGene||YES||||1:g.241667523C>T|0.03455|0.0205|0.02748|0.05361|0.04505|0.02293|0.02353|0.0351|0.08638|0.09|SAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:421:189:49,140:67,165:232,189:0.4489:2,2:28.6:1:36.5:1:0.51266:1.15976:59.9:93.5:0.4474:0:1.1	0/0:173:0:0,0:60,113:173,0:0:2,0:36.6:1:36.6:1:1:0:60:346:1:0:0.1
    481. 

  481. 1	241669271	241669271	G	A	intronic	FH	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs758146903	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	96	1	241669271	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=2;AF=0.0465;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.09415;SOR=inf;LSEQ=GACCACGTATAATGAGAAAT;RSEQ=AAAATGAGAAATAATTCACG;CSQ=A|intron_variant|MODIFIER|FH|2271|Transcript|NM_000143.4|protein_coding||6/9|NM_000143.4:c.904+32C>T|||||||rs758146903||-1||EntrezGene||YES||||1:g.241669271G>A|3.988e-06|0|0|0|5.439e-05|0|0|0|0|5.439e-05|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:43:2:1,1:31,10:41,2:0.0465:2,2:30:1:37:0:0.45072:3.003:60:4:0.0465:0:1	0/0:96:0:0,0:65,31:96,0:0:2,0:34.8:1:35.7:1:1:0:60:31:1:0:0.1
    482. 

  482. 1	241669280	241669280	A	G	intronic	FH	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	103	1	241669280	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=53;VD=2;AF=0.0377;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.11398;SOR=inf;LSEQ=TAATGAGAAATGAAAATGAG;RSEQ=AATAATTCACGTGATCACTA;CSQ=G|intron_variant|MODIFIER|FH|2271|Transcript|NM_000143.4|protein_coding||6/9|NM_000143.4:c.904+23T>C|||||||||-1||EntrezGene||YES||||1:g.241669280A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:53:2:1,1:36,15:51,2:0.0377:2,2:36.5:1:37:0:0.51669:2.35586:60:4:0.0385:0:1	0/0:103:0:0,0:68,35:103,0:0:2,0:35.9:1:36:1:1:0:60:33.333:1:0:0.1
    483. 

  483. 1	241669309	241669309	G	A	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon6:c.C898T:p.L300F	.	.	.	.	.	.	.	.	.	.	.	0.157	0.240	T	0.015	0.158	B	0.078	0.271	B	0.000	0.559	D	1	0.810	D	1.725	0.447	L	-5.77	0.993	D	-1.82	0.427	N	0.84	0.827	0.998	0.972	D	0.930	0.977	D	0.294	0.907	D	2.624	0.376	20.3	0.995	0.678	0.987	0.851	D	c	-0.023	0.127	1.000	0.747	0.707	0.730	0	4.85	0.622	6.227	0.720	0.143	0.228	1.000	0.715	0.917	0.393	12.443	0.548	Fumarate lyase, N-terminal|L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	125	1	241669309	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=2;AF=0.0163;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.24497;SOR=inf;LSEQ=ACGTGATCACTAACCTGTAA;RSEQ=TGCAGCCACTTTTGCAGCAA;CSQ=A|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|6/10||NM_000143.4:c.898C>T|NP_000134.2:p.Leu300Phe|931|898|300|L/F|Ctt/Ttt|||-1||EntrezGene||YES||||1:g.241669309G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:69,52:121,2:0.0163:2,2:18:0:37:0:1:1.32382:60:4:0.0167:0:1	0/0:125:0:0,0:73,52:125,0:0:2,0:39.3:1:36:1:1:0:60:61.5:1:0:0.1
    484. 

  484. 1	241669310	241669310	T	C	exonic	FH	.	synonymous SNV	FH:NM_000143:exon6:c.A897G:p.A299A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	472302	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	126	1	241669310	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=2;AF=0.0163;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.243;SOR=inf;LSEQ=CGTGATCACTAACCTGTAAG;RSEQ=GCAGCCACTTTTGCAGCAAC;CSQ=C|synonymous_variant|LOW|FH|2271|Transcript|NM_000143.4|protein_coding|6/10||NM_000143.4:c.897A>G|NP_000134.2:p.Ala299%3D|930|897|299|A|gcA/gcG|rs1553341151||-1||EntrezGene||YES||||1:g.241669310T>C||||||||||||likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:69,52:121,2:0.0163:2,2:19:1:37:0:1:1.32382:60:4:0.0167:0:1	0/0:126:0:0,0:74,52:126,0:0:2,0:39.3:1:36.6:1:1:0:60:252:1:0:0.1
    485. 

  485. 1	241669324	241669324	C	A	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon6:c.G883T:p.A295S	.	.	.	.	.	.	.	.	.	.	.	0.178	0.221	T	0.001	0.067	B	0.018	0.173	B	0.008	0.311	N	1.000	0.588	D	1.42	0.358	L	-6.3	0.996	D	-0.79	0.219	N	0.178	0.217	1.134	0.999	D	0.952	0.984	D	0.410	0.936	D	2.729	0.389	21.0	0.983	0.399	0.939	0.591	D	c	-0.106	0.044	1.000	0.489	0.707	0.730	0	4.83	0.617	2.761	0.470	0.935	0.490	0.994	0.380	0.943	0.417	13.719	0.620	Fumarate lyase, N-terminal|L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	127	1	241669324	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.26835;SOR=inf;LSEQ=TGTAAGTGCAGCCACTTTTG;RSEQ=AGCAACCTTTTCTGCAAAGC;CSQ=A|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|6/10||NM_000143.4:c.883G>T|NP_000134.2:p.Ala295Ser|916|883|295|A/S|Gca/Tca|||-1||EntrezGene||YES||||1:g.241669324C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:73,62:135,2:0.0146:2,2:30:0:37:0:1:1.17601:60:4:0.0149:0:1	0/0:127:0:0,0:70,57:127,0:0:2,0:41.8:1:35.6:1:1:0:60:24.4:1:0:0.1
    486. 

  486. 1	241669429	241669429	T	C	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon6:c.A778G:p.T260A	.	.	.	.	.	.	.	.	.	.	.	0.699	0.042	T	0.0	0.026	B	0.0	0.013	B	0.517	0.118	N	1	0.090	N	-1.47	0.005	N	-5.7	0.993	D	0.87	0.017	N	0.073	0.062	0.390	0.889	D	0.756	0.917	D	0.049	0.638	D	-1.502	0.017	0.003	0.302	0.016	0.037	0.089	N	c	-1.438	-1.307	0.991	0.322	0.707	0.730	0	1.19	0.200	1.185	0.315	-0.906	0.026	0.003	0.159	0.758	0.324	3.909	0.086	Fumarate lyase, N-terminal|L-Aspartase-like	.	.	ID=COSV100844992;OCCURENCE=1(breast)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU131709154	BRCA-US|1|1020|0.000980392	0.25	37	102	1	241669429	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.31974;SOR=0;LSEQ=CATGGCAGCTTTTATTCTTG;RSEQ=CATTGCATATTTTACTTGTT;CSQ=C|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|6/10||NM_000143.4:c.778A>G|NP_000134.2:p.Thr260Ala|811|778|260|T/A|Aca/Gca|COSV100844992||-1||EntrezGene||YES||||1:g.241669429T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:78:0:0,0:30,48:78,0:0:2,0:23:1:36.7:1:1:0:60:156:1:0:0	0/1:102:2:1,1:37,63:100,2:0.0196:2,2:24.5:1:37:0:1:1.69:60:4:0.0198:0:1
    487. 

  487. 1	241676963	241676963	T	C	exonic	FH	.	synonymous SNV	FH:NM_000143:exon3:c.A318G:p.V106V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	166	1	241676963	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.49387;SOR=0;LSEQ=TCAAGACCATAATCCTGGTT;RSEQ=ACTTCAGCGGCCGCTCGCTT;CSQ=C|synonymous_variant|LOW|FH|2271|Transcript|NM_000143.4|protein_coding|3/10||NM_000143.4:c.318A>G|NP_000134.2:p.Val106%3D|351|318|106|V|gtA/gtG|||-1||EntrezGene||YES||||1:g.241676963T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:70:0:0,0:28,42:70,0:0:2,0:32.6:1:36.7:1:1:0:60:140:1:0:0.3	0/1:166:2:1,1:84,80:164,2:0.012:2,2:32.5:1:37:0:1:1.04971:60:4:0.0121:0:1
    488. 

  488. 1	241680485	241680485	C	T	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon2:c.G264A:p.M88I	.	.	.	.	.	.	.	.	.	.	.	0.021	0.491	D	0.788	0.426	P	0.865	0.597	P	0.000	0.629	D	1	0.810	D	1.715	0.445	L	-6.21	0.996	D	-3.67	0.701	D	0.839	0.826	1.080	0.989	D	0.975	0.992	D	0.642	0.970	D	6.898	0.931	33	0.998	0.909	0.994	0.955	D	c	0.664	0.715	1.000	0.747	0.706	0.609	0	5.6	0.849	7.275	0.778	0.935	0.490	1.000	0.715	1.000	0.888	17.471	0.875	Fumarase/histidase, N-terminal|Fumarate lyase, N-terminal|L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	173	1	241680485	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=189;VD=2;AF=0.0106;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.2719;SOR=inf;LSEQ=CCACAAATGCCACTTACTGG;RSEQ=ATGCGTTCTGTCACACCTCC;CSQ=T|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|2/10||NM_000143.4:c.264G>A|NP_000134.2:p.Met88Ile|297|264|88|M/I|atG/atA|||-1||EntrezGene||YES||||1:g.241680485C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:189:2:1,1:103,84:187,2:0.0106:2,2:22:0:37:0:1:1.22485:60:4:0.0106:0:1	0/0:173:0:0,0:101,72:173,0:0:2,0:42.1:1:36.1:1:1:0:60:56.667:1:0:0.1
    489. 

  489. 1	241680562	241680562	G	T	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon2:c.C187A:p.P63T	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.99	0.774	D	0.000	0.843	D	1	0.810	D	4.425	0.988	H	-7.89	0.999	D	-6.77	0.928	D	0.95	0.946	0.928	0.961	D	0.997	0.999	D	0.819	0.986	D	5.568	0.757	26.4	0.998	0.889	0.990	0.900	D	c	1.117	1.017	1.000	0.747	0.706	0.609	0	5.75	0.904	9.455	0.968	1.048	0.713	1.000	0.715	0.980	0.490	17.794	0.884	Fumarase/histidase, N-terminal|Fumarate lyase, N-terminal|L-Aspartase-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	183	1	241680562	.	G	T	44	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=152;VD=1;AF=0.0066;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.38402;SOR=0.39835;LSEQ=GCCATAATACTTATCATTTG;RSEQ=CACCTTTAGTTCACCAAAGG;CSQ=T|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|2/10||NM_000143.4:c.187C>A|NP_000134.2:p.Pro63Thr|220|187|63|P/T|Cca/Aca|||-1||EntrezGene||YES||||1:g.241680562G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:152:1:1,0:68,83:151,1:0.0066:2,0:2:0:11:0:0.45395:0:60:0:0:0:5	0/1:183:3:1,2:86,94:180,3:0.0164:2,2:14.3:1:28.3:1:1:1.82399:60:2:0.011:0:2
    490. 

  490. 1	241680586	241680586	C	T	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon2:c.G163A:p.D55N	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	0	0.065	N	-6.5	0.997	D	-4.64	0.793	D	0.391	0.451	1.089	0.992	D	0.970	0.991	D	0.768	0.982	D	6.321	0.873	29.2	0.999	0.989	0.980	0.784	D	c	0.565	0.611	1.000	0.747	0.706	0.609	0	5.75	0.904	7.438	0.794	0.935	0.490	1.000	0.715	0.875	0.366	17.794	0.884	Fumarase/histidase, N-terminal|L-Aspartase-like	.	.	ID=COSV63818158;OCCURENCE=1(stomach)	921957	Fumarase_deficiency	MONDO:MONDO:0011730,MedGen:C0342770,OMIM:606812,Orphanet:ORPHA24,SNOMED_CT:237983002	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	164	1	241680586	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=98;VD=2;AF=0.0204;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13901;SOR=inf;LSEQ=CTTTAGTTCACCAAAGGTAT;RSEQ=ATATTCTATCCGGAAGGAAT;CSQ=T|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|2/10||NM_000143.4:c.163G>A|NP_000134.2:p.Asp55Asn|196|163|55|D/N|Gat/Aat|COSV63818158||-1||EntrezGene||YES||||1:g.241680586C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:98:2:1,1:39,57:96,2:0.0204:2,2:27:0:37:0:1:1.46:60:4:0.0206:0:1	0/0:164:0:0,0:67,97:164,0:0:2,0:35:1:36.1:1:1:0:60:53.667:1:0:0.1
    491. 

  491. 1	241682877	241682877	C	T	intronic	FH	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	120	1	241682877	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=596;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.02789;SOR=0;LSEQ=GCGGGGAGGCCGGGGGATGG;RSEQ=GGCCTGCGCTCACCATTCGA;CSQ=T|intron_variant|MODIFIER|FH|2271|Transcript|NM_000143.4|protein_coding||1/9|NM_000143.4:c.132+14G>A|||||||||-1||EntrezGene||YES||||1:g.241682877C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:596:0:0,0:401,194:595,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:120:2:1,1:73,45:118,2:0.0167:2,2:27.5:1:37:0:1:1.61538:60:4:0.0169:0:1
    492. 

  492. 1	241682965	241682965	C	T	exonic	FH	.	nonsynonymous SNV	FH:NM_000143:exon1:c.G58A:p.A20T	0.011	.	.	.	.	.	.	.	.	rs572324497	.	0.595	0.057	T	0.043	0.202	B	0.008	0.127	B	0.303	0.146	N	1	0.090	N	0	0.065	N	-6.28	0.996	D	0.19	0.050	N	0.229	0.281	0.832	0.948	D	0.864	0.955	D	0.471	0.947	D	0.863	0.176	9.849	0.931	0.221	0.070	0.129	N	c	-1.438	-1.450	1.000	0.747	0.442	0.072	0	-3.62	0.042	-0.131	0.104	-0.203	0.101	0.000	0.063	0.002	0.062	7.598	0.271	.	.	.	.	806587	Fumarase_deficiency|Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0011730,MedGen:C0342770,OMIM:606812,Orphanet:ORPHA24,SNOMED_CT:237983002|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	175	1	241682965	.	C	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1122;VD=1;AF=0.0009;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00872;SOR=0.05136;LSEQ=GGGAGCCGAAGCTAAGGCTG;RSEQ=GGCTGGAGCCCGCACGAGGG;CSQ=T|missense_variant|MODERATE|FH|2271|Transcript|NM_000143.4|protein_coding|1/10||NM_000143.4:c.58G>A|NP_000134.2:p.Ala20Thr|91|58|20|A/T|Gca/Aca|rs572324497||-1||EntrezGene||YES||||1:g.241682965C>T|2.744e-05|0|0.0001636|0|0|0|0|0|0|0.0014|AMR|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1122:1:0,1:635,485:1120,1:0.0009:2,0:22:0:37:0:0.43354:0:60:2:0.0009:0:1	0/1:175:3:1,2:91,81:172,3:0.0171:2,2:43:1:37:0:0.60427:2.23685:60:6:0.0173:0:1.3
    493. 

  493. 1	241683062	241683062	G	T	UTR5	FH	NM_000143:c.-40C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	176	1	241683062	.	G	T	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1229;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01561;SOR=0;LSEQ=TAGAATTTCTGGGCGGCTGT;RSEQ=GCCACGCCTCCACGCCGGTT;CSQ=T|upstream_gene_variant|MODIFIER|FH|2271|Transcript|NM_000143.4|protein_coding|||||||||||7|-1||EntrezGene||YES||||1:g.241683062G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1229:0:0,0:531,697:1228,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:176:2:0,2:79,95:174,2:0.0114:2,0:15.5:1:31:1:0.5024:0:60:4:0.0114:0:4
    494. 

  494. 1	243668558	243668558	C	T	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon13:c.G1433A:p.R478Q	0.0002	.	.	.	.	.	.	.	.	rs751275167	.	0.019	0.501	D	0.935	0.503	P	0.097	0.288	B	0.000	0.629	D	1.000	0.810	D	2	0.545	M	-0.28	0.676	T	-0.44	0.146	N	0.51	0.554	-0.423	0.713	T	0.239	0.607	T	0.026	0.488	D	5.376	0.728	25.9	0.999	0.984	0.977	0.762	D	c	0.418	0.460	1.000	0.747	0.722	0.854	0	5.27	0.737	4.088	0.572	0.935	0.490	0.999	0.424	0.999	0.750	19.091	0.932	AGC-kinase, C-terminal	.	.	ID=COSV55615010;OCCURENCE=3(large_intestine),1(biliary_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU124251	COAD-US|1|402|0.00248756,READ-US|1|143|0.00699301	0.25	37	178	1	243668558	.	C	T	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=174;VD=2;AF=0.0115;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.24364;SOR=inf;LSEQ=GAATGAAAGAGACTTATTCT;RSEQ=GTCCACTTGCAGAGTAGGAA;CSQ=T|intron_variant|MODIFIER|AKT3|10000|Transcript|NM_001206729.2|protein_coding||13/13|NM_001206729.2:c.1355-5470G>A|||||||rs751275167&COSV55615010||-1||EntrezGene||||||1:g.243668558C>T|3.978e-06|0|0|0|0|4.62e-05|0|0|0|4.62e-05|gnomAD_FIN||0&1|0&1,T|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|14/14||NM_001370074.1:c.1433G>A|NP_001357003.1:p.Arg478Gln|1576|1433|478|R/Q|cGa/cAa|rs751275167&COSV55615010||-1||EntrezGene||||||1:g.243668558C>T|3.978e-06|0|0|0|0|4.62e-05|0|0|0|4.62e-05|gnomAD_FIN||0&1|0&1,T|missense_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|14/14||NM_005465.7:c.1433G>A|NP_005456.1:p.Arg478Gln|1749|1433|478|R/Q|cGa/cAa|rs751275167&COSV55615010||-1||EntrezGene||YES||||1:g.243668558C>T|3.978e-06|0|0|0|0|4.62e-05|0|0|0|4.62e-05|gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|AKT3|10000|Transcript|NM_181690.2|protein_coding||12/13|NM_181690.2:c.1355-5470G>A|||||||rs751275167&COSV55615010||-1||EntrezGene||||||1:g.243668558C>T|3.978e-06|0|0|0|0|4.62e-05|0|0|0|4.62e-05|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:174:2:1,1:73,99:172,2:0.0115:2,2:5:0:37:0:1:1.35:60:4:0.0116:0:1	0/0:178:0:0,0:98,80:178,0:0:2,0:35.2:1:36.2:1:1:0:60:88:1:0:0.1
    495. 

  495. 1	243668593	243668593	C	T	exonic	AKT3	.	synonymous SNV	AKT3:NM_005465:exon13:c.G1398A:p.P466P	0.0008	0.0003	0.0001	0	0	0	0.0014	6.66e-05	0.0010	rs150573714	rs150573714	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55617471;OCCURENCE=2(large_intestine),1(urinary_tract),1(endometrium)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129131902	UCEC-US|1|531|0.00188324	0.25	37	199	1	243668593	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=172;VD=2;AF=0.0116;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.21426;SOR=inf;LSEQ=TAGGAAAATTGAGGGAAATG;RSEQ=GGCCGCCTCTCATTGTCCAT;CSQ=T|intron_variant|MODIFIER|AKT3|10000|Transcript|NM_001206729.2|protein_coding||13/13|NM_001206729.2:c.1355-5505G>A|||||||rs150573714&COSV55617471||-1||EntrezGene||||||1:g.243668593C>T|0.0001313|0.0002462|0|0|5.437e-05|0.0007854|7.914e-05|0.0001629|3.268e-05|0.0007854|gnomAD_FIN||0&1|0&1,T|synonymous_variant|LOW|AKT3|10000|Transcript|NM_001370074.1|protein_coding|14/14||NM_001370074.1:c.1398G>A|NP_001357003.1:p.Pro466%3D|1541|1398|466|P|ccG/ccA|rs150573714&COSV55617471||-1||EntrezGene||||||1:g.243668593C>T|0.0001313|0.0002462|0|0|5.437e-05|0.0007854|7.914e-05|0.0001629|3.268e-05|0.0007854|gnomAD_FIN||0&1|0&1,T|synonymous_variant|LOW|AKT3|10000|Transcript|NM_005465.7|protein_coding|14/14||NM_005465.7:c.1398G>A|NP_005456.1:p.Pro466%3D|1714|1398|466|P|ccG/ccA|rs150573714&COSV55617471||-1||EntrezGene||YES||||1:g.243668593C>T|0.0001313|0.0002462|0|0|5.437e-05|0.0007854|7.914e-05|0.0001629|3.268e-05|0.0007854|gnomAD_FIN||0&1|0&1,T|intron_variant|MODIFIER|AKT3|10000|Transcript|NM_181690.2|protein_coding||12/13|NM_181690.2:c.1355-5505G>A|||||||rs150573714&COSV55617471||-1||EntrezGene||||||1:g.243668593C>T|0.0001313|0.0002462|0|0|5.437e-05|0.0007854|7.914e-05|0.0001629|3.268e-05|0.0007854|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:172:2:1,1:63,107:170,2:0.0116:2,2:23:0:37:0:1:1.69:60:4:0.0118:0:1	0/0:199:0:0,0:101,98:199,0:0:2,0:42.6:1:36.7:1:1:0:60:198:1:0:0.1
    496. 

  496. 1	243708891	243708891	C	A	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon11:c.G1172T:p.G391V,AKT3:NM_181690:exon11:c.G1172T:p.G391V,AKT3:NM_001206729:exon12:c.G1172T:p.G391V	.	.	.	.	.	.	.	.	.	.	.	0.036	0.574	D	0.994	0.647	D	0.965	0.695	D	0.000	0.843	D	1	0.810	D	0.39	0.122	N	0.65	0.527	T	-7.72	0.957	D	0.838	0.831	-0.700	0.604	T	0.183	0.531	T	0.033	0.551	D	7.187	0.945	34	0.997	0.831	0.990	0.904	D	c	0.663	0.738	1.000	0.747	0.644	0.439	0	5.86	0.939	7.905	0.864	0.935	0.490	1.000	0.715	0.998	0.697	20.199	0.982	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	97	1	243708891	.	C	A	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.92043;SOR=0;LSEQ=CTTTTGCATCATCTGGTCCT;RSEQ=CACCAAGGCTATGAGAACAG;CSQ=A|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001206729.2|protein_coding|12/14||NM_001206729.2:c.1172G>T|NP_001193658.1:p.Gly391Val|1325|1172|391|G/V|gGa/gTa|COSV55637940||-1||EntrezGene||||||1:g.243708891C>A|||||||||||||1|1,A|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|12/14||NM_001370074.1:c.1172G>T|NP_001357003.1:p.Gly391Val|1315|1172|391|G/V|gGa/gTa|COSV55637940||-1||EntrezGene||||||1:g.243708891C>A|||||||||||||1|1,A|missense_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|12/14||NM_005465.7:c.1172G>T|NP_005456.1:p.Gly391Val|1488|1172|391|G/V|gGa/gTa|COSV55637940||-1||EntrezGene||YES||||1:g.243708891C>A|||||||||||||1|1,A|missense_variant|MODERATE|AKT3|10000|Transcript|NM_181690.2|protein_coding|11/14||NM_181690.2:c.1172G>T|NP_859029.1:p.Gly391Val|1284|1172|391|G/V|gGa/gTa|COSV55637940||-1||EntrezGene||||||1:g.243708891C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:1:0:37:0:1:0:60:4:1:0:0	0/1:97:4:2,2:43,50:93,4:0.0412:2,2:42.2:1:37:0:1:1.16:60:8:0.0417:0:1
    497. 

  497. 1	243716167	243716167	T	C	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon10:c.A1027G:p.R343G,AKT3:NM_181690:exon10:c.A1027G:p.R343G,AKT3:NM_001206729:exon11:c.A1027G:p.R343G	.	.	.	.	.	.	.	.	.	.	.	0.025	0.524	D	0.997	0.689	D	0.936	0.654	D	0.000	0.843	D	1	0.810	D	1.29	0.325	L	-0.23	0.667	T	-6.78	0.928	D	0.979	0.986	-0.449	0.705	T	0.332	0.700	T	0.052	0.652	D	5.768	0.788	27.0	0.999	0.948	0.902	0.510	D	c	0.347	0.340	1.000	0.446	0.644	0.439	0	4.24	0.493	1.880	0.390	0.060	0.166	1.000	0.715	0.997	0.653	11.376	0.488	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	191	1	243716167	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.88499;SOR=0;LSEQ=CTGGTTGTAGAAAGGTAACC;RSEQ=CCCACACATCATTTCATACA;CSQ=C|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001206729.2|protein_coding|11/14||NM_001206729.2:c.1027A>G|NP_001193658.1:p.Arg343Gly|1180|1027|343|R/G|Agg/Ggg|||-1||EntrezGene||||||1:g.243716167T>C||||||||||||||,C|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|11/14||NM_001370074.1:c.1027A>G|NP_001357003.1:p.Arg343Gly|1170|1027|343|R/G|Agg/Ggg|||-1||EntrezGene||||||1:g.243716167T>C||||||||||||||,C|missense_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|11/14||NM_005465.7:c.1027A>G|NP_005456.1:p.Arg343Gly|1343|1027|343|R/G|Agg/Ggg|||-1||EntrezGene||YES||||1:g.243716167T>C||||||||||||||,C|missense_variant|MODERATE|AKT3|10000|Transcript|NM_181690.2|protein_coding|10/14||NM_181690.2:c.1027A>G|NP_859029.1:p.Arg343Gly|1139|1027|343|R/G|Agg/Ggg|||-1||EntrezGene||||||1:g.243716167T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:5,7:12,0:0:2,0:48.1:1:36:1:1:0:60:24:1:0:0	0/1:191:2:1,1:97,92:189,2:0.0105:2,2:31:0:31:1:1:1.05408:60:4:0.0105:0:1
    498. 

  498. 1	243716209	243716209	A	G	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon10:c.T985C:p.W329R,AKT3:NM_181690:exon10:c.T985C:p.W329R,AKT3:NM_001206729:exon11:c.T985C:p.W329R	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	2.955	0.853	M	-0.16	0.654	T	-13.67	1.000	D	0.984	0.988	0.193	0.858	D	0.508	0.815	D	0.102	0.775	D	6.177	0.852	28.6	0.997	0.780	0.988	0.874	D	c	0.911	0.850	1.000	0.747	0.644	0.439	0	5.32	0.753	9.325	0.960	1.088	0.866	1.000	0.715	1.000	0.888	15.272	0.733	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	181	1	243716209	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.88842;SOR=0;LSEQ=GACAACCCCTAGGCCCCACC;RSEQ=GTCTACTGCTCGGCCATAGT;CSQ=G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001206729.2|protein_coding|11/14||NM_001206729.2:c.985T>C|NP_001193658.1:p.Trp329Arg|1138|985|329|W/R|Tgg/Cgg|||-1||EntrezGene||||||1:g.243716209A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|11/14||NM_001370074.1:c.985T>C|NP_001357003.1:p.Trp329Arg|1128|985|329|W/R|Tgg/Cgg|||-1||EntrezGene||||||1:g.243716209A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|11/14||NM_005465.7:c.985T>C|NP_005456.1:p.Trp329Arg|1301|985|329|W/R|Tgg/Cgg|||-1||EntrezGene||YES||||1:g.243716209A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_181690.2|protein_coding|10/14||NM_181690.2:c.985T>C|NP_859029.1:p.Trp329Arg|1097|985|329|W/R|Tgg/Cgg|||-1||EntrezGene||||||1:g.243716209A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:5,6:11,0:0:2,0:16.9:1:35.9:1:1:0:60:22:1:0:0	0/1:181:2:1,1:74,105:179,2:0.011:2,2:39.5:1:37:0:1:1.42:60:4:0.0112:0:1
    499. 

  499. 1	243716244	243716244	A	G	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon10:c.T950C:p.V317A,AKT3:NM_181690:exon10:c.T950C:p.V317A,AKT3:NM_001206729:exon11:c.T950C:p.V317A	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.994	0.807	D	0.000	0.843	D	1	0.810	D	1.26	0.320	L	-0.49	0.704	T	-3.85	0.723	D	0.836	0.833	0.105	0.843	D	0.515	0.818	D	0.031	0.537	D	5.738	0.784	26.9	0.999	0.960	0.998	0.992	D	c	0.807	0.782	1.000	0.747	0.644	0.439	0	5.32	0.753	9.246	0.945	1.088	0.866	1.000	0.715	1.000	0.888	15.272	0.733	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	136	1	243716244	.	A	G	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.9854;SOR=0;LSEQ=CATAGTCATTATCTTCTAAC;RSEQ=CCTAAAAGTGAAATCAGTAA;CSQ=G|missense_variant&splice_region_variant|MODERATE|AKT3|10000|Transcript|NM_001206729.2|protein_coding|11/14||NM_001206729.2:c.950T>C|NP_001193658.1:p.Val317Ala|1103|950|317|V/A|gTg/gCg|||-1||EntrezGene||||||1:g.243716244A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|11/14||NM_001370074.1:c.950T>C|NP_001357003.1:p.Val317Ala|1093|950|317|V/A|gTg/gCg|||-1||EntrezGene||||||1:g.243716244A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|11/14||NM_005465.7:c.950T>C|NP_005456.1:p.Val317Ala|1266|950|317|V/A|gTg/gCg|||-1||EntrezGene||YES||||1:g.243716244A>G||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|AKT3|10000|Transcript|NM_181690.2|protein_coding|10/14||NM_181690.2:c.950T>C|NP_859029.1:p.Val317Ala|1062|950|317|V/A|gTg/gCg|||-1||EntrezGene||||||1:g.243716244A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:70:0:37:0:1:0:60:2:1:0:0	0/1:136:2:1,1:49,85:134,2:0.0147:2,2:42:1:37:0:1:1.73:60:4:0.0149:0:1
    500. 

  500. 1	243727127	243727127	T	-	exonic	AKT3	.	frameshift deletion	AKT3:NM_005465:exon9:c.843delA:p.D282Mfs*4,AKT3:NM_181690:exon9:c.843delA:p.D282Mfs*4,AKT3:NM_001206729:exon10:c.843delA:p.D282Mfs*4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	96	1	243727126	.	CT	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=11;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.80409;SOR=0;LSEQ=TGTAATTTTTATGTGGCCAT;RSEQ=TTGTCCAGCATTAGATTCTC;CSQ=-|frameshift_variant|HIGH|AKT3|10000|Transcript|NM_001206729.2|protein_coding|10/14||NM_001206729.2:c.843del|NP_001193658.1:p.Asp282MetfsTer4|996|843|281|K/X|aaA/aa|||-1||EntrezGene||||||1:g.243727129del||||||||||||||,-|frameshift_variant|HIGH|AKT3|10000|Transcript|NM_001370074.1|protein_coding|10/14||NM_001370074.1:c.843del|NP_001357003.1:p.Asp282MetfsTer4|986|843|281|K/X|aaA/aa|||-1||EntrezGene||||||1:g.243727129del||||||||||||||,-|frameshift_variant|HIGH|AKT3|10000|Transcript|NM_005465.7|protein_coding|10/14||NM_005465.7:c.843del|NP_005456.1:p.Asp282MetfsTer4|1159|843|281|K/X|aaA/aa|||-1||EntrezGene||YES||||1:g.243727129del||||||||||||||,-|frameshift_variant|HIGH|AKT3|10000|Transcript|NM_181690.2|protein_coding|9/14||NM_181690.2:c.843del|NP_859029.1:p.Asp282MetfsTer4|955|843|281|K/X|aaA/aa|||-1||EntrezGene||||||1:g.243727129del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:2,9:11,0:0:2,0:26.2:1:35.9:1:1:0:60:22:1:0:0.1	0/1:96:2:1,1:35,59:94,2:0.0208:2,2:48:1:37:0:1:1.68:60:4:0.0208:0:0
    501. 

  501. 1	243736320	243736320	A	G	exonic	AKT3	.	nonsynonymous SNV	AKT3:NM_005465:exon8:c.T727C:p.F243L,AKT3:NM_181690:exon8:c.T727C:p.F243L,AKT3:NM_001206729:exon9:c.T727C:p.F243L	.	.	.	.	.	.	.	.	.	.	.	0.008	0.586	D	0.989	0.609	D	0.869	0.600	P	0.000	0.843	D	1	0.810	D	-0.13	0.045	N	0.17	0.605	T	-5.67	0.871	D	0.852	0.853	-0.598	0.649	T	0.209	0.569	T	0.016	0.379	T	6.405	0.884	29.6	0.999	0.945	0.954	0.645	D	c	0.611	0.694	1.000	0.747	0.644	0.439	0	5.87	0.942	9.325	0.960	1.199	0.960	1.000	0.715	1.000	0.888	16.27	0.824	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	252	1	243736320	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=2;AF=0.0339;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.03549;SOR=inf;LSEQ=ACGTGTGCGGTCCTCAGAGA;RSEQ=CACCCGCTCTCTCGACAAAT;CSQ=G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001206729.2|protein_coding|9/14||NM_001206729.2:c.727T>C|NP_001193658.1:p.Phe243Leu|880|727|243|F/L|Ttc/Ctc|||-1||EntrezGene||||||1:g.243736320A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_001370074.1|protein_coding|9/14||NM_001370074.1:c.727T>C|NP_001357003.1:p.Phe243Leu|870|727|243|F/L|Ttc/Ctc|||-1||EntrezGene||||||1:g.243736320A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_005465.7|protein_coding|9/14||NM_005465.7:c.727T>C|NP_005456.1:p.Phe243Leu|1043|727|243|F/L|Ttc/Ctc|||-1||EntrezGene||YES||||1:g.243736320A>G||||||||||||||,G|missense_variant|MODERATE|AKT3|10000|Transcript|NM_181690.2|protein_coding|8/14||NM_181690.2:c.727T>C|NP_859029.1:p.Phe243Leu|839|727|243|F/L|Ttc/Ctc|||-1||EntrezGene||||||1:g.243736320A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:59:2:1,1:30,27:57,2:0.0339:2,2:44:0:37:0:1:1.10912:60:4:0.0357:0:1	0/0:252:0:0,0:126,126:252,0:0:2,0:39.4:1:35.4:1:1:0:60:35:1:0:0.2
    502. 

  502. 1	246670333	246670333	A	G	intronic	SMYD3	.	.	.	1.	0.9833	0.9731	0.9868	0.9570	0.9987	0.9948	0.9851	0.9846	rs6426303	rs6426303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81725256	COCA-CN|5|321|0.0155763	0.5	74	0	1	246670333	.	A	G	74	d5	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGCTCGCGACTCAGGT;RSEQ=GGCGAGGGCGCTCCTTACGC;CSQ=G|intron_variant|MODIFIER|SMYD3|64754|Transcript|NM_001167740.2|protein_coding||1/11|NM_001167740.2:c.164+23T>C|||||||rs6426303||-1||EntrezGene||YES||||1:g.246670333A>G|0.9858|0.9693|0.9868|0.964|0.9992|0.9936|0.9824|0.9664|0.9958|1|EAS|||,G|intron_variant|MODIFIER|SMYD3|64754|Transcript|NM_001375962.1|protein_coding||1/10|NM_001375962.1:c.164+23T>C|||||||rs6426303||-1||EntrezGene||||||1:g.246670333A>G|0.9858|0.9693|0.9868|0.964|0.9992|0.9936|0.9824|0.9664|0.9958|1|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:1,3:0,0:0,4:1:0,2:39.5:1:37:0:1:0:60:8:1:0:1.5	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    503. 

  503. 2	16085556	16085556	T	C	intronic	MYCN	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	200	2	16085556	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=2;SSF=0.5776;SOR=0;LSEQ=CATACATATTAACATGGATA;RSEQ=ATATGTGAATTTCATTCAAA;CSQ=C|intron_variant|MODIFIER|MYCN|4613|Transcript|NM_001293228.2|protein_coding||2/2|NM_001293228.2:c.791-59T>C|||||||||1||EntrezGene||YES||||2:g.16085556T>C||||||||||||||,C|intron_variant|MODIFIER|MYCN|4613|Transcript|NM_001293231.2|protein_coding||1/1|NM_001293231.2:c.158-59T>C|||||||||1||EntrezGene||||||2:g.16085556T>C||||||||||||||,C|intron_variant|MODIFIER|MYCN|4613|Transcript|NM_001293233.2|protein_coding||2/2|NM_001293233.2:c.*726-59T>C|||||||||1||EntrezGene||||||2:g.16085556T>C||||||||||||||,C|intron_variant|MODIFIER|MYCN|4613|Transcript|NM_005378.6|protein_coding||2/2|NM_005378.6:c.791-59T>C|||||||||1||EntrezGene||||||2:g.16085556T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_110230.2|lncRNA|||||||||||3749|-1||EntrezGene||YES||||2:g.16085556T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_161162.1|lncRNA|||||||||||3749|-1||EntrezGene||||||2:g.16085556T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_161163.1|lncRNA|||||||||||3001|-1||EntrezGene||||||2:g.16085556T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:63:0:0,0:39,24:63,0:0:2,0:28.5:1:36:1:1:0:60:30.5:1:0:0.1	0/1:200:2:1,1:106,92:198,2:0.01:2,2:69:1:37:0:1:1.15135:60:4:0.0101:0:1
    504. 

  504. 2	16086265	16086265	T	-	UTR3	MYCN	NM_001293233:c.*1376delT;NM_001293231:c.*46delT;NM_005378:c.*46delT;NM_001293228:c.*46delT	.	.	0.027	6.581e-05	0.0001	0	0	0	0.0003	0	0	rs763183120	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	182	160	2	16086264	.	AT	A	182	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1453;VD=31;AF=0.0213;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.55949;SOR=1.14082;LSEQ=CTGCCACTTTGCACATTTTG;RSEQ=TTTTTTTTTAAACAAACATT;CSQ=-|3_prime_UTR_variant|MODIFIER|MYCN|4613|Transcript|NM_001293228.2|protein_coding|3/3||NM_001293228.2:c.*55del||2062|||||rs763183120||1||EntrezGene||YES||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|3_prime_UTR_variant|MODIFIER|MYCN|4613|Transcript|NM_001293231.2|protein_coding|2/2||NM_001293231.2:c.*55del||845|||||rs763183120||1||EntrezGene||||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|3_prime_UTR_variant|MODIFIER|MYCN|4613|Transcript|NM_001293233.2|protein_coding|3/3||NM_001293233.2:c.*1385del||1752|||||rs763183120||1||EntrezGene||||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|3_prime_UTR_variant|MODIFIER|MYCN|4613|Transcript|NM_005378.6|protein_coding|3/3||NM_005378.6:c.*55del||1752|||||rs763183120||1||EntrezGene||||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_110230.2|lncRNA||||||||||rs763183120|4458|-1||EntrezGene||YES||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_161162.1|lncRNA||||||||||rs763183120|4458|-1||EntrezGene||||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||,-|upstream_gene_variant|MODIFIER|MYCNOS|10408|Transcript|NR_161163.1|lncRNA||||||||||rs763183120|3710|-1||EntrezGene||||||2:g.16086274del|0.000563|8.07e-05|0.0007189|0.0005855|0.0008219|0|0.0006991|0.0006012|0.0003934|0.02706|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1453:31:7,24:359,1062:1421,31:0.0213:2,2:29.3:1:36.9:1:0.8368:1.15888:60:62:0.0216:0.0028:0.2	0/1:160:3:0,3:39,118:157,3:0.0187:2,0:53.3:1:37:0:1:0:60:6:0.0187:0:0
    505. 

  505. 2	25462063	25462063	C	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320893:exon15:c.G1888T:p.A630S,DNMT3A:NM_153759:exon16:c.G1777T:p.A593S,DNMT3A:NM_022552:exon20:c.G2344T:p.A782S,DNMT3A:NM_175629:exon20:c.G2344T:p.A782S	.	.	.	.	.	.	.	.	.	.	.	0.309	0.388	T	0.702	0.670	P	0.606	0.790	P	0.000	0.843	D	1	0.810	D	1.295	0.326	L	-4.54	0.977	D	-2.68	0.574	D	0.68	0.733	1.006	0.973	D	0.920	0.974	D	0.254	0.893	D	6.015	0.827	27.9	0.997	0.839	0.974	0.741	D	c	0.564	0.623	1.000	0.747	0.707	0.730	0	5.36	0.765	7.867	0.854	0.852	0.362	1.000	0.715	1.000	0.888	16.588	0.845	ADD domain;S-adenosyl-L-methionine-dependent methyltransferase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	300	2	25462063	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3671;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00043;SOR=0;LSEQ=TGCAGCTGACACTTCTTTGG;RSEQ=ATCAATCATCACAGGGTTGG;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|15/18||NM_001320893.1:c.1888G>T|NP_001307822.1:p.Ala630Ser|1925|1888|630|A/S|Gcc/Tcc|||-1||EntrezGene||||||2:g.25462063C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|15/18||NM_001375819.1:c.1675G>T|NP_001362748.1:p.Ala559Ser|1775|1675|559|A/S|Gcc/Tcc|||-1||EntrezGene||||||2:g.25462063C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|20/23||NM_022552.5:c.2344G>T|NP_072046.2:p.Ala782Ser|2621|2344|782|A/S|Gcc/Tcc|||-1||EntrezGene||YES||||2:g.25462063C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|16/19||NM_153759.3:c.1777G>T|NP_715640.2:p.Ala593Ser|1895|1777|593|A/S|Gcc/Tcc|||-1||EntrezGene||||||2:g.25462063C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|20/23||NM_175629.2:c.2344G>T|NP_783328.1:p.Ala782Ser|2682|2344|782|A/S|Gcc/Tcc|||-1||EntrezGene||||||2:g.25462063C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|21/24||NR_135490.2:n.2774G>T||2774|||||||-1||EntrezGene||||||2:g.25462063C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3671:0:0,0:1849,1822:3671,0:0:2,0:37.7:1:36.2:1:1:0:60:64.554:1:0:0.1	0/1:300:3:1,2:133,164:297,3:0.01:2,2:51:1:28.3:1:1:1.61944:60:2:0.0068:0:1.3
    506. 

  506. 2	25463147	25463147	C	T	intronic	DNMT3A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	144	2	25463147	.	C	T	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2113;VD=2;AF=0.0009;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.02228;SOR=0.06749;LSEQ=AGAAGCCATTAGTGAGCTGG;RSEQ=CAAACCAAGGTTGCTGGCTA;CSQ=T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding||14/17|NM_001320893.1:c.1866+24G>A|||||||rs1460252454||-1||EntrezGene||||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding||14/17|NM_001375819.1:c.1653+24G>A|||||||rs1460252454||-1||EntrezGene||||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||19/22|NM_022552.5:c.2322+24G>A|||||||rs1460252454||-1||EntrezGene||YES||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_153759.3|protein_coding||15/18|NM_153759.3:c.1755+24G>A|||||||rs1460252454||-1||EntrezGene||||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||19/22|NM_175629.2:c.2322+24G>A|||||||rs1460252454||-1||EntrezGene||||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||19/23|NR_135490.2:n.2553+24G>A|||||||rs1460252454||-1||EntrezGene||||||2:g.25463147C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2113:2:1,1:1256,854:2110,2:0.0009:2,2:63.5:1:37:0:1:1.47042:60:4:0.001:0:1	0/1:144:2:1,1:101,41:142,2:0.0139:2,2:9.5:1:37:0:0.49971:2.44594:60:4:0.014:0:1
    507. 

  507. 2	25463225	25463225	C	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320893:exon14:c.G1812T:p.E604D,DNMT3A:NM_153759:exon15:c.G1701T:p.E567D,DNMT3A:NM_022552:exon19:c.G2268T:p.E756D,DNMT3A:NM_175629:exon19:c.G2268T:p.E756D	0.	.	.	.	.	.	.	.	.	rs769718039	.	0.003	0.912	D	1.0	0.899	D	0.998	0.875	D	0.000	0.843	D	1.000	0.588	D	4.1	0.974	H	-4.74	0.981	D	-2.95	0.617	D	0.831	0.874	1.055	0.982	D	0.966	0.989	D	0.617	0.967	D	5.900	0.809	27.5	0.999	0.931	0.822	0.411	D	c	0.693	0.563	0.329	0.195	0.707	0.730	0	3.31	0.369	1.419	0.342	0.935	0.490	1.000	0.715	1.000	0.888	7.024	0.240	ADD domain;S-adenosyl-L-methionine-dependent methyltransferase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	245	2	25463225	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2774;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00053;SOR=0;LSEQ=ACGCCCATGGCCACCACATT;RSEQ=TCAAAGAGCCAGAAGAAGGG;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|14/18||NM_001320893.1:c.1812G>T|NP_001307822.1:p.Glu604Asp|1849|1812|604|E/D|gaG/gaT|rs769718039||-1||EntrezGene||||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|14/18||NM_001375819.1:c.1599G>T|NP_001362748.1:p.Glu533Asp|1699|1599|533|E/D|gaG/gaT|rs769718039||-1||EntrezGene||||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|19/23||NM_022552.5:c.2268G>T|NP_072046.2:p.Glu756Asp|2545|2268|756|E/D|gaG/gaT|rs769718039||-1||EntrezGene||YES||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|15/19||NM_153759.3:c.1701G>T|NP_715640.2:p.Glu567Asp|1819|1701|567|E/D|gaG/gaT|rs769718039||-1||EntrezGene||||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|19/23||NM_175629.2:c.2268G>T|NP_783328.1:p.Glu756Asp|2606|2268|756|E/D|gaG/gaT|rs769718039||-1||EntrezGene||||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|19/24||NR_135490.2:n.2499G>T||2499|||||rs769718039||-1||EntrezGene||||||2:g.25463225C>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2774:0:0,0:1411,1363:2774,0:0:2,0:38.5:1:36.8:1:1:0:60:307.222:1:0:0.1	0/1:245:3:3,0:137,105:242,3:0.0122:2,0:35.3:1:28.3:1:0.2623:0:60:2:0.0083:0:3
    508. 

  508. 2	25464411	25464411	G	T	intronic	DNMT3A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	139	2	25464411	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1254;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00989;SOR=0;LSEQ=GGGAGGGGAAGACGGGCTGC;RSEQ=CCCCACAGCATGGACATACA;CSQ=T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding||12/17|NM_001320893.1:c.1626+20C>A|||||||||-1||EntrezGene||||||2:g.25464411G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding||12/17|NM_001375819.1:c.1413+20C>A|||||||||-1||EntrezGene||||||2:g.25464411G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||17/22|NM_022552.5:c.2082+20C>A|||||||||-1||EntrezGene||YES||||2:g.25464411G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_153759.3|protein_coding||13/18|NM_153759.3:c.1515+20C>A|||||||||-1||EntrezGene||||||2:g.25464411G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||17/22|NM_175629.2:c.2082+20C>A|||||||||-1||EntrezGene||||||2:g.25464411G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||17/23|NR_135490.2:n.2313+20C>A|||||||||-1||EntrezGene||||||2:g.25464411G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1254:0:0,0:842,412:1254,0:0:2,0:36.5:1:36.6:1:1:0:60:208:1:0:0.1	0/1:139:2:1,1:88,49:137,2:0.0144:2,2:19.5:1:37:0:1:1.78785:60:4:0.0145:0:1
    509. 

  509. 2	25467477	25467477	G	C	exonic	DNMT3A	.	stopgain	DNMT3A:NM_001320893:exon9:c.C1143G:p.Y381X,DNMT3A:NM_153759:exon10:c.C1032G:p.Y344X,DNMT3A:NM_022552:exon14:c.C1599G:p.Y533X,DNMT3A:NM_175629:exon14:c.C1599G:p.Y533X	0.0001	.	.	.	.	.	.	.	.	rs757057121	.	.	.	.	.	.	.	.	.	.	0.000	0.629	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.388	0.882	29.5	0.975	0.338	0.911	0.525	D	c	-0.439	-0.773	1.000	0.747	0.707	0.730	0	-10.3	0.003	0.479	0.218	-1.115	0.018	0.993	0.376	0.817	0.342	22.095	1.000	ADD domain;PWWP domain	.	.	.	.	.	.	.	.	Uncertain significance	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	199	252	2	25467477	.	G	C	199	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3531;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGATGGTGCAGTAGGACTG;RSEQ=TAGCCGTCGTCGTCGTACTG;CSQ=C|stop_gained|HIGH|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|9/18||NM_001320893.1:c.1143C>G|NP_001307822.1:p.Tyr381Ter|1180|1143|381|Y/*|taC/taG|rs757057121&COSV99265600||-1||EntrezGene||||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|stop_gained|HIGH|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|9/18||NM_001375819.1:c.930C>G|NP_001362748.1:p.Tyr310Ter|1030|930|310|Y/*|taC/taG|rs757057121&COSV99265600||-1||EntrezGene||||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|stop_gained|HIGH|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|14/23||NM_022552.5:c.1599C>G|NP_072046.2:p.Tyr533Ter|1876|1599|533|Y/*|taC/taG|rs757057121&COSV99265600||-1||EntrezGene||YES||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|stop_gained|HIGH|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|10/19||NM_153759.3:c.1032C>G|NP_715640.2:p.Tyr344Ter|1150|1032|344|Y/*|taC/taG|rs757057121&COSV99265600||-1||EntrezGene||||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|stop_gained|HIGH|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|14/23||NM_175629.2:c.1599C>G|NP_783328.1:p.Tyr533Ter|1937|1599|533|Y/*|taC/taG|rs757057121&COSV99265600||-1||EntrezGene||||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|14/24||NR_135490.2:n.1830C>G||1830|||||rs757057121&COSV99265600||-1||EntrezGene||||||2:g.25467477G>C|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3531:0:0,0:1754,1777:3531,0:0:2,0:37.8:1:36.7:1:1:0:60:184.842:1:0:0.1	0/1:252:42:18,24:88,122:210,42:0.1667:2,2:41.1:1:37:0:1:1.04:60:84:0.1694:0:1
    510. 

  510. 2	25469147	25469147	C	A	exonic	DNMT3A	.	synonymous SNV	DNMT3A:NM_001320893:exon6:c.G855T:p.T285T,DNMT3A:NM_153759:exon7:c.G744T:p.T248T,DNMT3A:NM_022552:exon11:c.G1311T:p.T437T,DNMT3A:NM_175629:exon11:c.G1311T:p.T437T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	197	2	25469147	.	C	A	37	v3;f0.01;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2037;VD=2;AF=0.001;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04121;SOR=0.09604;LSEQ=TCAGGTTCCACCCACATGTC;RSEQ=GTGTACACTTCTTTGTAGGG;CSQ=A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|6/18||NM_001320893.1:c.855G>T|NP_001307822.1:p.Thr285%3D|892|855|285|T|acG/acT|COSV53078428||-1||EntrezGene||||||2:g.25469147C>A|||||||||||||1|1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|6/18||NM_001375819.1:c.642G>T|NP_001362748.1:p.Thr214%3D|742|642|214|T|acG/acT|COSV53078428||-1||EntrezGene||||||2:g.25469147C>A|||||||||||||1|1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|11/23||NM_022552.5:c.1311G>T|NP_072046.2:p.Thr437%3D|1588|1311|437|T|acG/acT|COSV53078428||-1||EntrezGene||YES||||2:g.25469147C>A|||||||||||||1|1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|7/19||NM_153759.3:c.744G>T|NP_715640.2:p.Thr248%3D|862|744|248|T|acG/acT|COSV53078428||-1||EntrezGene||||||2:g.25469147C>A|||||||||||||1|1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|11/23||NM_175629.2:c.1311G>T|NP_783328.1:p.Thr437%3D|1649|1311|437|T|acG/acT|COSV53078428||-1||EntrezGene||||||2:g.25469147C>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|11/24||NR_135490.2:n.1542G>T||1542|||||COSV53078428||-1||EntrezGene||||||2:g.25469147C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2037:2:1,1:904,1131:2035,2:0.001:2,2:33.5:1:18:1:1:1.25:60:1:0.0005:0:1.5	0/1:197:2:1,1:82,113:195,2:0.0102:2,2:54.5:1:37:0:1:1.38:60:4:0.0103:0:1
    511. 

  511. 2	25469451	25469451	C	T	intronic	DNMT3A	.	.	.	0.011	.	.	.	.	.	.	.	.	rs201436991	rs201436991	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53036466;OCCURENCE=1(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	108	17	2	25469451	.	C	T	108	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=156;VD=9;AF=0.0577;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.38504;SOR=inf;LSEQ=CCTGGTGTGGATCTGCCTGG;RSEQ=GGGCAGGGGTCCCAGAAAGC;CSQ=T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding||5/17|NM_001320893.1:c.823+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding||5/17|NM_001375819.1:c.610+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||10/22|NM_022552.5:c.1279+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||YES||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_153759.3|protein_coding||6/18|NM_153759.3:c.712+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||10/22|NM_175629.2:c.1279+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||10/23|NR_135490.2:n.1510+38G>A|||||||rs201436991&COSV53036466||-1||EntrezGene||||||2:g.25469451C>T|0.0008191|0|0|0|0.0006654|0|3.806e-05|0.0003519|0.006157|0.0072|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:156:9:4,5:101,46:147,9:0.0577:2,2:39.9:1:34.3:1:0.15363:2.72496:60:18:0.0577:0:1.7	0/0:17:0:0,0:12,5:17,0:0:2,0:29.2:1:37:0:1:0:60:34:1:0:0.1
    512. 

  512. 2	25469502	25469502	C	T	exonic	DNMT3A	.	synonymous SNV	DNMT3A:NM_001320893:exon5:c.G810A:p.L270L,DNMT3A:NM_153759:exon6:c.G699A:p.L233L,DNMT3A:NM_022552:exon10:c.G1266A:p.L422L,DNMT3A:NM_175629:exon10:c.G1266A:p.L422L	0.32	0.2202	0.2884	0.2124	0.1921	0.3213	0.2285	0.1702	0.1984	rs2276598	rs2276598	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53040646;OCCURENCE=1(breast),1(liver),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU778215	LICA-CN|1|402|0.00248756,LUSC-KR|2|170|0.0117647,COCA-CN|6|321|0.0186916,BRCA-KR|1|50|0.02	0.25	162	28	2	25469502	.	C	T	162	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=257;VD=21;AF=0.0817;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.10474;SOR=inf;LSEQ=CATTTACCTTCTGGTGGCTC;RSEQ=AGGCCCTTAGGGCCAGAAGG;CSQ=T|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|5/18||NM_001320893.1:c.810G>A|NP_001307822.1:p.Leu270%3D|847|810|270|L|ctG/ctA|rs2276598&COSV53040646||-1||EntrezGene||||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1,T|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|5/18||NM_001375819.1:c.597G>A|NP_001362748.1:p.Leu199%3D|697|597|199|L|ctG/ctA|rs2276598&COSV53040646||-1||EntrezGene||||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1,T|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|10/23||NM_022552.5:c.1266G>A|NP_072046.2:p.Leu422%3D|1543|1266|422|L|ctG/ctA|rs2276598&COSV53040646||-1||EntrezGene||YES||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1,T|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|6/19||NM_153759.3:c.699G>A|NP_715640.2:p.Leu233%3D|817|699|233|L|ctG/ctA|rs2276598&COSV53040646||-1||EntrezGene||||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1,T|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|10/23||NM_175629.2:c.1266G>A|NP_783328.1:p.Leu422%3D|1604|1266|422|L|ctG/ctA|rs2276598&COSV53040646||-1||EntrezGene||||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1,T|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|10/24||NR_135490.2:n.1497G>A||1497|||||rs2276598&COSV53040646||-1||EntrezGene||||||2:g.25469502C>T|0.19|0.2952|0.2067|0.1961|0.3155|0.2159|0.1642|0.1859|0.1172|0.3204|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:257:21:14,7:164,71:235,21:0.0817:2,2:24.7:1:37:0:0.80613:1.15425:60:42:0.0827:0:1.4	0/0:28:0:0,0:22,6:28,0:0:2,0:32:1:36.6:1:1:0:60:56:1:0:0.1
    513. 

  513. 2	25469569	25469569	T	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320893:exon5:c.A743T:p.E248V,DNMT3A:NM_153759:exon6:c.A632T:p.E211V,DNMT3A:NM_022552:exon10:c.A1199T:p.E400V,DNMT3A:NM_175629:exon10:c.A1199T:p.E400V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.949	0.518	P	0.54	0.470	P	0.000	0.843	D	1	0.810	D	2.685	0.788	M	-4.2	0.969	D	-3.79	0.716	D	0.622	0.719	0.885	0.955	D	0.861	0.954	D	0.572	0.961	D	6.465	0.892	29.9	0.990	0.500	0.990	0.893	D	c	0.535	0.561	1.000	0.747	0.707	0.730	0	4.87	0.627	7.887	0.857	1.061	0.807	1.000	0.715	0.999	0.750	12.466	0.549	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	58	2	25469569	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=575;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00826;SOR=0;LSEQ=TCATGGGCTTGTTCTGCACC;RSEQ=CCACGGCCTTGGCAGTGTCA;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|5/18||NM_001320893.1:c.743A>T|NP_001307822.1:p.Glu248Val|780|743|248|E/V|gAg/gTg|||-1||EntrezGene||||||2:g.25469569T>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|5/18||NM_001375819.1:c.530A>T|NP_001362748.1:p.Glu177Val|630|530|177|E/V|gAg/gTg|||-1||EntrezGene||||||2:g.25469569T>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|10/23||NM_022552.5:c.1199A>T|NP_072046.2:p.Glu400Val|1476|1199|400|E/V|gAg/gTg|||-1||EntrezGene||YES||||2:g.25469569T>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|6/19||NM_153759.3:c.632A>T|NP_715640.2:p.Glu211Val|750|632|211|E/V|gAg/gTg|||-1||EntrezGene||||||2:g.25469569T>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|10/23||NM_175629.2:c.1199A>T|NP_783328.1:p.Glu400Val|1537|1199|400|E/V|gAg/gTg|||-1||EntrezGene||||||2:g.25469569T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|10/24||NR_135490.2:n.1430A>T||1430|||||||-1||EntrezGene||||||2:g.25469569T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:575:0:0,0:340,235:575,0:0:2,0:35.2:1:36.2:1:1:0:60:56.5:1:0:0.1	0/1:58:2:1,1:35,21:56,2:0.0345:2,2:38:1:37:0:1:1.65138:60:4:0.0345:0:1
    514. 

  514. 2	25469913	25469913	C	T	intronic	DNMT3A	.	.	.	0.83	0.7006	0.5654	0.7363	0.6656	0.6001	0.8238	0.7565	0.7525	rs2276599	rs2276599	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53038205;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU778192	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,COCA-CN|6|321|0.0186916	0.75	319	329	2	25469913	.	C	T	319	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4984;VD=555;AF=0.1114;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCGAGCTCCCAGCAGGGA;RSEQ=ACTCACCTGCAGGACCTCGT;CSQ=T|splice_region_variant&intron_variant|LOW|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding||4/17|NM_001320893.1:c.666+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1,T|splice_region_variant&intron_variant|LOW|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding||4/17|NM_001375819.1:c.453+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1,T|splice_region_variant&intron_variant|LOW|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||9/22|NM_022552.5:c.1122+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||YES||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1,T|splice_region_variant&intron_variant|LOW|DNMT3A|1788|Transcript|NM_153759.3|protein_coding||5/18|NM_153759.3:c.555+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1,T|splice_region_variant&intron_variant|LOW|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||9/22|NM_175629.2:c.1122+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1,T|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||9/23|NR_135490.2:n.1353+7G>A|||||||rs2276599&COSV53038205||-1||EntrezGene||||||2:g.25469913C>T|0.7125|0.5573|0.7516|0.6761|0.5973|0.8176|0.7546|0.7207|0.6006|0.8176|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:4984:555:306,249:2433,1993:4426,555:0.1114:2,2:37.6:1:35.1:1:0.96391:1.01:60:22.125:0.1074:0:1.1	1/1:329:329:193,136:0,0:0,329:1:0,2:35.9:1:35.6:1:1:0:60:35.556:1:0:1.1
    515. 

  515. 2	25470472	25470472	G	A	exonic	DNMT3A	.	synonymous SNV	DNMT3A:NM_001320893:exon3:c.C546T:p.G182G,DNMT3A:NM_153759:exon4:c.C435T:p.G145G,DNMT3A:NM_022552:exon8:c.C1002T:p.G334G,DNMT3A:NM_175629:exon8:c.C1002T:p.G334G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	145	2	25470472	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2014;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.00448;SOR=0;LSEQ=CAACTTACCACTGAGAATTT;RSEQ=CCGTCTCCGAACCACATGAC;CSQ=A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|3/18||NM_001320893.1:c.546C>T|NP_001307822.1:p.Gly182%3D|583|546|182|G|ggC/ggT|||-1||EntrezGene||||||2:g.25470472G>A||||||||||||||,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|3/18||NM_001375819.1:c.333C>T|NP_001362748.1:p.Gly111%3D|433|333|111|G|ggC/ggT|||-1||EntrezGene||||||2:g.25470472G>A||||||||||||||,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|8/23||NM_022552.5:c.1002C>T|NP_072046.2:p.Gly334%3D|1279|1002|334|G|ggC/ggT|||-1||EntrezGene||YES||||2:g.25470472G>A||||||||||||||,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|4/19||NM_153759.3:c.435C>T|NP_715640.2:p.Gly145%3D|553|435|145|G|ggC/ggT|||-1||EntrezGene||||||2:g.25470472G>A||||||||||||||,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|8/23||NM_175629.2:c.1002C>T|NP_783328.1:p.Gly334%3D|1340|1002|334|G|ggC/ggT|||-1||EntrezGene||||||2:g.25470472G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|8/24||NR_135490.2:n.1233C>T||1233|||||||-1||EntrezGene||||||2:g.25470472G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2014:0:0,0:1089,923:2012,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:145:2:1,1:82,61:143,2:0.0138:2,2:42.5:1:37:0:1:1.34147:60:4:0.0142:0:1
    516. 

  516. 2	25470548	25470548	C	T	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320893:exon3:c.G470A:p.R157H,DNMT3A:NM_153759:exon4:c.G359A:p.R120H,DNMT3A:NM_022552:exon8:c.G926A:p.R309H,DNMT3A:NM_175629:exon8:c.G926A:p.R309H	.	.	.	.	.	.	.	.	.	.	.	0.05	0.564	D	0.988	0.899	D	0.465	0.655	P	0.000	0.843	D	1	0.810	D	1.48	0.373	L	-0.63	0.720	T	-1.75	0.414	N	0.863	0.872	-0.281	0.755	T	0.377	0.735	T	0.052	0.651	D	6.118	0.843	28.3	1.000	1.000	0.940	0.595	D	c	0.407	0.425	1.000	0.747	0.707	0.730	0	4.07	0.466	1.594	0.361	0.935	0.490	1.000	0.715	1.000	0.888	12.666	0.560	PWWP domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	80	170	2	25470548	.	C	T	80	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1985;VD=5;AF=0.0025;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.09987;SOR=0.2124;LSEQ=TCATCCACCAAGACACAATG;RSEQ=GGCCTGGCCACCAGGAGAAG;CSQ=T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|3/18||NM_001320893.1:c.470G>A|NP_001307822.1:p.Arg157His|507|470|157|R/H|cGc/cAc|COSV53048863&COSV53067843||-1||EntrezGene||||||2:g.25470548C>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|3/18||NM_001375819.1:c.257G>A|NP_001362748.1:p.Arg86His|357|257|86|R/H|cGc/cAc|COSV53048863&COSV53067843||-1||EntrezGene||||||2:g.25470548C>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|8/23||NM_022552.5:c.926G>A|NP_072046.2:p.Arg309His|1203|926|309|R/H|cGc/cAc|COSV53048863&COSV53067843||-1||EntrezGene||YES||||2:g.25470548C>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|4/19||NM_153759.3:c.359G>A|NP_715640.2:p.Arg120His|477|359|120|R/H|cGc/cAc|COSV53048863&COSV53067843||-1||EntrezGene||||||2:g.25470548C>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|8/23||NM_175629.2:c.926G>A|NP_783328.1:p.Arg309His|1264|926|309|R/H|cGc/cAc|COSV53048863&COSV53067843||-1||EntrezGene||||||2:g.25470548C>T|||||||||||||1&1|1&1,T|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|8/24||NR_135490.2:n.1157G>A||1157|||||COSV53048863&COSV53067843||-1||EntrezGene||||||2:g.25470548C>T|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1985:5:2,3:908,1072:1980,5:0.0025:2,2:46.8:1:34.6:1:1:1.27037:60:10:0.0025:0:1	0/1:170:2:1,1:87,81:168,2:0.0118:2,2:28:1:37:0:1:1.07359:60:4:0.0118:0:1
    517. 

  517. 2	25471014	25471014	C	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320893:exon2:c.G291T:p.Q97H,DNMT3A:NM_153759:exon3:c.G180T:p.Q60H,DNMT3A:NM_022552:exon7:c.G747T:p.Q249H,DNMT3A:NM_175629:exon7:c.G747T:p.Q249H	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.99	0.615	D	0.846	0.668	P	0.000	0.843	D	1.000	0.588	D	2.005	0.547	M	-3.29	0.937	D	-1.16	0.326	N	0.517	0.596	0.638	0.924	D	0.795	0.931	D	0.308	0.911	D	5.337	0.722	25.8	0.997	0.789	0.910	0.524	D	c	0.407	0.413	1.000	0.747	0.707	0.730	0	3.51	0.391	3.504	0.529	0.071	0.179	1.000	0.715	0.997	0.653	12.096	0.529	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	112	2	25471014	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=984;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.01036;SOR=0;LSEQ=GGGGATGCGGGGTCAGTGGG;RSEQ=TGCTGCACAGCAGGAGGGCT;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|2/18||NM_001320893.1:c.291G>T|NP_001307822.1:p.Gln97His|328|291|97|Q/H|caG/caT|||-1||EntrezGene||||||2:g.25471014C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|2/18||NM_001375819.1:c.78G>T|NP_001362748.1:p.Gln26His|178|78|26|Q/H|caG/caT|||-1||EntrezGene||||||2:g.25471014C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|7/23||NM_022552.5:c.747G>T|NP_072046.2:p.Gln249His|1024|747|249|Q/H|caG/caT|||-1||EntrezGene||YES||||2:g.25471014C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|3/19||NM_153759.3:c.180G>T|NP_715640.2:p.Gln60His|298|180|60|Q/H|caG/caT|||-1||EntrezGene||||||2:g.25471014C>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|7/23||NM_175629.2:c.747G>T|NP_783328.1:p.Gln249His|1085|747|249|Q/H|caG/caT|||-1||EntrezGene||||||2:g.25471014C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|7/24||NR_135490.2:n.978G>T||978|||||||-1||EntrezGene||||||2:g.25471014C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:984:0:0,0:466,518:984,0:0:2,0:37.8:1:36.7:1:1:0:60:163:1:0:0.1	0/1:112:2:1,1:44,66:110,2:0.0179:2,2:47.5:1:37:0:1:1.49:60:4:0.018:0:1
    518. 

  518. 2	25475127	25475127	G	T	UTR5	DNMT3A	NM_153759:c.-61C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	19	2	25475127	.	G	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=196;VD=2;AF=0.0102;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.83069;SOR=inf;LSEQ=AGCCGCGGCCCTGAAGCTCT;RSEQ=GAAGTAGCTGCCCGTCTTGG;CSQ=T|upstream_gene_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|||||||||||127|-1||EntrezGene||||||2:g.25475127G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|1/18||NM_001375819.1:c.-95C>A||6|||||||-1||EntrezGene||||||2:g.25475127G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||6/22|NM_022552.5:c.640-4006C>A|||||||||-1||EntrezGene||YES||||2:g.25475127G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|1/19||NM_153759.3:c.-61C>A||58|||||||-1||EntrezGene||||||2:g.25475127G>T||||||||||||||,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||6/22|NM_175629.2:c.640-4006C>A|||||||||-1||EntrezGene||||||2:g.25475127G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||6/23|NR_135490.2:n.871-4006C>A|||||||||-1||EntrezGene||||||2:g.25475127G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:196:2:1,1:52,142:194,2:0.0102:2,2:43.5:1:31:1:0.46871:2.71:60:4:0.0103:0:1	0/0:19:0:0,0:4,15:19,0:0:2,0:22.7:1:37:0:1:0:60:38:1:0:0.1
    519. 

  519. 2	25475149	25475149	G	A	UTR5	DNMT3A	NM_153759:c.-83C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	10	2	25475149	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.01176;SOR=0;LSEQ=AAGTAGCTGCCCGTCTTGGG;RSEQ=GAGGGGAAGGGGGCGATGGG;CSQ=A|upstream_gene_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320893.1|protein_coding|||||||||||149|-1||EntrezGene||||||2:g.25475149G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001375819.1|protein_coding|||||||||||17|-1||EntrezGene||||||2:g.25475149G>A||||||||||||||,A|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||6/22|NM_022552.5:c.640-4028C>T|||||||||-1||EntrezGene||YES||||2:g.25475149G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|DNMT3A|1788|Transcript|NM_153759.3|protein_coding|1/19||NM_153759.3:c.-83C>T||36|||||||-1||EntrezGene||||||2:g.25475149G>A||||||||||||||,A|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||6/22|NM_175629.2:c.640-4028C>T|||||||||-1||EntrezGene||||||2:g.25475149G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||6/23|NR_135490.2:n.871-4028C>T|||||||||-1||EntrezGene||||||2:g.25475149G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:78:0:0,0:13,64:77,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:10:2:1,1:1,7:8,2:0.2:2,2:6:0:37:0:0.37778:5.29:60:4:0.2:0:1
    520. 

  520. 2	25498398	25498398	C	T	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_022552:exon5:c.G463A:p.E155K,DNMT3A:NM_175629:exon5:c.G463A:p.E155K	.	.	.	.	.	.	.	.	.	.	.	0.008	0.586	D	0.88	0.464	P	0.899	0.620	P	0.096	0.201	N	0.978	0.394	D	0.695	0.181	N	-3.38	0.942	D	-1.04	0.273	N	0.326	0.387	0.441	0.897	D	0.739	0.911	D	0.065	0.694	D	3.273	0.452	22.8	0.992	0.563	0.739	0.358	D	c	0.194	0.213	1.000	0.747	0.696	0.573	0	3.73	0.418	1.970	0.399	-0.033	0.126	1.000	0.715	0.999	0.750	10.352	0.429	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	135	2	25498398	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1748;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0051;SOR=0;LSEQ=CATGGATTCGATGTTGGTCT;RSEQ=CTTCTGTTCTTTGCCTGTGG;CSQ=T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|5/23||NM_022552.5:c.463G>A|NP_072046.2:p.Glu155Lys|740|463|155|E/K|Gag/Aag|||-1||EntrezGene||YES||||2:g.25498398C>T||||||||||||||,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|5/23||NM_175629.2:c.463G>A|NP_783328.1:p.Glu155Lys|801|463|155|E/K|Gag/Aag|||-1||EntrezGene||||||2:g.25498398C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|5/24||NR_135490.2:n.694G>A||694|||||||-1||EntrezGene||||||2:g.25498398C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1748:0:0,0:791,955:1746,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:135:2:1,1:62,71:133,2:0.0148:2,2:32:1:37:0:1:1.14:60:4:0.0155:0:1
    521. 

  521. 2	25505261	25505261	G	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320892:exon4:c.C497T:p.P166L,DNMT3A:NM_175630:exon4:c.C497T:p.P166L	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.176	0.272	B	0.086	0.280	B	.	.	.	1	0.090	N	.	.	.	.	.	.	-2.44	0.534	N	0.135	0.156	-1.011	0.267	T	0.074	0.300	T	0.031	0.534	D	0.403	0.133	6.637	0.909	0.196	0.195	0.205	N	c	-0.577	-0.665	0.997	0.348	0.646	0.450	0	2.19	0.268	3.259	0.510	0.154	0.240	0.143	0.233	0.002	0.062	5.17	0.143	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	36	2	25505261	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=317;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01014;SOR=0;LSEQ=GCCAAGTCCCTGACTCTCAG;RSEQ=GTATGCTGGTGGGCCCAGAA;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding|4/4||NM_001320892.2:c.497C>T|NP_001307821.1:p.Pro166Leu|774|497|166|P/L|cCc/cTc|||-1||EntrezGene||||||2:g.25505261G>A||||||||||||||,A|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||4/22|NM_022552.5:c.448+49C>T|||||||||-1||EntrezGene||YES||||2:g.25505261G>A||||||||||||||,A|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||4/22|NM_175629.2:c.448+49C>T|||||||||-1||EntrezGene||||||2:g.25505261G>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175630.1|protein_coding|4/4||NM_175630.1:c.497C>T|NP_783329.1:p.Pro166Leu|835|497|166|P/L|cCc/cTc|||-1||EntrezGene||||||2:g.25505261G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||4/23|NR_135490.2:n.679+49C>T|||||||||-1||EntrezGene||||||2:g.25505261G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:317:0:0,0:200,117:317,0:0:2,0:34.4:1:36.4:1:1:0:60:78.25:1:0:0.1	0/1:36:2:1,1:28,6:34,2:0.0556:2,2:30.5:1:37:0:0.35556:4.39698:60:4:0.0571:0:1
    522. 

  522. 2	25505366	25505366	G	A	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320892:exon4:c.C392T:p.A131V,DNMT3A:NM_022552:exon4:c.C392T:p.A131V,DNMT3A:NM_175629:exon4:c.C392T:p.A131V,DNMT3A:NM_175630:exon4:c.C392T:p.A131V	.	.	.	.	.	.	.	.	.	.	.	0.206	0.199	T	0.872	0.459	P	0.395	0.425	B	0.014	0.286	N	0.841	0.351	D	0.695	0.181	N	-3.59	0.950	D	0.01	0.730	N	0.264	0.334	0.413	0.893	D	0.642	0.875	D	0.059	0.675	D	2.859	0.404	21.7	0.999	0.972	0.907	0.517	D	c	-0.003	0.156	1.000	0.747	0.707	0.730	0	4.81	0.613	4.293	0.586	1.048	0.713	1.000	0.715	0.978	0.483	13.406	0.602	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	82	2	25505366	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=571;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.0156;SOR=0;LSEQ=TGCAGCAGCCATTTTCCACT;RSEQ=CTCTTGAGGCTTCAGGCAGG;CSQ=A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding|4/4||NM_001320892.2:c.392C>T|NP_001307821.1:p.Ala131Val|669|392|131|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.25505366G>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|4/23||NM_022552.5:c.392C>T|NP_072046.2:p.Ala131Val|669|392|131|A/V|gCa/gTa|||-1||EntrezGene||YES||||2:g.25505366G>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|4/23||NM_175629.2:c.392C>T|NP_783328.1:p.Ala131Val|730|392|131|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.25505366G>A||||||||||||||,A|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175630.1|protein_coding|4/4||NM_175630.1:c.392C>T|NP_783329.1:p.Ala131Val|730|392|131|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.25505366G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|4/24||NR_135490.2:n.623C>T||623|||||||-1||EntrezGene||||||2:g.25505366G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:571:0:0,0:328,243:571,0:0:2,0:35:1:36.8:1:1:0:60:1142:1:0:0.1	0/1:82:2:1,1:52,28:80,2:0.0244:2,2:55:1:37:0:1:1.84238:60:4:0.0244:0:1
    523. 

  523. 2	25505572	25505572	G	T	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320892:exon4:c.C186A:p.S62R,DNMT3A:NM_022552:exon4:c.C186A:p.S62R,DNMT3A:NM_175629:exon4:c.C186A:p.S62R,DNMT3A:NM_175630:exon4:c.C186A:p.S62R	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.986	0.596	D	0.783	0.556	P	0.002	0.373	N	0.880	0.360	D	0.695	0.181	N	-3.7	0.954	D	-0.79	0.685	N	0.284	0.343	0.738	0.937	D	0.790	0.929	D	0.321	0.915	D	3.259	0.451	22.8	0.997	0.803	0.833	0.422	D	c	-0.202	-0.127	1.000	0.420	0.719	0.830	0	4.04	0.461	1.418	0.342	-0.733	0.036	1.000	0.715	0.948	0.423	9.461	0.378	.	.	.	ID=COSV53068730;OCCURENCE=1(liver)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU84100146	LICA-CN|1|402|0.00248756	0.25	37	82	2	25505572	.	G	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=740;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00984;SOR=0;LSEQ=GGGTCCTTTGGCGTGTCACC;RSEQ=CTTTCCACCTGCAAATGTAA;CSQ=T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding|4/4||NM_001320892.2:c.186C>A|NP_001307821.1:p.Ser62Arg|463|186|62|S/R|agC/agA|COSV53068730||-1||EntrezGene||||||2:g.25505572G>T|||||||||||||1|1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|4/23||NM_022552.5:c.186C>A|NP_072046.2:p.Ser62Arg|463|186|62|S/R|agC/agA|COSV53068730||-1||EntrezGene||YES||||2:g.25505572G>T|||||||||||||1|1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|4/23||NM_175629.2:c.186C>A|NP_783328.1:p.Ser62Arg|524|186|62|S/R|agC/agA|COSV53068730||-1||EntrezGene||||||2:g.25505572G>T|||||||||||||1|1,T|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175630.1|protein_coding|4/4||NM_175630.1:c.186C>A|NP_783329.1:p.Ser62Arg|524|186|62|S/R|agC/agA|COSV53068730||-1||EntrezGene||||||2:g.25505572G>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|4/24||NR_135490.2:n.417C>A||417|||||COSV53068730||-1||EntrezGene||||||2:g.25505572G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:740:0:0,0:296,443:739,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:82:2:1,1:30,50:80,2:0.0244:2,2:59.5:1:37:0:1:1.66:60:4:0.0247:0:1
    524. 

  524. 2	25536770	25536770	C	T	intronic	DNMT3A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	28	2	25536770	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=2;AF=0.0101;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.76804;SOR=inf;LSEQ=CCAGAGGGTCCCCAGCAGAG;RSEQ=CCGCTGCTCACCTTTCGGTC;CSQ=T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding||2/3|NM_001320892.2:c.72+12G>A|||||||COSV53080461||-1||EntrezGene||||||2:g.25536770C>T|||||||||||||1|1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||2/22|NM_022552.5:c.72+12G>A|||||||COSV53080461||-1||EntrezGene||YES||||2:g.25536770C>T|||||||||||||1|1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||2/22|NM_175629.2:c.72+12G>A|||||||COSV53080461||-1||EntrezGene||||||2:g.25536770C>T|||||||||||||1|1,T|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175630.1|protein_coding||2/3|NM_175630.1:c.72+12G>A|||||||COSV53080461||-1||EntrezGene||||||2:g.25536770C>T|||||||||||||1|1,T|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||2/23|NR_135490.2:n.303+12G>A|||||||COSV53080461||-1||EntrezGene||||||2:g.25536770C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:199:2:1,1:116,81:197,2:0.0101:2,2:13:0:37:0:1:1.42943:60:4:0.0101:0:1	0/0:28:0:0,0:18,10:28,0:0:2,0:41.4:1:36.1:1:1:0:60:56:1:0:0
    525. 

  525. 2	25536827	25536827	G	A	exonic	DNMT3A	.	synonymous SNV	DNMT3A:NM_001320892:exon2:c.C27T:p.P9P,DNMT3A:NM_022552:exon2:c.C27T:p.P9P,DNMT3A:NM_175629:exon2:c.C27T:p.P9P,DNMT3A:NM_175630:exon2:c.C27T:p.P9P	0.2	0.0809	0.0589	0.0610	0.0894	0.0871	0.0619	0.0972	0.0990	rs41284843	rs41284843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53040679;OCCURENCE=1(liver),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU2248925	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,LIAD-FR|1|32|0.03125	0.25	162	29	2	25536827	.	G	A	162	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=234;VD=23;AF=0.0983;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.05996;SOR=inf;LSEQ=GCAGAGCTGCTGGTGTCCCC;RSEQ=GGGCCGCTGGAGGGCATGGC;CSQ=A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding|2/4||NM_001320892.2:c.27C>T|NP_001307821.1:p.Pro9%3D|304|27|9|P|ccC/ccT|rs41284843&COSV53040679||-1||EntrezGene||||||2:g.25536827G>A|0.09596|0.06129|0.04896|0.1021|0.09414|0.06046|0.1004|0.1017|0.1697|0.1697|gnomAD_SAS||0&1|0&1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|2/23||NM_022552.5:c.27C>T|NP_072046.2:p.Pro9%3D|304|27|9|P|ccC/ccT|rs41284843&COSV53040679||-1||EntrezGene||YES||||2:g.25536827G>A|0.09596|0.06129|0.04896|0.1021|0.09414|0.06046|0.1004|0.1017|0.1697|0.1697|gnomAD_SAS||0&1|0&1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|2/23||NM_175629.2:c.27C>T|NP_783328.1:p.Pro9%3D|365|27|9|P|ccC/ccT|rs41284843&COSV53040679||-1||EntrezGene||||||2:g.25536827G>A|0.09596|0.06129|0.04896|0.1021|0.09414|0.06046|0.1004|0.1017|0.1697|0.1697|gnomAD_SAS||0&1|0&1,A|synonymous_variant|LOW|DNMT3A|1788|Transcript|NM_175630.1|protein_coding|2/4||NM_175630.1:c.27C>T|NP_783329.1:p.Pro9%3D|365|27|9|P|ccC/ccT|rs41284843&COSV53040679||-1||EntrezGene||||||2:g.25536827G>A|0.09596|0.06129|0.04896|0.1021|0.09414|0.06046|0.1004|0.1017|0.1697|0.1697|gnomAD_SAS||0&1|0&1,A|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|2/24||NR_135490.2:n.258C>T||258|||||rs41284843&COSV53040679||-1||EntrezGene||||||2:g.25536827G>A|0.09596|0.06129|0.04896|0.1021|0.09414|0.06046|0.1004|0.1017|0.1697|0.1697|gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:234:23:12,11:108,103:211,23:0.0983:2,2:41.5:1:35.9:1:1:1.04:60:22:0.0952:0:1.1	0/0:29:0:0,0:14,15:29,0:0:2,0:34.7:1:36.6:1:1:0:60:58:1:0:0
    526. 

  526. 2	25536843	25536843	A	G	exonic	DNMT3A	.	nonsynonymous SNV	DNMT3A:NM_001320892:exon2:c.T11C:p.M4T,DNMT3A:NM_022552:exon2:c.T11C:p.M4T,DNMT3A:NM_175629:exon2:c.T11C:p.M4T,DNMT3A:NM_175630:exon2:c.T11C:p.M4T	.	.	.	.	.	.	.	.	.	.	.	0.116	0.912	T	0.96	0.533	D	0.888	0.612	P	0.000	0.454	D	0.813	0.347	D	0.55	0.145	N	-3.31	0.938	D	-0.27	0.699	N	0.701	0.705	0.751	0.938	D	0.737	0.910	D	0.547	0.958	D	3.310	0.457	22.9	0.991	0.509	0.767	0.373	D	c	0.097	0.209	1.000	0.747	0.722	0.854	0	4.8	0.610	4.616	0.607	1.088	0.866	1.000	0.715	0.985	0.512	11.013	0.467	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	30	2	25536843	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=229;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01302;SOR=0;LSEQ=CCCCGGGGCCGCTGGAGGGC;RSEQ=TGGCGGGCATCTGGGCGCCG;CSQ=G|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding|2/4||NM_001320892.2:c.11T>C|NP_001307821.1:p.Met4Thr|288|11|4|M/T|aTg/aCg|||-1||EntrezGene||||||2:g.25536843A>G||||||||||||||,G|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_022552.5|protein_coding|2/23||NM_022552.5:c.11T>C|NP_072046.2:p.Met4Thr|288|11|4|M/T|aTg/aCg|||-1||EntrezGene||YES||||2:g.25536843A>G||||||||||||||,G|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175629.2|protein_coding|2/23||NM_175629.2:c.11T>C|NP_783328.1:p.Met4Thr|349|11|4|M/T|aTg/aCg|||-1||EntrezGene||||||2:g.25536843A>G||||||||||||||,G|missense_variant|MODERATE|DNMT3A|1788|Transcript|NM_175630.1|protein_coding|2/4||NM_175630.1:c.11T>C|NP_783329.1:p.Met4Thr|349|11|4|M/T|aTg/aCg|||-1||EntrezGene||||||2:g.25536843A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA|2/24||NR_135490.2:n.242T>C||242|||||||-1||EntrezGene||||||2:g.25536843A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:229:0:0,0:111,117:228,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:30:2:1,1:13,15:28,2:0.0667:2,2:16.5:1:37:0:1:1.15:60:4:0.0741:0:1
    527. 

  527. 2	25537367	25537367	A	C	intronic	DNMT3A	.	.	.	.	0.0002	0.0001	0	0	0	0.0007	7.666e-05	0.0012	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53078368;OCCURENCE=1(prostate)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU23701985	EOPC-DE|1|202|0.0049505	0.25	31	1	2	25537367	.	A	C	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=2;AF=0.1429;SHIFT3=2;MSI=4;MSILEN=1;SSF=0.86667;SOR=inf;LSEQ=CTTCCCGCATCCTCCCTCCC;RSEQ=CCCCAACCAGCCCCTGGGAA;CSQ=C|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_001320892.2|protein_coding||1/3|NM_001320892.2:c.-177-337T>G|||||||rs1480279824&COSV53078368||-1||EntrezGene||||||2:g.25537367A>C|||||||||||||0&1|0&1,C|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_022552.5|protein_coding||1/22|NM_022552.5:c.-177-337T>G|||||||rs1480279824&COSV53078368||-1||EntrezGene||YES||||2:g.25537367A>C|||||||||||||0&1|0&1,C|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175629.2|protein_coding||1/22|NM_175629.2:c.-177-337T>G|||||||rs1480279824&COSV53078368||-1||EntrezGene||||||2:g.25537367A>C|||||||||||||0&1|0&1,C|intron_variant|MODIFIER|DNMT3A|1788|Transcript|NM_175630.1|protein_coding||1/3|NM_175630.1:c.-177-337T>G|||||||rs1480279824&COSV53078368||-1||EntrezGene||||||2:g.25537367A>C|||||||||||||0&1|0&1,C|intron_variant&non_coding_transcript_variant|MODIFIER|DNMT3A|1788|Transcript|NR_135490.2|misc_RNA||1/23|NR_135490.2:n.55-337T>G|||||||rs1480279824&COSV53078368||-1||EntrezGene||||||2:g.25537367A>C|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:14:2:2,0:4,8:12,2:0.1429:2,0:15.5:1:31:1:0.16484:0:60:4:0.1818:0:3.5	0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:37:0:1:0:60:2:1:0:0
    528. 

  528. 2	29416366	29416366	G	C	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon29:c.C4587G:p.D1529E	0.75	0.4808	0.6142	0.6055	0.3377	0.7553	0.4851	0.3704	0.4510	rs1881421	rs1881421	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.119	0.191	N	1	0.090	P	-0.695	0.019	N	1.7	0.269	T	1.22	0.011	N	0.008	0.000	-0.993	0.319	T	0.000	0.000	T	.	.	.	-1.393	0.019	0.003	0.594	0.061	0.000	0.004	N	c	-1.813	-1.750	0.923	0.267	0.487	0.133	0	-3.42	0.045	-0.102	0.108	-1.050	0.020	0.000	0.063	0.000	0.016	11.802	0.512	.	.	.	ID=COSV66569695;OCCURENCE=1(breast),8(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(pancreas)	137215	Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU151094	LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.75	406	294	2	29416366	.	G	C	406	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2473;VD=2189;AF=0.8852;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=10.2644;LSEQ=TCCAGCCCCAGGTTACCCCT;RSEQ=TCGTGTGGCTCCTTCTTTGC;CSQ=C|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|10/10||NM_001353765.2:c.1383C>G|NP_001340694.1:p.Asp461Glu|1710|1383|461|D/E|gaC/gaG|rs1881421&COSV66569695||-1||EntrezGene||||||2:g.29416366G>C|0.4685|0.6262|0.6596|0.3048|0.7457|0.4895|0.3588|0.417|0.4582|0.7457|gnomAD_EAS|benign&likely_pathogenic|0&1|1&1,C|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|29/29||NM_004304.5:c.4587C>G|NP_004295.2:p.Asp1529Glu|5514|4587|1529|D/E|gaC/gaG|rs1881421&COSV66569695||-1||EntrezGene||YES||||2:g.29416366G>C|0.4685|0.6262|0.6596|0.3048|0.7457|0.4895|0.3588|0.417|0.4582|0.7457|gnomAD_EAS|benign&likely_pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2473:2189:1050,1139:145,135:280,2189:0.8852:2,2:33:1:36.6:1:0.253:1.16504:60:135.812:0.8851:0:1.3	0/1:294:126:59,67:81,87:168,126:0.4286:2,2:38.4:1:36.9:1:0.90611:1.05705:60:252:0.4286:0:2.2
    529. 

  529. 2	29416380	29416380	T	C	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon29:c.A4573G:p.K1525E	0.0096	0.0008	0.0001	0	0	0.0129	0	6.666e-05	0.0010	rs139437088	rs139437088	0.154	0.242	T	0.039	0.197	B	0.014	0.158	B	0.357	0.137	N	1	0.090	N	0.345	0.112	N	1.27	0.361	T	-1.74	0.412	N	0.124	0.140	-1.026	0.218	T	0.042	0.180	T	0.018	0.400	T	-0.372	0.063	0.452	0.678	0.082	0.305	0.239	N	c	-1.075	-1.095	0.841	0.248	0.487	0.133	0	-2.07	0.068	0.050	0.139	-0.242	0.092	0.001	0.137	0.001	0.043	6.414	0.208	.	.	.	ID=COSV66585220;OCCURENCE=1(upper_aerodigestive_tract)	137214	Neuroblastoma_3|not_specified	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	.	.	0.25	255	292	2	29416380	.	T	C	255	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2449;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCCTGTCGTGTGGCTCCT;RSEQ=CTTTGCTATAGGATTATTCT;CSQ=C|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|10/10||NM_001353765.2:c.1369A>G|NP_001340694.1:p.Lys457Glu|1696|1369|457|K/E|Aag/Gag|rs139437088&COSV66585220||-1||EntrezGene||||||2:g.29416380T>C|0.0007603|0.000123|0.0001156|0|0.009677|0|1.762e-05|0.0003262|9.799e-05|0.009677|gnomAD_EAS|benign&not_provided|0&1|1&1,C|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|29/29||NM_004304.5:c.4573A>G|NP_004295.2:p.Lys1525Glu|5500|4573|1525|K/E|Aag/Gag|rs139437088&COSV66585220||-1||EntrezGene||YES||||2:g.29416380T>C|0.0007603|0.000123|0.0001156|0|0.009677|0|1.762e-05|0.0003262|9.799e-05|0.009677|gnomAD_EAS|benign&not_provided|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2449:0:0,0:1177,1269:2446,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:292:129:64,65:77,84:161,129:0.4418:2,2:36.1:1:36.4:1:0.81341:1.07:60:128:0.4539:0:2.3
    530. 

  530. 2	29416481	29416481	T	C	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon29:c.A4472G:p.K1491R	0.75	0.2737	0.2434	0.5334	0.2067	0.7540	0.3057	0.2181	0.2882	rs1881420	rs1881420	0.408	0.102	T	0.0	0.026	B	0.003	0.080	B	0.003	0.352	U	1.000	0.266	P	1.475	0.372	L	-1.1	0.773	T	-0.42	0.142	N	0.046	0.026	-0.933	0.438	T	0.000	0.000	T	.	.	.	1.619	0.256	13.96	0.987	0.440	0.922	0.549	D	c	-0.425	-0.343	0.883	0.256	0.487	0.133	0	1.9	0.247	1.813	0.384	0.121	0.210	1.000	0.715	0.987	0.523	6.850	0.230	.	.	.	ID=COSV66555753;OCCURENCE=2(breast),6(meninges),1(haematopoietic_and_lymphoid_tissue),8(soft_tissue),1(pancreas),3(prostate),1(lung)	137213	Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU3888415	ESAD-UK|1|409|0.00244499,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.75	407	318	2	29416481	.	T	C	407	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2593;VD=2250;AF=0.8677;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=6.80518;LSEQ=TGTTTCTGGATCCGTGGACC;RSEQ=TGTGCAACTCCGAAGGAGGG;CSQ=C|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|10/10||NM_001353765.2:c.1268A>G|NP_001340694.1:p.Lys423Arg|1595|1268|423|K/R|aAg/aGg|rs1881420&COSV66555753||-1||EntrezGene||||||2:g.29416481T>C|0.3437|0.249|0.5879|0.1666|0.7467|0.3043|0.2229|0.2819|0.4227|0.7467|gnomAD_EAS|likely_pathogenic&benign|0&1|1&1,C|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|29/29||NM_004304.5:c.4472A>G|NP_004295.2:p.Lys1491Arg|5399|4472|1491|K/R|aAg/aGg|rs1881420&COSV66555753||-1||EntrezGene||YES||||2:g.29416481T>C|0.3437|0.249|0.5879|0.1666|0.7467|0.3043|0.2229|0.2819|0.4227|0.7467|gnomAD_EAS|likely_pathogenic&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2593:2250:1089,1161:166,171:337,2250:0.8677:2,2:37.3:1:36.6:1:0.77053:1.03494:60:186.5:0.8732:0:1.6	0/1:318:156:81,75:79,81:160,156:0.4906:2,2:44.4:1:36.8:1:0.65465:1.11:60:312:0.5065:0:1.8
    531. 

  531. 2	29416572	29416572	T	C	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon29:c.A4381G:p.I1461V	1.	0.9907	0.9680	0.9940	0.9934	1	1	0.9999	0.9990	rs1670283	rs1670283	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.683	0.061	N	1	0.090	P	-1.1	0.010	N	-0.89	0.748	T	0.37	0.036	N	0.012	0.001	-0.987	0.333	T	0.000	0.000	T	.	.	.	-2.014	0.008	0.001	0.529	0.047	0.005	0.023	N	c	-1.265	-1.247	0.774	0.237	0.487	0.133	0	-0.134	0.128	-0.984	0.038	-1.039	0.021	0.000	0.063	0.001	0.043	8.386	0.315	.	.	.	ID=COSV101201052;OCCURENCE=18(meninges),1(large_intestine),1(central_nervous_system)	137211	Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU81730341	COCA-CN|5|321|0.0155763	1	406	299	2	29416572	.	T	C	406	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2146;VD=2142;AF=0.9981;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.59327;SOR=0;LSEQ=TCTAGGGACTCGAACAGAGA;RSEQ=CTCTGCAGCTGTGGGTTTCT;CSQ=C|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|10/10||NM_001353765.2:c.1177A>G|NP_001340694.1:p.Ile393Val|1504|1177|393|I/V|Atc/Gtc|rs1670283&COSV101201052||-1||EntrezGene||||||2:g.29416572T>C|0.9976|0.9689|0.999|0.9959|1|1|0.9998|0.9987|1|1|AMR&EAS&EUR&gnomAD_EAS&gnomAD_FIN&gnomAD_SAS|benign&likely_pathogenic|0&1|1&1,C|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|29/29||NM_004304.5:c.4381A>G|NP_004295.2:p.Ile1461Val|5308|4381|1461|I/V|Atc/Gtc|rs1670283&COSV101201052||-1||EntrezGene||YES||||2:g.29416572T>C|0.9976|0.9689|0.999|0.9959|1|1|0.9998|0.9987|1|1|AMR&EAS&EUR&gnomAD_EAS&gnomAD_FIN&gnomAD_SAS|benign&likely_pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2146:2142:971,1171:0,0:0,2142:0.9981:0,2:35.5:1:36.7:1:1:0:60:213.2:0.9986:0:1.4	1/1:299:299:144,155:0,0:0,299:1:0,2:34.4:1:36.7:1:1:0:60:148.5:1:0:1.3
    532. 

  532. 2	29419658	29419658	T	C	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon28:c.A4142G:p.E1381G	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.998	0.715	D	0.994	0.807	D	0.000	0.473	U	1	0.810	D	1.24	0.311	L	-2.55	0.896	D	-6.66	0.923	D	0.872	0.860	0.713	0.933	D	0.807	0.935	D	0.391	0.932	D	6.527	0.899	31	0.999	0.993	0.909	0.521	D	c	0.760	0.746	1.000	0.747	0.422	0.057	0	5.79	0.917	8.017	0.886	1.061	0.807	1.000	0.715	1.000	0.888	16.129	0.811	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	216	2	29419658	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.1946;SOR=inf;LSEQ=GGGTGCAGTATTCAATCCTC;RSEQ=CCAAAATGATGGCAAAGTTG;CSQ=C|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|9/10||NM_001353765.2:c.938A>G|NP_001340694.1:p.Glu313Gly|1265|938|313|E/G|gAg/gGg|||-1||EntrezGene||||||2:g.29419658T>C||||||||||||||,C|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|28/29||NM_004304.5:c.4142A>G|NP_004295.2:p.Glu1381Gly|5069|4142|1381|E/G|gAg/gGg|||-1||EntrezGene||YES||||2:g.29419658T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:96,73:169,2:0.0117:2,2:50.5:1:37:0:1:1.31293:60:4:0.0118:0:1	0/0:216:0:0,0:114,102:216,0:0:2,0:38.3:1:36.7:1:1:0:60:215:1:0:0.2
    533. 

  533. 2	29420442	29420442	G	A	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon27:c.C4039T:p.R1347W	.	.	.	.	.	.	.	.	.	rs865887581	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.001	0.424	U	1	0.810	D	3.015	0.864	M	-2.01	0.855	D	-7.89	0.962	D	0.871	0.859	0.816	0.946	D	0.812	0.937	D	0.173	0.851	D	7.781	0.955	35	0.999	0.977	0.792	0.389	D	c	0.853	0.794	0.998	0.364	0.554	0.246	0	5.8	0.921	3.911	0.558	1.048	0.713	1.000	0.715	1.000	0.888	13.021	0.580	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV66574303;OCCURENCE=1(endometrium)	1024437	Neuroblastoma_3	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	172	2	29420442	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=773;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03297;SOR=0;LSEQ=GTTCTTGGGTGGGTCCATCC;RSEQ=GCCTCCACTGGTGACAAACT;CSQ=A|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|8/10||NM_001353765.2:c.835C>T|NP_001340694.1:p.Arg279Trp|1162|835|279|R/W|Cgg/Tgg|rs865887581&COSV66574303||-1||EntrezGene||||||2:g.29420442G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|27/29||NM_004304.5:c.4039C>T|NP_004295.2:p.Arg1347Trp|4966|4039|1347|R/W|Cgg/Tgg|rs865887581&COSV66574303||-1||EntrezGene||YES||||2:g.29420442G>A|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:773:0:0,0:427,346:773,0:0:2,0:36:1:36.6:1:1:0:60:153.6:1:0:0.1	0/1:172:2:1,1:91,79:170,2:0.0116:2,2:62:1:37:0:1:1.15095:60:4:0.012:0:1
    534. 

  534. 2	29445276	29445276	T	C	splicing	ALK	NM_004304:exon22:c.3451-2A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.472	0.599	24.2	0.995	0.685	0.996	0.981	D	c	1.047	0.879	1.000	0.747	0.054	0.004	0	5.15	0.702	8.017	0.886	1.061	0.807	1.000	0.715	0.992	0.562	15.002	0.710	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	52	298	2	29445276	.	T	C	52	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1967;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00226;SOR=0;LSEQ=AGCACACTTCAGGCAGCGTC;RSEQ=GGGCAGAGAAGGGGAGGGTG;CSQ=C|splice_acceptor_variant|HIGH|ALK|238|Transcript|NM_001353765.2|protein_coding||2/9|NM_001353765.2:c.247-2A>G|||||||||-1||EntrezGene||||||2:g.29445276T>C||||||||||||||,C|splice_acceptor_variant|HIGH|ALK|238|Transcript|NM_004304.5|protein_coding||21/28|NM_004304.5:c.3451-2A>G|||||||||-1||EntrezGene||YES||||2:g.29445276T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1967:0:0,0:1078,853:1931,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:298:3:2,1:162,127:289,3:0.0101:2,2:25.7:1:33:1:1:1.57:60:6:0.0121:0:1
    535. 

  535. 2	29445298	29445300	GGA	-	intronic	ALK	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs775243091	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	861299	Squamous_cell_lung_carcinoma	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782	no_assertion_criteria_provided	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU128852794	GACA-JP|1|585|0.0017094	0.25	58	293	2	29445297	.	GGGA	G	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1889;VD=2;AF=0.0011;SHIFT3=11;MSI=4;MSILEN=3;SSF=0.01946;SOR=0.10265;LSEQ=GGGCAGAGAAGGGGAGGGTG;RSEQ=GGAGGAGGAGGCTGTGAGCT;CSQ=-|intron_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||2/9|NM_001353765.2:c.247-26_247-24del|||||||rs775243091||-1||EntrezGene||||||2:g.29445309_29445311del|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,-|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||21/28|NM_004304.5:c.3451-26_3451-24del|||||||rs775243091||-1||EntrezGene||YES||||2:g.29445309_29445311del|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1889:2:1,1:944,940:1884,2:0.0011:2,2:29:1:37:0:1:1.00425:60:4:0.0011:0:0	0/1:293:3:2,1:153,137:290,3:0.0102:2,2:66:1:37:0:1:1.79:60:6:0.0103:0:1
    536. 

  536. 2	29445458	29445458	G	T	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon21:c.C3375A:p.G1125G	0.74	0.2742	0.2537	0.5383	0.2119	0.7426	0.3158	0.2119	0.2827	rs3795850	rs3795850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66569704;OCCURENCE=6(meninges),1(haematopoietic_and_lymphoid_tissue),1(kidney),1(pancreas)	289376	Squamous_cell_lung_carcinoma|Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU18066530	ESAD-UK|1|409|0.00244499,COCA-CN|4|321|0.0124611	0.75	377	203	2	29445458	.	G	T	377	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1519;VD=1310;AF=0.8624;SHIFT3=2;MSI=2;MSILEN=1;SSF=0;SOR=5.72732;LSEQ=TCATACACCTCCCCAAAGGC;RSEQ=CCATGGCCCAGACCCCTGTG;CSQ=T|synonymous_variant|LOW|ALK|238|Transcript|NM_001353765.2|protein_coding|2/10||NM_001353765.2:c.171C>A|NP_001340694.1:p.Gly57%3D|498|171|57|G|ggC/ggA|rs3795850&COSV66569704||-1||EntrezGene||||||2:g.29445458G>T|0.3369|0.2586|0.5962|0.1606|0.7373|0.3145|0.2133|0.273|0.3907|0.7373|gnomAD_EAS|likely_benign&benign|0&1|1&1,T|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|21/29||NM_004304.5:c.3375C>A|NP_004295.2:p.Gly1125%3D|4302|3375|1125|G|ggC/ggA|rs3795850&COSV66569704||-1||EntrezGene||YES||||2:g.29445458G>T|0.3369|0.2586|0.5962|0.1606|0.7373|0.3145|0.2133|0.273|0.3907|0.7373|gnomAD_EAS|likely_benign&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1519:1310:607,703:94,115:209,1310:0.8624:2,2:36.3:1:36.5:1:0.76515:1.06:60:162.75:0.8617:0:1.1	1/0:203:106:38,68:36,61:97,106:0.5222:2,2:39.1:1:37:0:0.88462:1.05577:60:212:0.5248:0:1.1
    537. 

  537. 2	29445466	29445466	C	A	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon21:c.G3367T:p.G1123C	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.491	D	1	0.810	D	3.625	0.941	H	-3.62	0.951	D	-8.89	0.981	D	0.971	0.972	1.105	0.998	D	0.950	0.984	D	0.719	0.977	D	7.327	0.949	34	0.997	0.811	0.991	0.918	D	c	0.949	0.851	1.000	0.747	0.554	0.246	0	5.15	0.702	7.905	0.864	0.935	0.490	1.000	0.715	0.997	0.653	18.654	0.914	Protein kinase domain|Protein kinase, ATP binding site|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain;Protein kinase, ATP binding site|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	199	2	29445466	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1497;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01371;SOR=0;LSEQ=CTCCCCAAAGGCGCCATGGC;RSEQ=CAGACCCCTGTGCAAAGGAG;CSQ=A|missense_variant|MODERATE|ALK|238|Transcript|NM_001353765.2|protein_coding|2/10||NM_001353765.2:c.163G>T|NP_001340694.1:p.Gly55Cys|490|163|55|G/C|Ggc/Tgc|COSV66561781||-1||EntrezGene||||||2:g.29445466C>A|||||||||||||1|1,A|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|21/29||NM_004304.5:c.3367G>T|NP_004295.2:p.Gly1123Cys|4294|3367|1123|G/C|Ggc/Tgc|COSV66561781||-1||EntrezGene||YES||||2:g.29445466C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1497:0:0,0:673,824:1497,0:0:2,0:35.9:1:36.6:1:1:0:60:212.857:1:0:0.9	0/1:199:2:1,1:70,127:197,2:0.0101:2,2:42:1:37:0:1:1.81:60:4:0.0102:0:2
    538. 

  538. 2	29446184	29446184	C	G	intronic	ALK	.	.	.	0.76	0.2763	0.2548	0.5418	0.2185	0.7584	0.3162	0.2133	0.2844	rs2276550	rs2276550	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	861300	Squamous_cell_lung_carcinoma	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782	no_assertion_criteria_provided	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU21150305	ESAD-UK|1|409|0.00244499,COCA-CN|4|321|0.0124611	0.75	366	134	2	29446184	.	C	G	366	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1220;VD=1062;AF=0.8705;SHIFT3=1;MSI=3;MSILEN=1;SSF=0;SOR=6.90956;LSEQ=TACACTGCACCCCTCTCCTC;RSEQ=CAGGACGGCAGCAGGGCGCT;CSQ=G|intron_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||1/9|NM_001353765.2:c.155+24G>C|||||||rs2276550||-1||EntrezGene||||||2:g.29446184C>G|0.3424|0.2606|0.5982|0.1652|0.7603|0.3146|0.2167|0.2755|0.3983|0.7603|gnomAD_EAS|uncertain_significance||1,G|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||20/28|NM_004304.5:c.3359+24G>C|||||||rs2276550||-1||EntrezGene||YES||||2:g.29446184C>G|0.3424|0.2606|0.5982|0.1652|0.7603|0.3146|0.2167|0.2755|0.3983|0.7603|gnomAD_EAS|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1220:1062:708,354:100,54:154,1062:0.8705:2,2:33.2:1:36.5:1:0.71501:1.08:60:95.545:0.8693:0:1.1	0/1:134:66:42,24:40,26:66,66:0.4925:2,2:36.3:1:36.8:1:0.85771:1.14:60:132:0.4925:0:1.1
    539. 

  539. 2	29446389	29446389	G	A	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon20:c.C3178T:p.R1060C	0.	.	.	.	.	.	.	.	.	rs774836034	.	0.006	0.614	D	0.999	0.764	D	0.856	0.592	P	0.041	0.240	N	1	0.810	D	1.4	0.355	L	-1.32	0.798	T	-5.47	0.856	D	0.815	0.803	0.057	0.834	D	0.561	0.840	D	0.151	0.833	D	7.331	0.949	34	0.999	0.993	0.826	0.415	D	c	0.494	0.485	1.000	0.500	0.487	0.133	0	4.65	0.575	3.335	0.516	1.048	0.713	1.000	0.715	0.995	0.604	17.738	0.883	.	.	.	.	558033	Neuroblastoma_3	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	197	2	29446389	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1455;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01416;SOR=0;LSEQ=CAGCTCCTGGTGCTTCCGGC;RSEQ=GTACACTGCAGGTGGGTGGT;CSQ=A|5_prime_UTR_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding|1/10||NM_001353765.2:c.-27C>T||301|||||rs774836034||-1||EntrezGene||||||2:g.29446389G>A|4.023e-06|0|0|0|0|0|8.965e-06|0|0|8.965e-06|gnomAD_NFE|uncertain_significance||1,A|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|20/29||NM_004304.5:c.3178C>T|NP_004295.2:p.Arg1060Cys|4105|3178|1060|R/C|Cgc/Tgc|rs774836034||-1||EntrezGene||YES||||2:g.29446389G>A|4.023e-06|0|0|0|0|0|8.965e-06|0|0|8.965e-06|gnomAD_NFE|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1455:0:0,0:582,873:1455,0:0:2,0:35.9:1:36.6:1:1:0:60:206.857:1:0:0.1	0/1:197:2:1,1:81,114:195,2:0.0102:2,2:17.5:1:37:0:1:1.4:60:4:0.0103:0:1
    540. 

  540. 2	29446701	29446701	T	C	intronic	ALK	.	.	.	0.43	0.3932	0.4174	0.2649	0.4205	0.1656	0.3302	0.4251	0.3939	rs12619049	rs12619049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66558292;OCCURENCE=15(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU22244114	LAML-KR|1|205|0.00487805	0.5	283	398	2	29446701	.	T	C	283	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=765;VD=100;AF=0.1307;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.12444;LSEQ=AGATGGGATTAGACCCAATA;RSEQ=GGTCTGCAGATTTTATTAGA;CSQ=C|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs12619049&COSV66558292|12|-1||EntrezGene||||||2:g.29446701T>C||||||||||0.4259|AFR||0&1|0&1,C|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3173-307A>G|||||||rs12619049&COSV66558292||-1||EntrezGene||YES||||2:g.29446701T>C||||||||||0.4259|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:765:100:75,25:449,214:663,100:0.1307:2,2:34.6:1:36.5:1:0.16533:1.43:60:200:0.134:0:2.1	1/0:398:218:116,102:108,72:180,218:0.5477:2,2:38.9:1:36.5:1:0.18773:1.31803:60:217:0.5564:0:2.1
    541. 

  541. 2	29446721	29446721	A	G	intronic	ALK	.	.	.	0.98	0.8794	0.6369	0.9617	0.9669	0.9340	0.9759	0.9801	0.9622	rs4665447	rs4665447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	359	417	2	29446721	.	A	G	359	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=949;VD=947;AF=0.9979;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.35755;SOR=2.28042;LSEQ=TGGTCTGCAGATTTTATTAG;RSEQ=AGAAATGCCCATGAGAGGAA;CSQ=G|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs4665447|32|-1||EntrezGene||||||2:g.29446721A>G||||||||||0.9826|SAS|||,G|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3173-327T>C|||||||rs4665447||-1||EntrezGene||YES||||2:g.29446721A>G||||||||||0.9826|SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:949:947:615,332:0,0:0,947:0.9979:0,2:38:1:36.4:1:1:0:60:117.375:0.9989:0:1.2	1/1:417:415:219,196:0,0:0,415:0.9952:0,2:38.4:1:36:1:1:0:60:40.5:0.9951:0:1.6
    542. 

  542. 2	29446880	29446880	C	A	intronic	ALK	.	.	.	0.1	0.0094	0.0006	0.0012	0.0066	0.1117	0.0183	0.0016	0.0153	rs12615096	rs12615096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	279	475	2	29446880	.	C	A	279	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2970;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGGAAGTTTCAGCAAGGCC;RSEQ=TAAGGGGTTCTGGAGCCAAA;CSQ=A|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs12615096|191|-1||EntrezGene||||||2:g.29446880C>A||||||||||0.1032|EAS|||,A|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3173-486G>T|||||||rs12615096||-1||EntrezGene||YES||||2:g.29446880C>A||||||||||0.1032|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2970:0:0,0:1641,1329:2970,0:0:2,0:35.3:1:36.5:1:1:0:60:246.5:1:0:0.1	1/0:475:255:131,124:116,103:219,255:0.5368:2,2:35:1:35:1:0.78215:1.06588:60:27.333:0.5313:0:1.1
    543. 

  543. 2	29447108	29447108	G	A	intronic	ALK	.	.	.	0.83	0.7086	0.6098	0.7947	0.7152	0.7670	0.8268	0.7242	0.7495	rs4387740	rs4387740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114075717	LAML-KR|1|205|0.00487805	0.75	383	378	2	29447108	.	G	A	383	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2848;VD=2489;AF=0.8739;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=6.78104;LSEQ=CACATCATGAAAAGATCTCT;RSEQ=AATTGGTGTCTGGGGATCTG;CSQ=A|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs4387740|419|-1||EntrezGene||||||2:g.29447108G>A||||||||||0.8272|SAS|||,A|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3173-714C>T|||||||rs4387740||-1||EntrezGene||YES||||2:g.29447108G>A||||||||||0.8272|SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2848:2489:1163,1326:149,183:332,2489:0.8739:2,2:36.4:1:34:1:0.55816:1.08:60:13.728:0.8725:0:1.1	1/0:378:191:90,101:85,99:184,191:0.5053:2,2:36.6:1:35:1:0.91759:1.04:60:22.875:0.4986:0:1.1
    544. 

  544. 2	29447253	29447253	A	G	intronic	ALK	.	.	.	0.86	0.5322	0.4892	0.7375	0.5364	0.8872	0.5295	0.5070	0.5439	rs6723311	rs6723311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	394	269	2	29447253	.	A	G	394	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1797;VD=1790;AF=0.9961;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37606;SOR=0;LSEQ=CCTGCCCTGTTTCCCTAACC;RSEQ=CTGCCACTCCCCACCCTCTA;CSQ=G|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs6723311|564|-1||EntrezGene||||||2:g.29447253A>G||||||||||0.8581|EAS|||,G|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3173-859T>C|||||||rs6723311||-1||EntrezGene||YES||||2:g.29447253A>G||||||||||0.8581|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1797:1790:821,969:2,2:4,1790:0.9961:2,2:36:1:36.5:1:1:1.18016:60:104.294:0.9961:0:1.1	1/1:269:269:132,137:0,0:0,269:1:0,2:36:1:36.3:1:1:0:60:52.8:1:0:1.2
    545. 

  545. 2	29447454	29447454	C	A	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	258	2	29447454	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1782;VD=0;AF=0;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.002;SOR=0;LSEQ=TGTGTGTAAAGCCCAGCCCC;RSEQ=CAACACATGGGCCAGGGCAA;CSQ=A|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding|||||||||||765|-1||EntrezGene||||||2:g.29447454C>A||||||||||||||,A|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3172+873G>T|||||||||-1||EntrezGene||YES||||2:g.29447454C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1782:0:0,0:874,908:1782,0:0:2,0:38:1:36.5:1:1:0:60:103.824:1:0:0.1	0/1:258:3:1,2:105,150:255,3:0.0116:2,2:48.7:1:28.3:1:1:1.39824:60:2:0.0079:0:1.3
    546. 

  546. 2	29447513	29447513	C	T	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	195	2	29447513	.	C	T	31	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1504;VD=1;AF=0.0007;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03636;SOR=0.06441;LSEQ=GCTCAGTTCCCTCCTCTATG;RSEQ=AATGGACCGACCGTGATCAG;CSQ=T|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs1272635608|824|-1||EntrezGene||||||2:g.29447513C>T||||||||||||||,T|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3172+814G>A|||||||rs1272635608||-1||EntrezGene||YES||||2:g.29447513C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1504:1:1,0:693,810:1503,1:0.0007:2,0:11:0:37:0:0.46144:0:60:2:0.0007:0:1	0/1:195:2:1,1:67,126:193,2:0.0103:2,2:16.5:1:31:1:1:1.87:60:4:0.0105:0:1
    547. 

  547. 2	29447656	29447656	C	A	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	177	2	29447656	.	C	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1595;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.00993;SOR=0;LSEQ=GATGGCACCATATGGGGACA;RSEQ=AGTGTGTGCTGCCATCTCCC;CSQ=A|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding|||||||||||967|-1||EntrezGene||||||2:g.29447656C>A||||||||||||||,A|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3172+671G>T|||||||||-1||EntrezGene||YES||||2:g.29447656C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1595:0:0,0:888,705:1593,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:177:2:1,1:95,80:175,2:0.0113:2,2:56:1:37:0:1:1.18634:60:4:0.0115:0:1
    548. 

  548. 2	29447657	29447657	A	G	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	180	2	29447657	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1607;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0101;SOR=0;LSEQ=ATGGCACCATATGGGGACAC;RSEQ=GTGTGTGCTGCCATCTCCCT;CSQ=G|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding|||||||||||968|-1||EntrezGene||||||2:g.29447657A>G||||||||||||||,G|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||19/28|NM_004304.5:c.3172+670T>C|||||||||-1||EntrezGene||YES||||2:g.29447657A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1607:0:0,0:894,708:1602,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:180:2:1,1:98,80:178,2:0.0111:2,2:39:1:37:0:1:1.22361:60:4:0.0112:0:1
    549. 

  549. 2	29448760	29448760	C	T	intronic	ALK	.	.	.	0.26	0.2081	0.2094	0.1691	0.2384	0.1400	0.1163	0.2386	0.1939	rs34935102	rs34935102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66558297;OCCURENCE=11(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	301	276	2	29448760	.	C	T	301	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3152;VD=315;AF=0.0999;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0.10339;LSEQ=TCTGGAAGAGATGTGGGGGC;RSEQ=GCAGGTGACCAAACAACAGG;CSQ=T|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs34935102&COSV66558297|2071|-1||EntrezGene||||||2:g.29448760C>T||||||||||0.2555|EUR||0&1|0&1,T|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||18/28|NM_004304.5:c.3068-329G>A|||||||rs34935102&COSV66558297||-1||EntrezGene||YES||||2:g.29448760C>T||||||||||0.2555|EUR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3152:315:153,162:1278,1559:2837,315:0.0999:2,2:33.3:1:36.3:1:0.23368:1.15:60:104:0.0996:0:1	1/0:276:143:60,83:60,72:132,143:0.5181:2,2:36.7:1:35.9:1:0.62661:1.15218:60:70.5:0.5184:0:1.1
    550. 

  550. 2	29449005	29449005	G	T	intronic	ALK	.	.	.	0.17	0.1288	0.1719	0.0621	0.1457	0.1359	0.0960	0.1143	0.1245	rs1317902	rs1317902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66564624;OCCURENCE=3(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU22244224	LAML-KR|1|205|0.00487805	0.5	275	250	2	29449005	.	G	T	275	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1962;VD=203;AF=0.1035;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.11196;LSEQ=CACAAAACTGCATCTTGTAT;RSEQ=AACTGCTGCAAACAAATGGG;CSQ=T|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs1317902&COSV66564624|2316|-1||EntrezGene||||||2:g.29449005G>T||||||||||0.1702|AFR||0&1|0&1,T|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||18/28|NM_004304.5:c.3068-574C>A|||||||rs1317902&COSV66564624||-1||EntrezGene||YES||||2:g.29449005G>T||||||||||0.1702|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1962:203:73,130:613,1143:1756,203:0.1035:2,2:37.1:1:36:1:0.75662:1.05:60:66.667:0.1028:0:1.1	1/0:250:127:47,80:44,79:123,127:0.508:2,2:38.8:1:36.7:1:0.89564:1.05:60:254:0.508:0:1.1
    551. 

  551. 2	29449526	29449526	C	T	intronic	ALK	.	.	.	0.69	0.3004	0.1990	0.5	0.2649	0.6807	0.3245	0.2992	0.3480	rs1881419	rs1881419	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	397	467	2	29449526	.	C	T	397	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3245;VD=2805;AF=0.8644;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=7.53133;LSEQ=GTAAGATCCCTGTCACTGGG;RSEQ=ATGTTTAAGTGGAGGCAGGA;CSQ=T|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs1881419|2837|-1||EntrezGene||||||2:g.29449526C>T||||||||||0.6855|EAS|||,T|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||18/28|NM_004304.5:c.3067+262G>A|||||||rs1881419||-1||EntrezGene||YES||||2:g.29449526C>T||||||||||0.6855|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3245:2805:1418,1387:214,204:418,2805:0.8644:2,2:37:1:34.7:1:0.83392:1.02608:60:18.894:0.8621:0:1.1	0/1:467:214:112,102:126,127:253,214:0.4582:2,2:36.8:1:36.3:1:0.64239:1.11:60:213:0.461:0:1.1
    552. 

  552. 2	29449819	29449819	C	T	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon18:c.G3036A:p.T1012T	0.23	0.1686	0.2114	0.1122	0.2550	0.1228	0.1180	0.1624	0.1592	rs2293563	rs2293563	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66557745;OCCURENCE=5(meninges),1(stomach),2(haematopoietic_and_lymphoid_tissue),1(urinary_tract),5(soft_tissue),2(lung)	250718	Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU584959	LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,COCA-CN|1|321|0.00311526	0.5	295	379	2	29449819	.	C	T	295	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3193;VD=311;AF=0.0974;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.10975;LSEQ=ACGCCATCCTCAGCCAGCAC;RSEQ=GTCCCGTGGTCACAGAAGCA;CSQ=T|upstream_gene_variant|MODIFIER|ALK|238|Transcript|NM_001353765.2|protein_coding||||||||||rs2293563&COSV66557745|3130|-1||EntrezGene||||||2:g.29449819C>T|0.1562|0.2082|0.1073|0.2435|0.1207|0.1086|0.172|0.1915|0.1444|0.2435|gnomAD_ASJ|benign|0&1|1&1,T|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|18/29||NM_004304.5:c.3036G>A|NP_004295.2:p.Thr1012%3D|3963|3036|1012|T|acG/acA|rs2293563&COSV66557745||-1||EntrezGene||YES||||2:g.29449819C>T|0.1562|0.2082|0.1073|0.2435|0.1207|0.1086|0.172|0.1915|0.1444|0.2435|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3193:311:152,159:1423,1459:2882,311:0.0974:2,2:38:1:35.7:1:0.905:1.02024:60:50.833:0.0962:0:1.1	0/1:379:188:98,90:88,100:188,188:0.496:2,2:35.2:1:36:1:0.35325:1.24:60:93:0.4987:0:1.1
    553. 

  553. 2	29451807	29451807	C	G	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon16:c.G2758C:p.G920R	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.998	0.715	D	0.99	0.774	D	0.000	0.491	D	1	0.810	D	3.39	0.917	M	-0.69	0.727	T	-5.21	0.837	D	0.774	0.766	0.432	0.896	D	0.626	0.869	D	0.300	0.909	D	6.697	0.916	32	0.999	0.997	0.997	0.990	D	c	0.861	0.799	1.000	0.747	0.487	0.133	0	5.22	0.722	7.376	0.788	0.935	0.490	1.000	0.715	1.000	0.888	18.788	0.919	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	29	2	29451807	.	C	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=261;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.00969;SOR=0;LSEQ=CCCTCCACCCCCTCCGAAAC;RSEQ=CCCTCTTGTCTCCCACCCCC;CSQ=G|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|16/29||NM_004304.5:c.2758G>C|NP_004295.2:p.Gly920Arg|3685|2758|920|G/R|Ggt/Cgt|COSV66557810||-1||EntrezGene||YES||||2:g.29451807C>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:261:0:0,0:97,164:261,0:0:2,0:23.1:1:36.2:1:1:0:60:51.2:1:0:0.4	0/1:29:2:1,1:10,17:27,2:0.069:2,2:8:0:37:0:1:1.67:60:4:0.0714:0:1
    554. 

  554. 2	29455267	29455267	A	G	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon15:c.T2535C:p.G845G	0.72	0.6208	0.5538	0.4880	0.7583	0.1811	0.6663	0.7009	0.6288	rs2256740	rs2256740	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66555763;OCCURENCE=1(breast),1(liver),16(meninges),1(bone),1(stomach),1(haematopoietic_and_lymphoid_tissue),19(soft_tissue)	250719	Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU584960	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,COCA-CN|2|321|0.00623053,BRCA-KR|1|50|0.02	0.25	269	241	2	29455267	.	A	G	269	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1729;VD=159;AF=0.092;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=TTGGCCCCGTAGGCCCTGCC;RSEQ=CCACCTCCGGCTGCAATGAT;CSQ=G|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|15/29||NM_004304.5:c.2535T>C|NP_004295.2:p.Gly845%3D|3462|2535|845|G|ggT/ggC|rs2256740&COSV66555763||-1||EntrezGene||YES||||2:g.29455267A>G|0.6073|0.5415|0.4451|0.7996|0.1767|0.6506|0.7101|0.6609|0.5979|0.7996|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1729:159:66,93:680,889:1569,159:0.092:2,2:37.4:1:36.8:1:0.67526:1.0778:60:158:0.0927:0:1.1	0/0:241:0:0,0:95,146:241,0:0:2,0:36.4:1:36.7:1:1:0:60:240:1:0:0
    555. 

  555. 2	29456474	29456474	G	A	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon14:c.C2444T:p.A815V	.	.	.	.	.	.	.	.	.	.	.	0.141	0.255	T	0.977	0.566	D	0.934	0.652	D	0.000	0.477	D	1.000	0.810	D	2.855	0.832	M	0.89	0.456	T	-2.89	0.606	D	0.645	0.660	-0.531	0.675	T	0.280	0.652	T	0.049	0.638	D	5.448	0.739	26.1	0.999	0.979	0.942	0.603	D	c	0.803	0.778	1.000	0.747	0.487	0.133	0	5.29	0.743	7.814	0.846	1.048	0.713	1.000	0.715	0.995	0.604	18.958	0.926	.	.	.	ID=COSV66561157;OCCURENCE=2(thyroid)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU89000166	THCA-CN|1|50|0.02	0.25	37	162	2	29456474	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1211;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01385;SOR=0;LSEQ=CCCCTCCTCCTCCGCCTCCT;RSEQ=CCCACTCATGCACGCTTCTG;CSQ=A|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|14/29||NM_004304.5:c.2444C>T|NP_004295.2:p.Ala815Val|3371|2444|815|A/V|gCa/gTa|COSV66561157||-1||EntrezGene||YES||||2:g.29456474G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1211:0:0,0:674,535:1209,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:162:2:1,1:85,75:160,2:0.0123:2,2:66:1:37:0:1:1.13245:60:4:0.0124:0:1
    556. 

  556. 2	29473934	29473934	G	A	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	114	2	29473934	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=804;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.0153;SOR=0;LSEQ=TCCAGGCTTCTTCGGAAGGG;RSEQ=TGGTCTGCCCCTCCCCTCCC;CSQ=A|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||12/28|NM_004304.5:c.2204+37C>T|||||||rs193064534||-1||EntrezGene||YES||||2:g.29473934G>A|4.169e-06|0|0|0|0|0|9.32e-06|0|0|9.32e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:804:0:0,0:494,310:804,0:0:2,0:36.7:1:36.7:1:1:0:60:267:1:0:0.1	0/1:114:2:1,1:74,38:112,2:0.0175:2,2:39:1:37:0:1:1.93525:60:4:0.0175:0:1
    557. 

  557. 2	29543663	29543663	T	C	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon7:c.A1500G:p.Q500Q	0.92	0.8023	0.5071	0.8771	0.8808	0.9086	0.9241	0.9216	0.8939	rs2293564	rs2293564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66566490;OCCURENCE=18(meninges),1(thyroid)	250720	Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4556178	LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763	1	418	362	2	29543663	.	T	C	418	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2822;VD=2819;AF=0.9989;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.10216;SOR=5.21574;LSEQ=TTTAGGGTCCTGACCTGCCA;RSEQ=TGAGGAGTGTGGGGTGACAG;CSQ=C|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|7/29||NM_004304.5:c.1500A>G|NP_004295.2:p.Gln500%3D|2427|1500|500|Q|caA/caG|rs2293564&COSV66566490||-1||EntrezGene||YES||||2:g.29543663T>C|0.8777|0.5039|0.8853|0.8957|0.9073|0.9138|0.9184|0.8961|0.8633|0.9235|EUR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2822:2819:1430,1389:0,0:0,2819:0.9989:0,2:39.1:1:36.5:1:1:0:60:147.368:0.9989:0:1.1	1/1:362:360:190,170:0,0:0,360:0.9945:0,2:38.4:1:36.4:1:1:0:60:179:0.9944:0:1.1
    558. 

  558. 2	29606543	29606543	G	T	intronic	ALK	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	56	187	2	29606543	.	G	T	56	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1531;VD=5;AF=0.0033;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.17178;SOR=0.30338;LSEQ=AAACATGGTTGCAGGTTATT;RSEQ=ACACATCTAACACAATAGGC;CSQ=T|intron_variant|MODIFIER|ALK|238|Transcript|NM_004304.5|protein_coding||5/28|NM_004304.5:c.1282+55C>A|||||||||-1||EntrezGene||YES||||2:g.29606543G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1531:5:3,2:908,618:1526,5:0.0033:2,2:31:1:24.2:1:1:1.02:60:1.5:0.002:0:3.6	0/1:187:2:1,1:121,64:185,2:0.0107:2,2:45.5:1:37:0:1:1.88383:60:4:0.0109:0:1
    559. 

  559. 2	29917793	29917793	C	T	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon3:c.G875A:p.R292H	0.0008	0.0001	0.0003	0	0	0.0006	0	0	0	rs149145987	rs149145987	0.437	0.093	T	0.001	0.067	B	0.003	0.080	B	.	.	.	1.000	0.537	D	0	0.065	N	4.26	0.026	T	-0.76	0.212	N	0.204	0.250	-0.843	0.524	T	0.005	0.017	T	0.021	0.435	T	1.039	0.194	10.88	0.950	0.254	0.025	0.069	N	c	-1.098	-1.038	0.000	0.029	0.487	0.133	0	0.444	0.157	0.133	0.156	-0.319	0.077	0.046	0.210	0.170	0.210	9.532	0.382	Concanavalin A-like lectin/glucanase domain|MAM domain	.	.	ID=COSV66559404;OCCURENCE=1(stomach),1(pancreas),1(lung),1(large_intestine)	392773	Neuroblastoma_3	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	MU18374544	PACA-AU|1|391|0.00255754,LUSC-US|1|485|0.00206186	0.25	37	174	2	29917793	.	C	T	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=765;VD=2;AF=0.0026;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.15831;SOR=0.22593;LSEQ=AGGCCTCCTCGGAGGGGATG;RSEQ=GGCGCCAGGACCAGCTCTGG;CSQ=T|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|3/29||NM_004304.5:c.875G>A|NP_004295.2:p.Arg292His|1802|875|292|R/H|cGc/cAc|rs149145987&COSV66559404||-1||EntrezGene||YES||||2:g.29917793C>T|5.186e-05|0.0001232|0.0001446|0|0.0002721|0|0|0|3.268e-05|0.0008|AFR|uncertain_significance|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:765:2:1,1:445,317:762,2:0.0026:2,2:42:1:37:0:1:1.40313:60:4:0.0026:0:1	0/1:174:2:1,1:95,77:172,2:0.0115:2,2:41:1:37:0:1:1.23226:60:4:0.0115:0:1
    560. 

  560. 2	29940529	29940529	A	T	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon2:c.T702A:p.P234P	0.81	0.6361	0.2397	0.7224	0.7881	0.7342	0.7362	0.8163	0.7633	rs2246745	rs2246745	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66584548;OCCURENCE=17(meninges),1(haematopoietic_and_lymphoid_tissue)	250722	Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU13471149	COCA-CN|5|321|0.0155763	1	305	412	2	29940529	.	A	T	305	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=420;VD=419;AF=0.9976;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.50481;SOR=0;LSEQ=AAATAATCAGGAGAAGGAGA;RSEQ=GGCATGTTTGTTGGTGATTC;CSQ=T|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|2/29||NM_004304.5:c.702T>A|NP_004295.2:p.Pro234%3D|1629|702|234|P|ccT/ccA|rs2246745&COSV66584548||-1||EntrezGene||YES||||2:g.29940529A>T|0.7408|0.2347|0.7288|0.8203|0.7455|0.7466|0.8139|0.7818|0.7106|0.8203|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:420:419:236,183:0,0:0,419:0.9976:0,2:38.4:1:35.1:1:1:0:60:19.95:1:0:1.1	1/1:412:412:199,213:0,0:0,412:1:0,2:39.2:1:36.2:1:1:0:60:67.667:1:0:1.1
    561. 

  561. 2	30142907	30142907	C	T	exonic	ALK	.	nonsynonymous SNV	ALK:NM_004304:exon1:c.G619A:p.A207T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.996	0.832	D	.	.	.	1.000	0.508	D	0.55	0.145	N	-2.07	0.860	D	-0.56	0.170	N	0.902	0.891	0.164	0.853	D	0.624	0.868	D	0.107	0.784	D	4.867	0.654	24.9	0.998	0.887	0.836	0.424	D	c	0.459	0.440	1.000	0.747	0.497	0.185	0	5.33	0.756	6.706	0.743	0.925	0.434	1.000	0.715	0.439	0.261	17.976	0.890	.	.	.	ID=COSV66575135;OCCURENCE=1(central_nervous_system)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	197	2	30142907	.	C	T	58	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1965;VD=3;AF=0.0015;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0687;SOR=0.14935;LSEQ=GGGCTGGGAGGCGCGAATTG;RSEQ=CGCGGACAGCCTTCCCTCTC;CSQ=T|missense_variant|MODERATE|ALK|238|Transcript|NM_004304.5|protein_coding|1/29||NM_004304.5:c.619G>A|NP_004295.2:p.Ala207Thr|1546|619|207|A/T|Gca/Aca|COSV66575135||-1||EntrezGene||YES||||2:g.30142907C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1965:3:2,1:1182,780:1962,3:0.0015:2,2:55:1:37:0:1:1.32:60:6:0.0015:0:1	0/1:197:2:1,1:119,76:195,2:0.0102:2,2:41.5:1:37:0:1:1.56206:60:4:0.0103:0:1
    562. 

  562. 2	30143499	30143499	G	C	exonic	ALK	.	synonymous SNV	ALK:NM_004304:exon1:c.C27G:p.L9L	1.	0.8892	0.8349	0.9459	0.8245	1	0.8627	0.9123	0.9002	rs4358080	rs4358080	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV66573286;OCCURENCE=4(large_intestine)	250724	Neuroblastoma_3|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013083,MedGen:C2751681,OMIM:613014|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU84195	COCA-CN|5|321|0.0155763	1	326	80	2	30143499	.	G	C	326	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=493;VD=493;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAAAGCAGCAGCGGCAG;RSEQ=AGCCACAGGAGCCCGATGGC;CSQ=C|synonymous_variant|LOW|ALK|238|Transcript|NM_004304.5|protein_coding|1/29||NM_004304.5:c.27C>G|NP_004295.2:p.Leu9%3D|954|27|9|L|ctC/ctG|rs4358080&COSV66573286||-1||EntrezGene||YES||||2:g.30143499G>C|0.9066|0.8318|0.9382|0.8617|0.9996|0.8555|0.9078|0.894|0.8798|0.9996|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:493:493:112,381:0,0:0,493:1:0,2:33.5:1:36.5:1:1:0:60:122.25:1:0:1.1	1/1:80:80:14,66:0,0:0,80:1:0,2:35.9:1:36:1:1:0:60:39:1:0:1.1
    563. 

  563. 2	38298150	38298150	A	G	exonic	CYP1B1	.	synonymous SNV	CYP1B1:NM_000104:exon3:c.T1347C:p.D449D	0.91	0.5083	0.2469	0.7584	0.4834	0.8905	0.6354	0.5701	0.5959	rs1056837	rs1056837	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52226737;OCCURENCE=2(large_intestine)	177657	Irido-corneo-trabecular_dysgenesis|Glaucoma_3,_primary_congenital,_A|not_specified	Human_Phenotype_Ontology:HP:0000659,MONDO:MONDO:0011414,MedGen:C0344559,OMIM:604229,Orphanet:ORPHA708,SNOMED_CT:204153003|MONDO:MONDO:0009277,MedGen:C1856439,OMIM:231300|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	1	1	MU157484	COCA-CN|6|321|0.0186916	1	405	395	2	38298150	.	A	G	405	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2306;VD=2303;AF=0.9987;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.62219;SOR=0;LSEQ=AGGTCCTTGTTGATGAGGCC;RSEQ=TCCTTGTCCAAGAATCGAGC;CSQ=G|synonymous_variant|LOW|CYP1B1|1545|Transcript|NM_000104.4|protein_coding|3/3||NM_000104.4:c.1347T>C|NP_000095.2:p.Asp449%3D|1719|1347|449|D|gaT/gaC|rs1056837&COSV52226737||-1||EntrezGene||YES||||2:g.38298150A>G|0.6341|0.245|0.7855|0.5083|0.9011|0.6346|0.5703|0.6338|0.787|0.9087|EAS|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|RMDN2|151393|Transcript|NM_001322212.2|protein_coding||||||||||rs1056837&COSV52226737|3869|1||EntrezGene||||||2:g.38298150A>G|0.6341|0.245|0.7855|0.5083|0.9011|0.6346|0.5703|0.6338|0.787|0.9087|EAS|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|RMDN2|151393|Transcript|NM_144713.5|protein_coding||||||||||rs1056837&COSV52226737|3869|1||EntrezGene||YES||||2:g.38298150A>G|0.6341|0.245|0.7855|0.5083|0.9011|0.6346|0.5703|0.6338|0.787|0.9087|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2306:2303:1183,1120:0,0:0,2303:0.9987:0,2:37.5:1:36.3:1:1:0:60:81.25:1:0:1.8	1/1:395:395:200,195:0,0:0,395:1:0,2:35.4:1:36.4:1:1:0:60:196.5:1:0:1.8
    564. 

  564. 2	38298203	38298203	C	G	exonic	CYP1B1	.	nonsynonymous SNV	CYP1B1:NM_000104:exon3:c.G1294C:p.V432L	0.91	0.5025	0.2253	0.7590	0.4834	0.8888	0.6355	0.5710	0.5937	rs1056836	rs1056836	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52230252;OCCURENCE=1(large_intestine)	177658	not_specified|not_provided	MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	MU157492	COCA-CN|5|321|0.0155763	1	409	435	2	38298203	.	C	G	409	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2372;VD=2367;AF=0.9979;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.4306;SOR=0;LSEQ=CTCCGGGTTAGGCCACTTCA;RSEQ=TGGGTCATGATTCACAGACC;CSQ=G|missense_variant|MODERATE|CYP1B1|1545|Transcript|NM_000104.4|protein_coding|3/3||NM_000104.4:c.1294G>C|NP_000095.2:p.Val432Leu|1666|1294|432|V/L|Gtg/Ctg|rs1056836&CM004465&COSV52230252||-1||EntrezGene||YES||||2:g.38298203C>G|0.6317|0.2216|0.7843|0.5062|0.8995|0.6344|0.5694|0.6318|0.7864|0.9087|EAS|likely_benign&benign|0&0&1|1&1&1,G|downstream_gene_variant|MODIFIER|RMDN2|151393|Transcript|NM_001322212.2|protein_coding||||||||||rs1056836&CM004465&COSV52230252|3922|1||EntrezGene||||||2:g.38298203C>G|0.6317|0.2216|0.7843|0.5062|0.8995|0.6344|0.5694|0.6318|0.7864|0.9087|EAS|likely_benign&benign|0&0&1|1&1&1,G|downstream_gene_variant|MODIFIER|RMDN2|151393|Transcript|NM_144713.5|protein_coding||||||||||rs1056836&CM004465&COSV52230252|3922|1||EntrezGene||YES||||2:g.38298203C>G|0.6317|0.2216|0.7843|0.5062|0.8995|0.6344|0.5694|0.6318|0.7864|0.9087|EAS|likely_benign&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2372:2367:1189,1178:0,0:0,2367:0.9979:0,2:37.7:1:36.5:1:1:0:60:111.714:0.9983:0:1.7	1/1:435:435:225,210:0,0:0,435:1:0,2:37.9:1:36.5:1:1:0:60:144:1:0:1.7
    565. 

  565. 2	46583279	46583281	CCC	GCTCT	intronic	EPAS1	.	.	.	0.54	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	36	0	2	46583279	.	CCC	GCTCT	36	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=Complex;DP=2;VD=2;AF=1;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TGCAAGCTGTCCCACCCCCC;RSEQ=CTTTCCAGTTTGCTCTGAAA;CSQ=GCTCT|splice_polypyrimidine_tract_variant&intron_variant|LOW|EPAS1|2034|Transcript|NM_001430.5|protein_coding||2/15|NM_001430.5:c.218-11_218-9delinsGCTCT|||||||rs1553394867||1||EntrezGene||YES||||2:g.46583279_46583281delinsGCTCT||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:50.5:1:36:1:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    566. 

  566. 2	47601106	47601106	T	C	exonic	EPCAM	.	nonsynonymous SNV	EPCAM:NM_002354:exon3:c.T344C:p.M115T	0.89	0.6033	0.8316	0.4557	0.3775	0.8403	0.6001	0.4616	0.5545	rs1126497	rs1126497	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.060	0.222	N	1	0.090	P	-1.4	0.006	N	0.05	0.619	T	2.21	0.003	N	0.058	0.529	-0.934	0.436	T	0.000	0.000	T	.	.	.	-0.486	0.056	0.238	0.739	0.102	0.076	0.135	N	c	-1.157	-0.973	1.000	0.747	0.778	0.996	0	1.71	0.233	0.050	0.139	-0.318	0.077	0.559	0.272	0.815	0.341	11.894	0.517	Thyroglobulin type-1	ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8	Adipose_Subcutaneous|Artery_Tibial|Lung	ID=COSV55392922;OCCURENCE=1(urinary_tract),2(prostate)	181861	Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified	MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	1	0	1	0	MU3888690	ESAD-UK|1|409|0.00244499,COCA-CN|5|321|0.0155763	1	378	451	2	47601106	.	T	C	378	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1238;VD=1237;AF=0.9992;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.46286;SOR=2.74695;LSEQ=GCAGTGCAACGGCACCTCCA;RSEQ=GTGCTGGTGTGTGAACACTG;CSQ=C|missense_variant|MODERATE|EPCAM|4072|Transcript|NM_002354.3|protein_coding|3/9||NM_002354.3:c.344T>C|NP_002345.2:p.Met115Thr|539|344|115|M/T|aTg/aCg|rs1126497&CM1110060&COSV55392922||1||EntrezGene||YES||||2:g.47601106T>C|0.5131|0.8418|0.472|0.3635|0.832|0.5964|0.4359|0.4638|0.4807|0.8888|AFR|benign|0&0&1|1&1&1,C|upstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA||||||||||rs1126497&CM1110060&COSV55392922|3708|1||EntrezGene||YES||||2:g.47601106T>C|0.5131|0.8418|0.472|0.3635|0.832|0.5964|0.4359|0.4638|0.4807|0.8888|AFR|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1238:1237:545,692:0,0:0,1237:0.9992:0,2:38.8:1:36.8:1:1:0:60:411.333:0.9992:0:1.1	1/1:451:450:199,251:0,0:0,450:0.9978:0,2:36.6:1:36.5:1:1:0:60:74:1:0:1.1
    567. 

  567. 2	47602434	47602434	C	T	exonic	EPCAM	.	nonsynonymous SNV	EPCAM:NM_002354:exon4:c.C487T:p.R163W	0.0036	0.0009	0.0031	0	0	0.0006	0	6.662e-05	0	rs148725106	rs148725106	0.011	0.555	D	0.937	0.541	P	0.332	0.434	B	0.648	0.105	N	1	0.090	N	1.1	0.281	L	-0.64	0.721	T	-3.26	0.654	D	0.205	0.270	-0.912	0.466	T	0.194	0.548	T	0.083	0.741	D	5.189	0.700	25.5	0.996	0.736	0.134	0.177	N	c	-0.441	-0.546	0.001	0.081	0.732	0.924	0	1.83	0.242	-0.023	0.123	0.935	0.490	0.003	0.159	0.133	0.200	8.032	0.295	.	.	.	.	139735	not_provided	MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Likely_benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	1	0	MU91759152	LUSC-US|1|485|0.00206186	0.25	37	89	2	47602434	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.74548;SOR=0;LSEQ=CTTATGATAGTAAAAGTTTG;RSEQ=GGACGTAAGTGCAATTAAAT;CSQ=T|missense_variant|MODERATE|EPCAM|4072|Transcript|NM_002354.3|protein_coding|4/9||NM_002354.3:c.487C>T|NP_002345.2:p.Arg163Trp|682|487|163|R/W|Cgg/Tgg|rs148725106||1||EntrezGene||YES||||2:g.47602434C>T|0.000211|0.002772|5.787e-05|0|0|0|5.285e-05|0|0|0.003631|AA|likely_benign||1,T|upstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA||||||||||rs148725106|2380|1||EntrezGene||YES||||2:g.47602434C>T|0.000211|0.002772|5.787e-05|0|0|0|5.285e-05|0|0|0.003631|AA|likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:14:0:0,0:6,8:14,0:0:2,0:24.9:1:36.1:1:1:0:60:28:1:0:0.1	0/1:89:2:1,1:42,45:87,2:0.0225:2,2:46.5:1:37:0:1:1.07:60:4:0.0227:0:1
    568. 

  568. 2	47604230	47604230	A	G	intronic	EPCAM	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs373453367	rs373453367	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	2	47604230	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=92;VD=2;AF=0.0217;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13557;SOR=inf;LSEQ=TATTTTGGTATGATTTTTTA;RSEQ=TAAGTGAGCTTTAGCAGACA;CSQ=G|intron_variant|MODIFIER|EPCAM|4072|Transcript|NM_002354.3|protein_coding||5/8|NM_002354.3:c.555+14A>G|||||||rs373453367||1||EntrezGene||YES||||2:g.47604230A>G|2.388e-05|0|0|0|0|0|5.278e-05|0|0|0.0001163|EA|||,G|upstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA||||||||||rs373453367|584|1||EntrezGene||YES||||2:g.47604230A>G|2.388e-05|0|0|0|0|0|5.278e-05|0|0|0.0001163|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:92:2:1,1:47,43:90,2:0.0217:2,2:45:1:37:0:1:1.09196:60:4:0.0222:0:1	0/0:157:0:0,0:79,78:157,0:0:2,0:43.5:1:35.6:1:1:0:60:30.4:1:0:0
    569. 

  569. 2	47606107	47606107	A	-	exonic	EPCAM	.	frameshift deletion	EPCAM:NM_002354:exon6:c.571delA:p.I191Sfs*19	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	47	2	47606106	.	TA	T	37	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=2;VD=2;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00085;SOR=inf;LSEQ=CCCCAGTATGAGAATAATGT;RSEQ=TCACTATTGATCTGGTTCAA;CSQ=-|frameshift_variant|HIGH|EPCAM|4072|Transcript|NM_002354.3|protein_coding|6/9||NM_002354.3:c.571del|NP_002345.2:p.Ile191SerfsTer19|766|571|191|I/X|Atc/tc|||1||EntrezGene||YES||||2:g.47606107del||||||||||||||,-|downstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA|||||||||||1198|1||EntrezGene||YES||||2:g.47606107del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:37:0:1:0:60:4:1:0:3.5	0/0:47:0:0,0:28,19:47,0:0:2,0:36.7:1:36.5:1:1:0:60:94:1:0:0
    570. 

  570. 2	47606969	47606969	T	C	exonic	EPCAM	.	nonsynonymous SNV	EPCAM:NM_002354:exon7:c.T719C:p.L240P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.909	0.654	D	0.001	0.411	D	1	0.810	D	3.12	0.881	M	-1.52	0.815	D	-6.04	0.897	D	0.825	0.853	0.447	0.898	D	0.662	0.883	D	0.260	0.895	D	6.353	0.877	29.4	0.999	0.984	0.970	0.720	D	c	0.598	0.536	0.999	0.389	0.707	0.730	0	5.66	0.872	5.438	0.661	1.061	0.807	0.671	0.281	0.877	0.367	15.898	0.790	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	163	2	47606969	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=66;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.50575;SOR=0;LSEQ=GACAGTAAATGGGGAACAAC;RSEQ=GGATCTGGATCCTGGTCAAA;CSQ=C|missense_variant|MODERATE|EPCAM|4072|Transcript|NM_002354.3|protein_coding|7/9||NM_002354.3:c.719T>C|NP_002345.2:p.Leu240Pro|914|719|240|L/P|cTg/cCg|||1||EntrezGene||YES||||2:g.47606969T>C||||||||||||||,C|downstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA|||||||||||2060|1||EntrezGene||YES||||2:g.47606969T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:66:0:0,0:42,24:66,0:0:2,0:28.2:1:36.8:1:1:0:60:132:1:0:0.2	0/1:163:2:1,1:92,69:161,2:0.0123:2,2:40.5:1:37:0:1:1.33094:60:4:0.0123:0:1
    571. 

  571. 2	47606977	47606977	G	T	exonic	EPCAM	.	nonsynonymous SNV	EPCAM:NM_002354:exon7:c.G727T:p.D243Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.493	0.393	P	0.097	0.313	B	0.000	0.469	D	1.000	0.499	D	2.8	0.819	M	-0.8	0.739	T	-4.91	0.816	D	0.811	0.835	-0.363	0.732	T	0.305	0.676	T	0.030	0.523	D	4.866	0.653	24.9	0.992	0.551	0.992	0.924	D	c	0.366	0.476	0.998	0.367	0.707	0.730	0	5.66	0.872	5.390	0.658	1.048	0.713	1.000	0.715	0.998	0.697	15.251	0.731	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	176	2	47606977	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=73;VD=2;AF=0.0274;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08511;SOR=inf;LSEQ=ATGGGGAACAACTGGATCTG;RSEQ=ATCCTGGTCAAACTTTAATT;CSQ=T|missense_variant|MODERATE|EPCAM|4072|Transcript|NM_002354.3|protein_coding|7/9||NM_002354.3:c.727G>T|NP_002345.2:p.Asp243Tyr|922|727|243|D/Y|Gat/Tat|||1||EntrezGene||YES||||2:g.47606977G>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA|||||||||||2068|1||EntrezGene||YES||||2:g.47606977G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:73:2:1,1:45,26:71,2:0.0274:2,2:20:1:37:0:1:1.7171:60:4:0.0274:0:1	0/0:176:0:0,0:97,79:176,0:0:2,0:36.4:1:36.7:1:1:0:60:352:1:0:0.1
    572. 

  572. 2	47607034	47607034	C	T	exonic	EPCAM	.	stopgain	EPCAM:NM_002354:exon7:c.C784T:p.Q262X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.001	0.434	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.375	0.991	42	0.996	0.729	0.914	0.532	D	c	0.681	0.542	0.010	0.120	0.707	0.730	0	3.75	0.421	2.553	0.453	0.935	0.490	1.000	0.715	1.000	0.888	12.605	0.557	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	211	2	47607034	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=126;VD=2;AF=0.0159;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.13909;SOR=inf;LSEQ=AAGCACCTGAATTCTCAATG;RSEQ=AGGGTCTAAAAGCTGGTGTT;CSQ=T|stop_gained|HIGH|EPCAM|4072|Transcript|NM_002354.3|protein_coding|7/9||NM_002354.3:c.784C>T|NP_002345.2:p.Gln262Ter|979|784|262|Q/*|Cag/Tag|||1||EntrezGene||YES||||2:g.47607034C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MIR559|693144|Transcript|NR_030286.1|miRNA|||||||||||2125|1||EntrezGene||YES||||2:g.47607034C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:126:2:2,0:74,50:124,2:0.0159:2,0:33.5:1:37:0:0.51746:0:60:4:0.0161:0:1	0/0:211:0:0,0:103,108:211,0:0:2,0:37.8:1:35.7:1:1:0:60:34.167:1:0:0
    573. 

  573. 2	47613723	47613723	G	A	exonic	EPCAM	.	nonsynonymous SNV	EPCAM:NM_002354:exon9:c.G916A:p.G306S	.	.	.	.	.	.	.	.	.	.	.	0.087	0.324	T	0.991	0.689	D	0.79	0.617	P	0.084	0.207	N	0.659	0.309	N	2.65	0.778	M	-0.59	0.716	T	-2.13	0.483	N	0.437	0.492	-0.142	0.791	T	0.439	0.778	T	0.050	0.642	D	3.672	0.498	23.3	0.997	0.785	0.692	0.338	D	c	0.453	0.417	0.000	0.067	0.732	0.924	0	4.49	0.540	1.677	0.370	0.141	0.225	1.000	0.715	0.999	0.750	8.255	0.307	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	168	2	47613723	.	G	A	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.98817;SOR=0;LSEQ=TGTTTCAGATAAAGGAGATG;RSEQ=GTGAGATGCATAGGGAACTC;CSQ=A|missense_variant|MODERATE|EPCAM|4072|Transcript|NM_002354.3|protein_coding|9/9||NM_002354.3:c.916G>A|NP_002345.2:p.Gly306Ser|1111|916|306|G/S|Ggt/Agt|||1||EntrezGene||YES||||2:g.47613723G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:37:0:1:0:60:2:1:0:0	0/1:168:2:1,1:88,78:166,2:0.0119:2,2:63.5:1:37:0:1:1.12739:60:4:0.0121:0:1
    574. 

  574. 2	47613763	47613763	T	C	UTR3	EPCAM	NM_002354:c.*11T>C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	170	2	47613763	.	T	C	25	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.9883;SOR=0;LSEQ=CAATGCATAACTATATAATT;RSEQ=GAAGATTATAGAAGAAGGGA;CSQ=C|3_prime_UTR_variant|MODIFIER|EPCAM|4072|Transcript|NM_002354.3|protein_coding|9/9||NM_002354.3:c.*11T>C||1151|||||||1||EntrezGene||YES||||2:g.47613763T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:71:0:37:0:1:0:60:2:1:0:0	0/1:170:2:1,1:75,93:168,2:0.0118:2,2:30.5:1:25:0:1:1.24:60:4:0.0119:0:3.5
    575. 

  575. 2	47630378	47630378	G	T	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon1:c.G48T:p.E16D	.	.	.	.	.	.	.	.	.	.	.	0.071	0.351	T	0.199	0.689	B	0.084	0.725	B	0.000	0.843	D	0.991	0.810	D	1.85	0.492	L	-3.05	0.924	D	-1.52	0.370	N	0.791	0.784	0.541	0.911	D	0.791	0.929	D	0.494	0.951	D	2.877	0.406	21.7	0.992	0.537	0.811	0.403	D	c	-0.130	-0.118	1.000	0.747	0.442	0.072	0	2.57	0.298	0.865	0.274	-0.229	0.095	0.631	0.278	0.990	0.544	9.387	0.373	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	149	2	47630378	.	G	T	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1330;VD=1;AF=0.0008;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02826;SOR=0.05554;LSEQ=CAGTTGGAGAGCGCGGCCGA;RSEQ=GTCGGCTTCGTGCGCTTCTT;CSQ=T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|1/16||NM_000251.3:c.48G>T|NP_000242.1:p.Glu16Asp|84|48|16|E/D|gaG/gaT|COSV99253506||1||EntrezGene||YES||||2:g.47630378G>T|||||||||||||1|1,T|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||1/16|NM_001258281.1:c.-31+64G>T|||||||COSV99253506||1||EntrezGene||||||2:g.47630378G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1330:1:1,0:674,655:1329,1:0.0008:2,0:24:0:11:0:1:0:60:0:0:0:3	0/1:149:2:1,1:80,67:147,2:0.0134:2,2:10:1:37:0:1:1.1926:60:4:0.0134:0:1.5
    576. 

  576. 2	47630550	47630550	C	G	intronic	MSH2	.	.	.	0.81	0.5569	0.7546	0.4376	0.3477	0.8292	0.5805	0.4201	0.5295	rs2303426	rs2303426	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	45235	Carcinoma_of_colon|Lynch_syndrome|Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|none_provided	MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN235283	reviewed_by_expert_panel	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU16913554	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,COCA-CN|5|321|0.0155763	1	331	96	2	47630550	.	C	G	331	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=506;VD=506;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCCGGCAGGTGAGGGC;RSEQ=GGGACGGCGCGTGCTGGGGA;CSQ=G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||1/15|NM_000251.3:c.211+9C>G|||||||rs2303426||1||EntrezGene||YES||||2:g.47630550C>G|0.4735|0.7665|0.4531|0.3348|0.8155|0.5751|0.3857|0.4235|0.4569|0.8155|gnomAD_EAS|benign||1,G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||2/16|NM_001258281.1:c.13+9C>G|||||||rs2303426||1||EntrezGene||||||2:g.47630550C>G|0.4735|0.7665|0.4531|0.3348|0.8155|0.5751|0.3857|0.4235|0.4569|0.8155|gnomAD_EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:506:506:174,332:0,0:0,506:1:0,2:37.5:1:36.9:1:1:0:60:1012:1:0:1.3	1/1:96:96:39,57:0,0:0,96:1:0,2:37.3:1:36.2:1:1:0:60:47:1:0:1.4
    577. 

  577. 2	47635523	47635523	-	T	intronic	MSH2	.	.	.	0.2	0.0071	0.0012	0.0260	0	0	0.0772	0.0034	0.0170	rs757515274	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	483323	Hereditary_cancer-predisposing_syndrome|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU41422983	BTCA-SG|2|71|0.028169,ESCA-CN|1|332|0.00301205	0.5	92	56	2	47635523	.	C	CT	92	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=20;VD=5;AF=0.25;SHIFT3=13;MSI=14;MSILEN=1;SSF=0.07942;SOR=3.33463;LSEQ=TATCTCAAATCTGTAATGTA;RSEQ=TTTTTTTTTTTTTAAGGAGC;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||1/15|NM_000251.3:c.212-4dup|||||||rs746333570||1||EntrezGene||YES||||2:g.47635536dup|0.2036|0.1599|0.2545|0.2572|0.2199|0.1727|0.1769|0.2342|0.258|0.258|gnomAD_SAS|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||2/16|NM_001258281.1:c.14-4dup|||||||rs746333570||1||EntrezGene||||||2:g.47635536dup|0.2036|0.1599|0.2545|0.2572|0.2199|0.1727|0.1769|0.2342|0.258|0.258|gnomAD_SAS|benign&likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:20:5:2,3:11,4:15,5:0.25:2,2:33.9:1:40:1:0.2898:3.80519:64.8:10:0.2941:0.1:0.4	0/1:56:5:4,1:36,7:43,5:0.0893:2,2:34.8:1:40:0:1:1.27854:64.8:10:0.1087:0:0
    578. 

  578. 2	47641560	47641565	AAAAAA	-	intronic	MSH2	.	.	.	0.045	.	.	.	.	.	.	.	.	rs747112683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	685134	Lynch_syndrome_I|Breast_and/or_ovarian_cancer|none_provided|not_provided	MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MedGen:CN221562|MedGen:CN235283|MedGen:CN517202	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	12	2	47641559	.	TAAAAAA	T	37	d5;v3;MSI12	STATUS=AFDiff;SAMPLE=LibM078FTT;TYPE=Deletion;DP=4;VD=2;AF=0.5;SHIFT3=21;MSI=27;MSILEN=1;SSF=0.24451;SOR=4.40909;LSEQ=AGCCCTTAACCTTTTTCAGG;RSEQ=AAAAAAAAAAAAAAAAAAAA;CSQ=-|splice_donor_5th_base_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||5/15|NM_000251.3:c.942+24_942+29del|||||||rs11309117||1||EntrezGene||YES||||2:g.47641581_47641586del||||||||||||uncertain_significance&benign&likely_benign||1,-|splice_donor_5th_base_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||6/16|NM_001258281.1:c.744+24_744+29del|||||||rs11309117||1||EntrezGene||||||2:g.47641581_47641586del||||||||||||uncertain_significance&benign&likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:1,1:1,0:1,2:0.5:0,2:61.5:1:37:0:1:0:60:4:0.5:0:0	0/1:12:2:1,1:3,2:5,2:0.1667:2,2:30:1:37:0:1:1.41418:60:4:0.1667:0:0
    579. 

  579. 2	47642059	47642059	G	C	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	0	2	47642059	.	G	C	37	d5;v3;pSTD	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=2;AF=0.5;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTTGGTGGAGTGAAGTG;RSEQ=CAAGATCATAGCTCACTGCA;CSQ=C|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||5/15|NM_000251.3:c.942+502G>C|||||||||1||EntrezGene||YES||||2:g.47642059G>C||||||||||||||,C|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||6/16|NM_001258281.1:c.744+502G>C|||||||||1||EntrezGene||||||2:g.47642059G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:1,1:1,1:2,2:0.5:2,2:49:0:37:0:1:1:60:4:0.5:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    580. 

  580. 2	47643191	47643191	C	G	intronic	MSH2	.	.	.	0.87	0.6048	0.8136	0.4675	0.4238	0.8405	0.6229	0.4670	0.5724	rs11691516	rs11691516	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	659157	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	58	2	2	47643191	.	C	G	58	d5	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGTCTGGGCAATAGAGT;RSEQ=AGACCCTGTCTCAACAAATA;CSQ=G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||5/15|NM_000251.3:c.943-244C>G|||||||rs11691516||1||EntrezGene||YES||||2:g.47643191C>G||||||||||0.8676|AFR|benign||1,G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||6/16|NM_001258281.1:c.745-244C>G|||||||rs11691516||1||EntrezGene||||||2:g.47643191C>G||||||||||0.8676|AFR|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:1,2:0,0:0,3:1:0,2:22.7:1:37:0:1:0:60:6:1:0:1	1/1:2:2:2,0:0,0:0,2:1:0,0:40.5:1:37:0:1:0:60:4:1:0:1
    581. 

  581. 2	47643412	47643412	C	T	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	165	2	47643412	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=55;VD=2;AF=0.0364;SHIFT3=1;MSI=2;MSILEN=4;SSF=0.06164;SOR=inf;LSEQ=TAATGAGCTTGCCATTCTTT;RSEQ=TATTTTATTTTTTGTTTACT;CSQ=T|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||5/15|NM_000251.3:c.943-23C>T|||||||||1||EntrezGene||YES||||2:g.47643412C>T||||||||||||||,T|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||6/16|NM_001258281.1:c.745-23C>T|||||||||1||EntrezGene||||||2:g.47643412C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:55:2:1,1:35,18:53,2:0.0364:2,2:40.5:1:37:0:1:1.91949:60:4:0.0364:0:1	0/0:165:0:0,0:114,51:165,0:0:2,0:38.3:1:35.1:1:1:0:60:40.25:1:0:0
    582. 

  582. 2	47643524	47643524	G	T	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon6:c.G1032T:p.Q344H,MSH2:NM_001258281:exon7:c.G834T:p.Q278H	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.983	0.790	D	0.000	0.629	D	1.000	0.588	D	3.3	0.907	M	-2.87	0.915	D	-4.75	0.802	D	0.891	0.880	0.797	0.944	D	0.856	0.952	D	0.251	0.892	D	5.655	0.771	26.7	0.997	0.784	0.963	0.682	D	c	0.523	0.400	0.000	0.069	0.732	0.924	0	1.77	0.237	2.441	0.443	0.998	0.613	1.000	0.715	1.000	0.888	10.765	0.453	DNA mismatch repair protein MutS, connector domain;DNA mismatch repair protein MutS, core	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	278	2	47643524	.	G	T	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=111;VD=2;AF=0.018;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0809;SOR=inf;LSEQ=GGACAAAGACTTGTTAACCA;RSEQ=TGGATTAAGCAGCCTCTCAT;CSQ=T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|6/16||NM_000251.3:c.1032G>T|NP_000242.1:p.Gln344His|1068|1032|344|Q/H|caG/caT|||1||EntrezGene||YES||||2:g.47643524G>T||||||||||||||,T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|7/17||NM_001258281.1:c.834G>T|NP_001245210.1:p.Gln278His|973|834|278|Q/H|caG/caT|||1||EntrezGene||||||2:g.47643524G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:111:2:1,1:52,57:109,2:0.018:2,2:6:0:37:0:1:1.1:60:4:0.018:0:1	0/0:278:0:0,0:129,149:278,0:0:2,0:37.9:1:36.4:1:1:0:60:138:1:0:0.1
    583. 

  583. 2	47643540	47643540	C	G	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon6:c.C1048G:p.L350V,MSH2:NM_001258281:exon7:c.C850G:p.L284V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.971	D	0.000	0.843	D	1	0.810	D	3.24	0.899	M	-3.28	0.937	D	-2.98	0.620	D	0.857	0.910	1.053	0.982	D	0.922	0.974	D	0.318	0.914	D	5.683	0.775	26.8	0.998	0.922	0.987	0.863	D	c	0.836	0.734	1.000	0.405	0.732	0.924	0	5.62	0.857	4.897	0.627	0.892	0.403	1.000	0.715	0.990	0.544	13.898	0.631	DNA mismatch repair protein MutS, connector domain;DNA mismatch repair protein MutS, core	.	.	.	472806	Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	271	2	47643540	.	C	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=89;VD=2;AF=0.0225;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.0606;SOR=inf;LSEQ=ACCAGTGGATTAAGCAGCCT;RSEQ=TCATGGATAAGAACAGAATA;CSQ=G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|6/16||NM_000251.3:c.1048C>G|NP_000242.1:p.Leu350Val|1084|1048|350|L/V|Ctc/Gtc|rs771126636||1||EntrezGene||YES||||2:g.47643540C>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|7/17||NM_001258281.1:c.850C>G|NP_001245210.1:p.Leu284Val|989|850|284|L/V|Ctc/Gtc|rs771126636||1||EntrezGene||||||2:g.47643540C>G||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:89:2:1,1:40,47:87,2:0.0225:2,2:50:1:37:0:1:1.17:60:4:0.0227:0:1	0/0:271:0:0,0:118,153:271,0:0:2,0:35.6:1:36.4:1:1:0:60:134.5:1:0:0.1
    584. 

  584. 2	47656948	47656948	C	T	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon7:c.C1144T:p.R382C,MSH2:NM_001258281:exon8:c.C946T:p.R316C	0.	3.229e-05	0.0001	0	0	0	0	0	0	rs752373431	.	0.0	0.912	D	0.998	0.899	D	0.93	0.647	D	0.000	0.843	D	1	0.810	D	3.125	0.882	M	-2.92	0.918	D	-6.67	0.928	D	0.863	0.872	0.953	0.964	D	0.886	0.962	D	0.168	0.847	D	8.082	0.957	35	0.999	0.999	0.980	0.784	D	c	0.859	0.823	1.000	0.747	0.722	0.854	0	5.69	0.883	5.408	0.659	0.915	0.428	1.000	0.715	0.998	0.697	19.802	0.965	DNA mismatch repair protein MutS, core	.	.	ID=COSV99254668;OCCURENCE=1(upper_aerodigestive_tract)	232574	Lynch_syndrome|Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	MU131160614	HNSC-US|1|508|0.0019685	0.5	37	184	2	47656948	.	C	T	37	v3;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=51;VD=1;AF=0.0196;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.5217;SOR=1.81461;LSEQ=CTTTACAAGAAGATTTACTT;RSEQ=GTCGATTCCCAGATCTTAAC;CSQ=T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|7/16||NM_000251.3:c.1144C>T|NP_000242.1:p.Arg382Cys|1180|1144|382|R/C|Cgt/Tgt|rs752373431&COSV51876239&COSV99254668||1||EntrezGene||YES||||2:g.47656948C>T|3.182e-05|0|2.891e-05|0|5.437e-05|0|3.517e-05|0|6.533e-05|6.533e-05|gnomAD_SAS|uncertain_significance|0&1&1|1&1&1,T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|8/17||NM_001258281.1:c.946C>T|NP_001245210.1:p.Arg316Cys|1085|946|316|R/C|Cgt/Tgt|rs752373431&COSV51876239&COSV99254668||1||EntrezGene||||||2:g.47656948C>T|3.182e-05|0|2.891e-05|0|5.437e-05|0|3.517e-05|0|6.533e-05|6.533e-05|gnomAD_SAS|uncertain_significance|0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:51:1:1,0:28,22:50,1:0.0196:2,0:10:0:37:0:1:0:60:2:0.0213:0:1	0/1:184:2:1,1:105,77:182,2:0.0109:2,2:21:1:37:0:1:1.36129:60:4:0.0113:0:1
    585. 

  585. 2	47657029	47657029	C	T	exonic	MSH2	.	stopgain	MSH2:NM_000251:exon7:c.C1225T:p.Q409X,MSH2:NM_001258281:exon8:c.C1027T:p.Q343X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.140	0.989	41	0.999	0.932	0.925	0.557	D	c	1.176	1.031	1.000	0.747	0.719	0.830	0	5.45	0.796	7.145	0.768	0.915	0.428	1.000	0.715	1.000	0.888	19.274	0.940	DNA mismatch repair protein MutS, core	.	.	ID=COSV99253946;OCCURENCE=1(ovary)	483364	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Pathogenic	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU130526419	OV-US|1|426|0.00234742	0.25	37	160	2	47657029	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=90;VD=2;AF=0.0222;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.12867;SOR=inf;LSEQ=AAGATTGTTACCGACTCTAT;RSEQ=AGGGTATAAATCAACTACCT;CSQ=T|stop_gained|HIGH|MSH2|4436|Transcript|NM_000251.3|protein_coding|7/16||NM_000251.3:c.1225C>T|NP_000242.1:p.Gln409Ter|1261|1225|409|Q/*|Cag/Tag|rs151244108&CM036112&CM080441&COSV99253946||1||EntrezGene||YES||||2:g.47657029C>T||||||||||||pathogenic|0&0&0&1|1&1&1&1,T|stop_gained|HIGH|MSH2|4436|Transcript|NM_001258281.1|protein_coding|8/17||NM_001258281.1:c.1027C>T|NP_001245210.1:p.Gln343Ter|1166|1027|343|Q/*|Cag/Tag|rs151244108&CM036112&CM080441&COSV99253946||1||EntrezGene||||||2:g.47657029C>T||||||||||||pathogenic|0&0&0&1|1&1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:90:2:1,1:42,46:88,2:0.0222:2,2:64:1:37:0:1:1.09:60:4:0.0225:0:1	0/0:160:0:0,0:71,88:159,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    586. 

  586. 2	47690298	47690298	G	A	intronic	MSH2	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs756919331	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	266	2	47690298	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=2;AF=0.1429;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.00233;SOR=inf;LSEQ=GCAGCCAGAGATCTTGGTAA;RSEQ=AATGGGTCATTGGAGGTTGG;CSQ=A|splice_donor_5th_base_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||9/15|NM_000251.3:c.1510+5G>A|||||||rs756919331||1||EntrezGene||YES||||2:g.47690298G>A|7.964e-06|0|0|0|0|0|0|0|6.533e-05|6.533e-05|gnomAD_SAS|||,A|splice_donor_5th_base_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||10/16|NM_001258281.1:c.1312+5G>A|||||||rs756919331||1||EntrezGene||||||2:g.47690298G>A|7.964e-06|0|0|0|0|0|0|0|6.533e-05|6.533e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:14:2:1,1:9,3:12,2:0.1429:2,2:29:1:37:0:0.50549:2.73861:60:4:0.1429:0:2.5	0/0:266:0:0,0:123,143:266,0:0:2,0:38:1:36.3:1:1:0:60:65.5:1:0:0.5
    587. 

  587. 2	47693782	47693782	T	C	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	191	2	47693782	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.91181;SOR=0;LSEQ=ATGGAATACTTTTTCTTTTC;RSEQ=TCTTGATTATCAAGGCTTGG;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||9/15|NM_000251.3:c.1511-15T>C|||||||||1||EntrezGene||YES||||2:g.47693782T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||10/16|NM_001258281.1:c.1313-15T>C|||||||||1||EntrezGene||||||2:g.47693782T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:5,4:9,0:0:2,0:44.9:1:35.7:1:1:0:60:18:1:0:0.1	0/1:191:2:1,1:118,71:189,2:0.0105:2,2:43.5:1:31:1:1:1.6573:60:4:0.0105:0:1.5
    588. 

  588. 2	47693875	47693875	A	-	exonic	MSH2	.	frameshift deletion	MSH2:NM_000251:exon10:c.1589delA:p.V532Sfs*11,MSH2:NM_001258281:exon11:c.1391delA:p.V466Sfs*11	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	611020	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Likely_pathogenic	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	198	2	47693874	.	GA	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=9;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.91473;SOR=0;LSEQ=TTCGTGTAACCTGTAAGGAA;RSEQ=AAAAGTCCTTCGTAACAATA;CSQ=-|frameshift_variant|HIGH|MSH2|4436|Transcript|NM_000251.3|protein_coding|10/16||NM_000251.3:c.1593del|NP_000242.1:p.Val532SerfsTer11|1625|1589|530|E/X|gAa/ga|rs1558511051||1||EntrezGene||YES|||4|2:g.47693879del||||||||||||likely_pathogenic||1,-|frameshift_variant|HIGH|MSH2|4436|Transcript|NM_001258281.1|protein_coding|11/17||NM_001258281.1:c.1395del|NP_001245210.1:p.Val466SerfsTer11|1530|1391|464|E/X|gAa/ga|rs1558511051||1||EntrezGene|||||4|2:g.47693879del||||||||||||likely_pathogenic||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:3,6:9,0:0:2,0:41.1:1:37:0:1:0:60:18:1:0:0	0/1:198:2:1,1:76,120:196,2:0.0101:2,2:65:1:37:0:1:1.58:60:4:0.0102:0:0
    589. 

  589. 2	47693959	47693959	G	A	intronic	MSH2	.	.	.	0.67	0.4185	0.6166	0.2950	0.2285	0.6795	0.3975	0.2923	0.3961	rs3732183	rs3732183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99253307;OCCURENCE=3(meninges)	45229	Endometrial_carcinoma|Lynch_syndrome|Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|not_specified|none_provided	Human_Phenotype_Ontology:HP:0012114,MONDO:MONDO:0002447,MedGen:C0476089,OMIM:608089,SNOMED_CT:254878006|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN235283	reviewed_by_expert_panel	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13928740	SKCA-BR|1|100|0.01,COCA-CN|5|321|0.0155763	0.5	234	82	2	47693959	.	G	A	234	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00029;SOR=0;LSEQ=TACCAACAGGTTTGCAAGTC;RSEQ=TTATTATATTTTTAACCCTT;CSQ=A|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||10/15|NM_000251.3:c.1661+12G>A|||||||rs3732183&CS045476&COSV51881941&COSV99253307||1||EntrezGene||YES||||2:g.47693959G>A|0.343|0.6275|0.2949|0.2305|0.6569|0.3897|0.2736|0.3036|0.329|0.6725|AFR|benign|0&0&1&1|1&1&1&1,A|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||11/16|NM_001258281.1:c.1463+12G>A|||||||rs3732183&CS045476&COSV51881941&COSV99253307||1||EntrezGene||||||2:g.47693959G>A|0.343|0.6275|0.2949|0.2305|0.6569|0.3897|0.2736|0.3036|0.329|0.6725|AFR|benign|0&0&1&1|1&1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:0,2:2,0:0:0,0:29:1:37:0:1:0:60:4:1:0:0	1/1:82:82:8,74:0,0:0,82:1:0,2:31.7:1:36.9:1:1:0:60:164:1:0:1
    590. 

  590. 2	47702266	47702266	G	A	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon12:c.G1862A:p.R621Q,MSH2:NM_001258281:exon13:c.G1664A:p.R555Q	0.0002	.	.	.	.	.	.	.	.	rs759263820	.	0.002	0.721	D	1.0	0.899	D	0.991	0.850	D	0.000	0.843	D	1	0.810	D	3.185	0.891	M	-2.18	0.867	D	-3.59	0.704	D	0.878	0.934	0.857	0.951	D	0.839	0.946	D	0.210	0.873	D	7.625	0.954	34	1.000	1.000	0.995	0.970	D	c	0.988	0.937	1.000	0.747	0.732	0.924	0	5.61	0.853	9.134	0.937	1.048	0.713	1.000	0.715	1.000	0.888	19.643	0.957	DNA mismatch repair protein MutS, C-terminal|DNA mismatch repair protein MutS, core|P-loop containing nucleoside triphosphate hydrolase;DNA mismatch repair protein MutS, clamp|DNA mismatch repair protein MutS, core	.	.	ID=COSV51886143;OCCURENCE=1(endometrium)	451338	Lynch_syndrome|Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	58	175	2	47702266	.	G	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.26469;SOR=0;LSEQ=AGCACCTGTTCCATATGTAC;RSEQ=ACCAGCCATTTTGGAGAAAG;CSQ=A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|12/16||NM_000251.3:c.1862G>A|NP_000242.1:p.Arg621Gln|1898|1862|621|R/Q|cGa/cAa|rs759263820&COSV51885380&COSV51886143||1||EntrezGene||YES||||2:g.47702266G>A|7.953e-06|0|0|0|0|4.619e-05|8.791e-06|0|0|4.619e-05|gnomAD_FIN|uncertain_significance|0&1&1|1&1&1,A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|13/17||NM_001258281.1:c.1664G>A|NP_001245210.1:p.Arg555Gln|1803|1664|555|R/Q|cGa/cAa|rs759263820&COSV51885380&COSV51886143||1||EntrezGene||||||2:g.47702266G>A|7.953e-06|0|0|0|0|4.619e-05|8.791e-06|0|0|4.619e-05|gnomAD_FIN|uncertain_significance|0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:97:0:0,0:48,49:97,0:0:2,0:38:1:35.8:1:1:0:60:31.333:1:0:0	0/1:175:3:1,2:90,82:172,3:0.0171:2,2:57.3:1:37:0:0.60821:2.18559:60:6:0.0174:0:1
    591. 

  591. 2	47702271	47702271	G	A	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon12:c.G1867A:p.A623T,MSH2:NM_001258281:exon13:c.G1669A:p.A557T	.	.	.	.	.	.	.	.	.	.	.	0.474	0.107	T	0.0	0.067	B	0.002	0.080	B	0.182	0.171	N	1	0.090	N	-1.695	0.004	N	-1.97	0.852	D	1.06	0.013	N	0.344	0.405	-0.869	0.507	T	0.174	0.518	T	0.030	0.526	D	1.201	0.210	11.75	0.947	0.248	0.601	0.308	D	c	-0.863	-0.599	0.425	0.203	0.732	0.924	0	3.01	0.337	2.125	0.414	0.142	0.226	0.144	0.233	0.996	0.625	9.428	0.376	DNA mismatch repair protein MutS, C-terminal|DNA mismatch repair protein MutS, core|P-loop containing nucleoside triphosphate hydrolase;DNA mismatch repair protein MutS, clamp|DNA mismatch repair protein MutS, core	.	.	.	1024549	Hereditary_nonpolyposis_colorectal_neoplasms	MedGen:C0009405	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	177	2	47702271	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=95;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.42262;SOR=0;LSEQ=CTGTTCCATATGTACGACCA;RSEQ=CCATTTTGGAGAAAGGACAA;CSQ=A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|12/16||NM_000251.3:c.1867G>A|NP_000242.1:p.Ala623Thr|1903|1867|623|A/T|Gcc/Acc|||1||EntrezGene||YES||||2:g.47702271G>A||||||||||||||,A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|13/17||NM_001258281.1:c.1669G>A|NP_001245210.1:p.Ala557Thr|1808|1669|557|A/T|Gcc/Acc|||1||EntrezGene||||||2:g.47702271G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:95:0:0,0:46,49:95,0:0:2,0:37.2:1:36.5:1:1:0:60:94:1:0:0	0/1:177:2:1,1:91,84:175,2:0.0113:2,2:54:1:37:0:1:1.08283:60:4:0.0115:0:1
    592. 

  592. 2	47702309	47702309	A	G	exonic	MSH2	.	synonymous SNV	MSH2:NM_000251:exon12:c.A1905G:p.K635K,MSH2:NM_001258281:exon13:c.A1707G:p.K569K	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99253389;OCCURENCE=1(large_intestine)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU130249716	COAD-US|1|402|0.00248756	0.25	31	173	2	47702309	.	A	G	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=2;AF=0.0345;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06222;SOR=inf;LSEQ=CAAGGAAGAATTATATTAAA;RSEQ=GCATCCAGGCATGCTTGTGT;CSQ=G|synonymous_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding|12/16||NM_000251.3:c.1905A>G|NP_000242.1:p.Lys635%3D|1941|1905|635|K|aaA/aaG|COSV99253389||1||EntrezGene||YES||||2:g.47702309A>G|||||||||||||1|1,G|synonymous_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding|13/17||NM_001258281.1:c.1707A>G|NP_001245210.1:p.Lys569%3D|1846|1707|569|K|aaA/aaG|COSV99253389||1||EntrezGene||||||2:g.47702309A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:58:2:1,1:22,34:56,2:0.0345:2,2:57:1:31:1:1:1.53:60:4:0.0357:0:1	0/0:173:0:0,0:76,97:173,0:0:2,0:33.2:1:36.6:1:1:0:60:172:1:0:0.1
    593. 

  593. 2	47702455	47702455	T	G	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	rs1005837916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	67	76	2	47702455	.	T	G	67	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=6;AF=0.8571;SHIFT3=3;MSI=19;MSILEN=1;SSF=0;SOR=inf;LSEQ=GTGGGGGTAACGTTTTGTTT;RSEQ=TTTTTTTTTTTTTTTAATCT;CSQ=G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_000251.3|protein_coding||12/15|NM_000251.3:c.2005+46T>G|||||||rs1005837916||1||EntrezGene||YES||||2:g.47702455T>G|3.797e-05|0|0|0.0001369|7.008e-05|0|3.333e-05|0|8.919e-05|0.0001369|gnomAD_ASJ|||,G|intron_variant|MODIFIER|MSH2|4436|Transcript|NM_001258281.1|protein_coding||13/16|NM_001258281.1:c.1807+46T>G|||||||rs1005837916||1||EntrezGene||||||2:g.47702455T>G|3.797e-05|0|0|0.0001369|7.008e-05|0|3.333e-05|0|8.919e-05|0.0001369|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:7:6:3,3:0,1:1,6:0.8571:0,2:27.8:1:26.3:1:1:0:60:2:0.8:0:1.8	0/0:76:0:0,0:20,55:75,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    594. 

  594. 2	47703500	47703500	T	C	intronic	MSH2	.	.	.	0.36	0.0978	0.0271	0.0919	0.0728	0.3736	0.1151	0.1049	0.1133	rs2303428	rs2303428	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51876931;OCCURENCE=1(breast),1(stomach),2(haematopoietic_and_lymphoid_tissue),3(soft_tissue),15(prostate),1(lung),1(thymus)	45233	Lynch_syndrome|Lynch_syndrome_I|Turcot_syndrome|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|none_provided	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0010159,MedGen:C0265325,OMIM:276300,Orphanet:ORPHA252202,SNOMED_CT:61665008|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN235283	reviewed_by_expert_panel	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU585006	LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.5	251	278	2	47703500	.	T	C	251	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=6;AF=0.1071;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=0.12238;LSEQ=GCTTTCTGATATAATTTGTT;RSEQ=TGTAGGCCCCAATATGGGAG;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||12/15|NM_000251.3:c.2006-6T>C|||||||rs2303428&CS951474&CX060722&COSV51876931||1||EntrezGene||YES||||2:g.47703500T>C|0.1151|0.02138|0.07931|0.09486|0.3549|0.1048|0.0995|0.1075|0.1345|0.3631|EAS|benign|0&0&0&1|1&1&1&1,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||13/16|NM_001258281.1:c.1808-6T>C|||||||rs2303428&CS951474&CX060722&COSV51876931||1||EntrezGene||||||2:g.47703500T>C|0.1151|0.02138|0.07931|0.09486|0.3549|0.1048|0.0995|0.1075|0.1345|0.3631|EAS|benign|0&0&0&1|1&1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:56:6:5,1:40,10:50,6:0.1071:2,2:25.8:1:37:0:1:1.25:60:12:0.1132:0:1	0/1:278:138:93,45:96,44:140,138:0.4964:2,2:39:1:35.4:1:0.89786:1.05548:60:45:0.4963:0:1.1
    595. 

  595. 2	47703649	47703649	A	G	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon13:c.A2149G:p.S717G,MSH2:NM_001258281:exon14:c.A1951G:p.S651G	0.0001	.	.	.	.	.	.	.	.	rs778712654	.	0.008	0.632	D	0.942	0.629	P	0.843	0.622	P	0.000	0.843	D	1	0.810	D	3.295	0.906	M	-2.03	0.856	D	-3.42	0.672	D	0.723	0.753	0.641	0.924	D	0.746	0.913	D	0.135	0.819	D	5.353	0.725	25.9	0.999	0.955	0.976	0.757	D	c	0.785	0.764	1.000	0.473	0.707	0.730	0	4.82	0.615	7.048	0.761	1.140	0.893	1.000	0.715	1.000	0.888	13.742	0.622	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	826614	Hereditary_nonpolyposis_colorectal_neoplasms	MedGen:C0009405	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	417	2	47703649	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=188;VD=2;AF=0.0106;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.09621;SOR=inf;LSEQ=CCCGAGTAGGGGCTGGTGAC;RSEQ=GTCAATTGAAAGGAGTCTCC;CSQ=G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|13/16||NM_000251.3:c.2149A>G|NP_000242.1:p.Ser717Gly|2185|2149|717|S/G|Agt/Ggt|rs778712654||1||EntrezGene||YES||||2:g.47703649A>G|3.976e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|uncertain_significance||1,G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|14/17||NM_001258281.1:c.1951A>G|NP_001245210.1:p.Ser651Gly|2090|1951|651|S/G|Agt/Ggt|rs778712654||1||EntrezGene||||||2:g.47703649A>G|3.976e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:188:2:1,1:78,108:186,2:0.0106:2,2:67:1:37:0:1:1.38:60:4:0.0109:0:1	0/0:417:0:0,0:173,244:417,0:0:2,0:37.9:1:35.6:1:1:0:60:26.8:1:0:0.1
    596. 

  596. 2	47705488	47705488	C	T	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon14:c.C2288T:p.A763V,MSH2:NM_001258281:exon15:c.C2090T:p.A697V	0.0002	.	.	.	.	.	.	.	.	rs144412585	rs144412585	0.0	0.912	D	1.0	0.899	D	0.989	0.916	D	0.000	0.629	D	1	0.810	D	3.84	0.958	H	-2.6	0.899	D	-3.67	0.701	D	0.748	0.744	1.004	0.973	D	0.888	0.963	D	0.464	0.946	D	6.982	0.936	33	0.999	0.969	0.980	0.789	D	c	0.881	0.739	1.000	0.473	0.707	0.730	0	4.11	0.472	7.532	0.807	0.798	0.323	1.000	0.715	1.000	0.888	13.204	0.590	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	180027	Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	261	2	47705488	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=2;AF=0.0714;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00908;SOR=inf;LSEQ=CTACGATGGATTTGGGTTAG;RSEQ=ATGGGCTATATCAGAATACA;CSQ=T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|14/16||NM_000251.3:c.2288C>T|NP_000242.1:p.Ala763Val|2324|2288|763|A/V|gCa/gTa|rs144412585||1||EntrezGene||YES||||2:g.47705488C>T||||||||||0.000227|AA|uncertain_significance||1,T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|15/17||NM_001258281.1:c.2090C>T|NP_001245210.1:p.Ala697Val|2229|2090|697|A/V|gCa/gTa|rs144412585||1||EntrezGene||||||2:g.47705488C>T||||||||||0.000227|AA|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:28:2:1,1:14,12:26,2:0.0714:2,2:30.5:1:37:0:1:1.16024:60:4:0.0714:0:1	0/0:261:0:0,0:140,121:261,0:0:2,0:36:1:36.3:1:1:0:60:129.5:1:0:0.1
    597. 

  597. 2	47707820	47707820	C	T	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	915576	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	135	2	47707820	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=83;VD=2;AF=0.0241;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.14387;SOR=inf;LSEQ=TGCTGTCCCCTCACGCTTCC;RSEQ=CAAATTTCTTATAGGTGTCT;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||14/15|NM_000251.3:c.2459-15C>T|||||||||1||EntrezGene||YES||||2:g.47707820C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||15/16|NM_001258281.1:c.2261-15C>T|||||||||1||EntrezGene||||||2:g.47707820C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:83:2:1,1:51,30:81,2:0.0241:2,2:26.5:1:37:0:1:1.6886:60:4:0.025:0:3	0/0:135:0:0,0:97,38:135,0:0:2,0:36.3:1:36.3:1:1:0:60:66.5:1:0:0.1
    598. 

  598. 2	47707828	47707828	C	T	intronic	MSH2	.	.	.	.	.	.	.	.	.	.	.	.	rs201698097	rs201698097	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	147	2	47707828	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.15705;SOR=inf;LSEQ=CCTCACGCTTCCCCAAATTT;RSEQ=TTATAGGTGTCTGTGATCAA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding||14/15|NM_000251.3:c.2459-7C>T|||||||rs201698097||1||EntrezGene||YES||||2:g.47707828C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding||15/16|NM_001258281.1:c.2261-7C>T|||||||rs201698097||1||EntrezGene||||||2:g.47707828C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:55,40:95,2:0.0206:2,2:34.5:1:37:0:1:1.3704:60:4:0.0206:0:3	0/0:147:0:0,0:103,43:146,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    599. 

  599. 2	47707910	47707910	A	G	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon15:c.A2534G:p.K845R,MSH2:NM_001258281:exon16:c.A2336G:p.K779R	.	.	.	.	.	.	.	.	.	.	.	0.392	0.107	T	0.042	0.269	B	0.077	0.283	B	0.000	0.473	N	0.940	0.373	D	0.83	0.210	L	-1.99	0.853	D	-1.67	0.399	N	0.541	0.622	-0.668	0.619	T	0.348	0.713	T	0.020	0.425	T	2.159	0.321	17.24	0.988	0.467	0.697	0.340	D	c	-0.415	-0.236	0.982	0.303	0.707	0.730	0	3.5	0.390	1.078	0.302	1.088	0.866	0.982	0.353	0.997	0.653	9.076	0.355	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	246	2	47707910	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=115;VD=2;AF=0.0174;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.10088;SOR=inf;LSEQ=GCATGTAATAGAGTGTGCTA;RSEQ=ACAGAAAGCCCTGGAACTTG;CSQ=G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|15/16||NM_000251.3:c.2534A>G|NP_000242.1:p.Lys845Arg|2570|2534|845|K/R|aAa/aGa|||1||EntrezGene||YES||||2:g.47707910A>G||||||||||||||,G|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|16/17||NM_001258281.1:c.2336A>G|NP_001245210.1:p.Lys779Arg|2475|2336|779|K/R|aAa/aGa|||1||EntrezGene||||||2:g.47707910A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:115:2:1,1:59,54:113,2:0.0174:2,2:30.5:1:37:0:1:1.09174:60:4:0.0177:0:3	0/0:246:0:0,0:130,116:246,0:0:2,0:36.4:1:36.5:1:1:0:60:81:1:0:0.1
    600. 

  600. 2	47707961	47707961	G	T	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon15:c.G2585T:p.G862V,MSH2:NM_001258281:exon16:c.G2387T:p.G796V	.	.	.	.	.	.	.	.	.	.	.	0.052	0.496	T	0.006	0.126	B	0.006	0.154	B	0.714	0.100	N	0.822	0.288	N	0.895	0.225	L	-2.92	0.918	D	-2.15	0.524	N	0.588	0.616	-0.478	0.694	T	0.496	0.809	T	0.075	0.724	D	0.917	0.182	10.18	0.943	0.241	0.635	0.318	D	c	-0.792	-0.730	0.972	0.293	0.707	0.730	0	2.18	0.267	2.325	0.433	1.048	0.713	0.967	0.338	0.578	0.284	3.777	0.081	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	482458	Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	44	249	2	47707961	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.47432;SOR=0;LSEQ=GTATATTGGAGAATCGCAAG;RSEQ=ATATGATATCATGGAACCAG;CSQ=T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|15/16||NM_000251.3:c.2585G>T|NP_000242.1:p.Gly862Val|2621|2585|862|G/V|gGa/gTa|rs1216558739||1||EntrezGene||YES||||2:g.47707961G>T||||||||||||uncertain_significance||1,T|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|16/17||NM_001258281.1:c.2387G>T|NP_001245210.1:p.Gly796Val|2526|2387|796|G/V|gGa/gTa|rs1216558739||1||EntrezGene||||||2:g.47707961G>T||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:70:0:0,0:25,45:70,0:0:2,0:34.1:1:36.5:1:1:0:60:140:1:0:0.1	0/1:249:3:1,2:114,132:246,3:0.012:2,2:46.7:1:28.3:1:1:1.72364:60:2:0.0082:0:2.7
    601. 

  601. 2	47707979	47707979	C	A	exonic	MSH2	.	nonsynonymous SNV	MSH2:NM_000251:exon15:c.C2603A:p.P868Q,MSH2:NM_001258281:exon16:c.C2405A:p.P802Q	.	.	.	.	.	.	.	.	.	.	.	0.112	0.416	T	0.98	0.596	D	0.694	0.552	P	0.001	0.434	D	1.000	0.588	D	2.085	0.579	M	-2.82	0.912	D	-3.56	0.688	D	0.798	0.788	0.555	0.913	D	0.778	0.925	D	0.040	0.594	D	3.627	0.493	23.2	0.990	0.502	0.962	0.679	D	c	0.628	0.664	1.000	0.747	0.707	0.730	0	6.04	0.980	5.301	0.653	0.935	0.490	1.000	0.715	0.951	0.427	20.595	0.994	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	44	242	2	47707979	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=54;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.54523;SOR=0;LSEQ=AGGATATGATATCATGGAAC;RSEQ=AGCAGCAAAGAAGTGCTATC;CSQ=A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_000251.3|protein_coding|15/16||NM_000251.3:c.2603C>A|NP_000242.1:p.Pro868Gln|2639|2603|868|P/Q|cCa/cAa|||1||EntrezGene||YES||||2:g.47707979C>A||||||||||||||,A|missense_variant|MODERATE|MSH2|4436|Transcript|NM_001258281.1|protein_coding|16/17||NM_001258281.1:c.2405C>A|NP_001245210.1:p.Pro802Gln|2544|2405|802|P/Q|cCa/cAa|||1||EntrezGene||||||2:g.47707979C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:54:0:0,0:21,33:54,0:0:2,0:36.2:1:36.3:1:1:0:60:108:1:0:0.1	0/1:242:3:1,2:102,137:239,3:0.0124:2,2:18:1:28.3:1:1:1.4867:60:2:0.0083:0:2.7
    602. 

  602. 2	47739551	47739551	A	G	intergenic	MSH2;KCNK12	dist=29184;dist=8364	.	.	0.68	0.4826	0.6099	0.3341	0.3154	0.6993	0.4986	0.3940	0.4714	rs2303424	rs2303424	0.0	0.912	D	0.0	0.026	B	0.0	0.013	B	.	.	.	1	0.090	P	.	.	.	-2.79	0.910	D	-0.37	0.132	N	0.047	0.028	-0.971	0.370	T	0.000	0.000	T	.	.	.	-0.939	0.034	0.021	0.427	0.031	0.012	0.043	N	c	-1.771	-1.890	0.998	0.366	0.615	0.372	0	-3.02	0.051	0.310	0.190	-1.011	0.022	0.000	0.063	0.000	0.016	3.848	0.084	.	ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8|ENSG00000095002.8	Adipose_Subcutaneous|Artery_Tibial|Esophagus_Gastroesophageal_Junction|Lung|Nerve_Tibial	ID=COSV100009561;OCCURENCE=7(meninges)	50306	not_specified|not_provided	MedGen:CN169374|MedGen:CN517202	no_assertion_criteria_provided	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13928820	COCA-CN|5|321|0.0155763	0.75	284	215	2	47739551	.	A	G	284	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1783;VD=185;AF=0.1038;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0.00054;LSEQ=TCGGCCAGAGAGACAGAACC;RSEQ=GGGCAGTGGTGAGCTCTCAT;CSQ=G|3_prime_UTR_variant|MODIFIER|KCNK12|56660|Transcript|NM_022055.2|protein_coding|2/2||NM_022055.2:c.*8495T>C||10442|||||rs2303424&COSV100009561||-1||EntrezGene||YES||||2:g.47739551A>G|0.421|0.6076|0.3327|0.3374|0.6819|0.4979|0.372|0.403|0.4292|0.6819|gnomAD_EAS|benign&not_provided|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1783:185:73,112:636,960:1596,185:0.1038:2,2:37.2:1:36.3:1:0.93694:1.01643:60:60.667:0.1047:0:1.1	1/1:215:214:82,132:0,0:0,214:0.9953:0,2:38.7:1:36.7:1:1:0:60:213:0.9953:0:1.1
    603. 

  603. 2	48010472	48010472	G	A	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_000179:exon1:c.G100A:p.A34T,MSH6:NM_001281492:exon1:c.G100A:p.A34T	.	.	.	.	.	.	.	.	.	.	.	0.084	0.329	T	0.092	0.237	B	0.007	0.193	B	0.861	0.089	N	1	0.090	N	0.345	0.112	N	-1.96	0.864	D	0.21	0.048	N	0.127	0.144	-0.772	0.568	T	0.369	0.729	T	0.473	0.947	D	0.807	0.171	9.505	0.987	0.439	0.019	0.057	N	c	-1.110	-1.163	1.000	0.747	0.442	0.072	0	1.41	0.214	0.593	0.235	0.593	0.286	0.004	0.165	0.034	0.151	5.791	0.175	.	.	.	.	443261	Hereditary_cancer-predisposing_syndrome|not_provided	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	31	102	2	48010472	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=754;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01408;SOR=0;LSEQ=CCTCACGCGAAGGCGGCCGT;RSEQ=CCGCCGCTGCCCCCGGGGCC;CSQ=A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|1/10||NM_000179.3:c.100G>A|NP_000170.1:p.Ala34Thr|189|100|34|A/T|Gcc/Acc|rs1553408194||1||EntrezGene||YES||||2:g.48010472G>A||||||||||||uncertain_significance||1,A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|1/8||NM_001281492.2:c.100G>A|NP_001268421.1:p.Ala34Thr|189|100|34|A/T|Gcc/Acc|rs1553408194||1||EntrezGene||||||2:g.48010472G>A||||||||||||uncertain_significance||1,A|5_prime_UTR_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding|1/9||NM_001281493.2:c.-637G>A||189|||||rs1553408194||1||EntrezGene||||||2:g.48010472G>A||||||||||||uncertain_significance||1,A|upstream_gene_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding||||||||||rs1553408194|622|1||EntrezGene||||||2:g.48010472G>A||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:754:0:0,0:303,451:754,0:0:2,0:32.9:1:36.3:1:1:0:60:82.778:1:0:1	0/1:102:2:1,1:44,56:100,2:0.0196:2,2:27:0:31:1:1:1.27:60:4:0.0196:0:1.5
    604. 

  604. 2	48010488	48010488	G	A	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_000179:exon1:c.G116A:p.G39E,MSH6:NM_001281492:exon1:c.G116A:p.G39E	0.29	0.1903	0.2229	0.1214	0.2583	0.2398	0.1368	0.1813	0.1861	rs1042821	rs1042821	0.212	0.284	T	0.0	0.090	B	0.001	0.080	B	0.902	0.086	N	1.000	0.232	P	0.695	0.181	N	-1.77	0.862	D	-0.28	0.116	N	0.091	0.169	-1.097	0.044	T	0.000	0.000	T	.	.	.	-0.457	0.058	0.281	0.836	0.143	0.049	0.105	N	c	-0.592	-0.509	1.000	0.747	0.442	0.072	0	2.63	0.303	1.784	0.381	0.787	0.318	0.984	0.356	0.250	0.228	3.328	0.066	.	ENSG00000116062.10	Adipose_Subcutaneous	ID=COSV52274018;OCCURENCE=3(meninges),4(large_intestine),3(prostate),8(lung),22(upper_aerodigestive_tract)	45243	Breast_carcinoma|Carcinoma_of_colon|Lynch_syndrome|Lynch_syndrome_I|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|none_provided|not_provided	Human_Phenotype_Ontology:HP:0003002,MONDO:MONDO:0004989,MedGen:C0678222|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN235283|MedGen:CN517202	reviewed_by_expert_panel	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	0	0	1	0	MU113418	LUSC-KR|7|170|0.0411765,COCA-CN|4|321|0.0124611	0.5	310	91	2	48010488	.	G	A	310	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=625;VD=512;AF=0.8192;SHIFT3=2;MSI=4;MSILEN=1;SSF=0;SOR=inf;LSEQ=CCGTGCCGCCGCTGCCCCCG;RSEQ=GGCCTCTCCTTCCCCAGGCG;CSQ=A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|1/10||NM_000179.3:c.116G>A|NP_000170.1:p.Gly39Glu|205|116|39|G/E|gGg/gAg|rs1042821&CM092149&COSV52274018||1||EntrezGene||YES||||2:g.48010488G>A|0.182|0.2215|0.1042|0.2973|0.2531|0.1312|0.1809|0.1908|0.212|0.2973|gnomAD_ASJ|benign/likely_benign&benign|0&0&1|1&1&1,A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|1/8||NM_001281492.2:c.116G>A|NP_001268421.1:p.Gly39Glu|205|116|39|G/E|gGg/gAg|rs1042821&CM092149&COSV52274018||1||EntrezGene||||||2:g.48010488G>A|0.182|0.2215|0.1042|0.2973|0.2531|0.1312|0.1809|0.1908|0.212|0.2973|gnomAD_ASJ|benign/likely_benign&benign|0&0&1|1&1&1,A|5_prime_UTR_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding|1/9||NM_001281493.2:c.-621G>A||205|||||rs1042821&CM092149&COSV52274018||1||EntrezGene||||||2:g.48010488G>A|0.182|0.2215|0.1042|0.2973|0.2531|0.1312|0.1809|0.1908|0.212|0.2973|gnomAD_ASJ|benign/likely_benign&benign|0&0&1|1&1&1,A|upstream_gene_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding||||||||||rs1042821&CM092149&COSV52274018|606|1||EntrezGene||||||2:g.48010488G>A|0.182|0.2215|0.1042|0.2973|0.2531|0.1312|0.1809|0.1908|0.212|0.2973|gnomAD_ASJ|benign/likely_benign&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:625:512:178,334:39,58:97,512:0.8192:2,2:31.2:1:34.5:1:0.35498:1.2612:60:11.8:0.8252:0:1.3	0/0:91:0:0,0:34,56:90,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    605. 

  605. 2	48010551	48010551	T	G	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_000179:exon1:c.T179G:p.L60W,MSH6:NM_001281492:exon1:c.T179G:p.L60W	.	.	.	.	.	.	.	.	.	.	.	0.032	0.457	D	0.758	0.447	P	0.171	0.400	B	0.000	0.003	N	1	0.090	N	0.345	0.112	N	-1.89	0.856	D	-0.29	0.117	N	0.213	0.293	-0.534	0.674	T	0.369	0.729	T	0.809	0.985	D	-0.787	0.041	0.046	0.612	0.065	0.038	0.090	N	c	-1.399	-1.527	1.000	0.747	0.442	0.072	0	-4.33	0.034	-0.171	0.098	-0.674	0.039	0.002	0.151	0.026	0.142	6.747	0.225	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.5	30	47	2	48010551	.	T	G	30	q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=256;VD=7;AF=0.0273;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.41954;SOR=0.63364;LSEQ=TGGGCCTGGGCCCAGGCCCT;RSEQ=GGCGCGCTCCGCGTCACCGC;CSQ=G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|1/10||NM_000179.3:c.179T>G|NP_000170.1:p.Leu60Trp|268|179|60|L/W|tTg/tGg|||1||EntrezGene||YES||||2:g.48010551T>G||||||||||||||,G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|1/8||NM_001281492.2:c.179T>G|NP_001268421.1:p.Leu60Trp|268|179|60|L/W|tTg/tGg|||1||EntrezGene||||||2:g.48010551T>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding|1/9||NM_001281493.2:c.-558T>G||268|||||||1||EntrezGene||||||2:g.48010551T>G||||||||||||||,G|upstream_gene_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding|||||||||||543|1||EntrezGene||||||2:g.48010551T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:256:7:1,6:55,194:249,7:0.0273:2,2:40.3:1:11:0:1:1.69795:60:0:0:0:4.7	0/1:47:2:0,2:10,35:45,2:0.0426:2,0:9:1:25:0:1:0:60:4:0.0541:0:2.5
    606. 

  606. 2	48023031	48023031	A	G	splicing	MSH6	NM_000179:exon3:c.458-2A>G;NM_001281494:exon3:UTR5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.946	0.665	25.0	0.995	0.660	0.978	0.773	D	c	1.086	0.926	1.000	0.747	0.257	0.036	0	5.0	0.661	7.558	0.811	1.112	0.879	1.000	0.715	0.999	0.750	14.855	0.698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	171	2	48023031	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=524;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.06027;SOR=0;LSEQ=TTATAAATACATTTCTTTCT;RSEQ=GGTTCAAAATCAAAGGAAGC;CSQ=G|splice_acceptor_variant|HIGH|MSH6|2956|Transcript|NM_000179.3|protein_coding||2/9|NM_000179.3:c.458-2A>G|||||||||1||EntrezGene||YES||||2:g.48023031A>G||||||||||||||,G|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281492.2|protein_coding||1/7|NM_001281492.2:c.238-2719A>G|||||||||1||EntrezGene||||||2:g.48023031A>G||||||||||||||,G|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding||2/8|NM_001281493.2:c.-279-2719A>G|||||||||1||EntrezGene||||||2:g.48023031A>G||||||||||||||,G|splice_acceptor_variant|HIGH|MSH6|2956|Transcript|NM_001281494.2|protein_coding||2/9|NM_001281494.2:c.-445-2A>G|||||||||1||EntrezGene||||||2:g.48023031A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:524:0:0,0:348,175:523,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:171:2:1,1:119,50:169,2:0.0117:2,2:48.5:1:37:0:0.50877:2.36645:60:4:0.0123:0:2
    607. 

  607. 2	48025747	48025747	C	T	intronic	MSH6	.	.	.	0.0002	.	.	.	.	.	.	.	.	rs3136332	rs3136332	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	650937	Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	159	2	48025747	.	C	T	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=1;AF=0.0078;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.58098;SOR=0.61911;LSEQ=AATACTCTTTCCTTGCCTGG;RSEQ=AGGTAGGCACAACTTACGTA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_000179.3|protein_coding||3/9|NM_000179.3:c.628-3C>T|||||||rs3136332||1||EntrezGene||YES||||2:g.48025747C>T||||||||||0.000227|AA|uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281492.2|protein_coding||1/7|NM_001281492.2:c.238-3C>T|||||||rs3136332||1||EntrezGene||||||2:g.48025747C>T||||||||||0.000227|AA|uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281493.2|protein_coding||2/8|NM_001281493.2:c.-279-3C>T|||||||rs3136332||1||EntrezGene||||||2:g.48025747C>T||||||||||0.000227|AA|uncertain_significance||1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281494.2|protein_coding||3/9|NM_001281494.2:c.-275-7C>T|||||||rs3136332||1||EntrezGene||||||2:g.48025747C>T||||||||||0.000227|AA|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:128:1:1,0:107,20:127,1:0.0078:2,0:37:0:37:0:1:0:60:2:0.008:0:1	0/1:159:2:1,1:118,39:157,2:0.0126:2,2:39:1:37:0:0.44105:3.00021:60:4:0.013:0:1
    608. 

  608. 2	48025751	48025751	T	C	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_001281492:exon2:c.T239C:p.V80A,MSH6:NM_000179:exon4:c.T629C:p.V210A	0.0014	.	.	.	.	.	.	.	.	rs201431515	rs201431515	0.963	0.253	T	0.0	0.026	B	0.0	0.040	B	0.847	0.090	N	0.999	0.588	D	1.355	0.339	L	-1.83	0.844	D	-0.36	0.336	N	0.161	0.193	-0.783	0.562	T	0.365	0.726	T	0.093	0.762	D	-1.402	0.019	0.003	0.568	0.055	0.877	0.470	D	c	-0.998	-0.968	0.988	0.313	0.707	0.730	0	-0.55	0.112	2.489	0.447	1.061	0.807	1.000	0.715	0.378	0.251	4.849	0.128	.	.	.	.	518369	Hereditary_nonpolyposis_colorectal_neoplasms	MedGen:C0009405	criteria_provided,_single_submitter	Uncertain_significance	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	37	174	2	48025751	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=2;AF=0.0152;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.18528;SOR=inf;LSEQ=CTCTTTCCTTGCCTGGCAGG;RSEQ=AGGCACAACTTACGTAACAG;CSQ=C|missense_variant&splice_region_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|4/10||NM_000179.3:c.629T>C|NP_000170.1:p.Val210Ala|718|629|210|V/A|gTa/gCa|rs201431515||1||EntrezGene||YES||||2:g.48025751T>C|0|0|0|0|0|0|0|0|0|0.0014|AMR|uncertain_significance||1,C|missense_variant&splice_region_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|2/8||NM_001281492.2:c.239T>C|NP_001268421.1:p.Val80Ala|328|239|80|V/A|gTa/gCa|rs201431515||1||EntrezGene||||||2:g.48025751T>C|0|0|0|0|0|0|0|0|0|0.0014|AMR|uncertain_significance||1,C|splice_region_variant&5_prime_UTR_variant|LOW|MSH6|2956|Transcript|NM_001281493.2|protein_coding|3/9||NM_001281493.2:c.-278T>C||548|||||rs201431515||1||EntrezGene||||||2:g.48025751T>C|0|0|0|0|0|0|0|0|0|0.0014|AMR|uncertain_significance||1,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281494.2|protein_coding||3/9|NM_001281494.2:c.-275-3T>C|||||||rs201431515||1||EntrezGene||||||2:g.48025751T>C|0|0|0|0|0|0|0|0|0|0.0014|AMR|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:132:2:1,1:110,20:130,2:0.0152:2,2:32:1:37:0:0.29389:5.39189:60:4:0.0152:0:2	0/0:174:0:0,0:127,47:174,0:0:2,0:33.7:1:36.1:1:1:0:60:86:1:0:0.1
    609. 

  609. 2	48025765	48025765	G	A	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_001281492:exon2:c.G253A:p.V85I,MSH6:NM_000179:exon4:c.G643A:p.V215I	0.0014	9.683e-05	0.0003	0	0	0	0	0	0	rs145959653	rs145959653	0.263	0.164	T	0.103	0.243	B	0.006	0.133	B	0.139	0.029	U	1	0.090	N	1.245	0.315	L	-1.84	0.852	D	-0.15	0.131	N	0.077	0.068	-0.801	0.551	T	0.334	0.702	T	0.077	0.728	D	-0.107	0.084	1.681	0.793	0.122	0.118	0.167	N	c	-1.204	-1.281	0.998	0.357	0.707	0.730	0	-3.79	0.040	-0.583	0.059	-0.545	0.048	0.000	0.063	0.053	0.166	4.286	0.102	.	.	.	ID=COSV99029715;OCCURENCE=1(stomach),1(lung)	212222	Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	MU91801528	COAD-US|1|402|0.00248756,LUAD-US|1|516|0.00193798	0.25	37	193	2	48025765	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=159;VD=2;AF=0.0126;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20333;SOR=inf;LSEQ=GGCAGGTAGGCACAACTTAC;RSEQ=TAACAGATAAGAGTGAAGAA;CSQ=A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|4/10||NM_000179.3:c.643G>A|NP_000170.1:p.Val215Ile|732|643|215|V/I|Gta/Ata|rs145959653&COSV99029715||1||EntrezGene||YES||||2:g.48025765G>A|4.051e-05|0.0001244|0|0|0.0002732|0|8.877e-06|0.0001641|3.273e-05|0.0014|AMR|uncertain_significance&conflicting_interpretations_of_pathogenicity|0&1|1&1,A|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|2/8||NM_001281492.2:c.253G>A|NP_001268421.1:p.Val85Ile|342|253|85|V/I|Gta/Ata|rs145959653&COSV99029715||1||EntrezGene||||||2:g.48025765G>A|4.051e-05|0.0001244|0|0|0.0002732|0|8.877e-06|0.0001641|3.273e-05|0.0014|AMR|uncertain_significance&conflicting_interpretations_of_pathogenicity|0&1|1&1,A|5_prime_UTR_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding|3/9||NM_001281493.2:c.-264G>A||562|||||rs145959653&COSV99029715||1||EntrezGene||||||2:g.48025765G>A|4.051e-05|0.0001244|0|0|0.0002732|0|8.877e-06|0.0001641|3.273e-05|0.0014|AMR|uncertain_significance&conflicting_interpretations_of_pathogenicity|0&1|1&1,A|5_prime_UTR_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding|4/10||NM_001281494.2:c.-264G>A||530|||||rs145959653&COSV99029715||1||EntrezGene||||||2:g.48025765G>A|4.051e-05|0.0001244|0|0|0.0002732|0|8.877e-06|0.0001641|3.273e-05|0.0014|AMR|uncertain_significance&conflicting_interpretations_of_pathogenicity|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:159:2:1,1:129,27:156,2:0.0126:2,2:31.5:1:37:0:0.32395:4.70988:60:4:0.0136:0:1	0/0:193:0:0,0:138,54:192,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    610. 

  610. 2	48030640	48030640	C	-	exonic	MSH6	.	frameshift deletion	MSH6:NM_001281492:exon3:c.2864delC:p.F958Sfs*2,MSH6:NM_001281493:exon4:c.2348delC:p.F786Sfs*2,MSH6:NM_000179:exon5:c.3254delC:p.F1088Sfs*2,MSH6:NM_001281494:exon5:c.2348delC:p.F786Sfs*2	0.0033	3.256e-05	0	0	0	0	0.0003	0	0	rs267608078	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	94837	Lynch-like_syndrome|Carcinoma_of_colon|Lynch_syndrome|Hereditary_cancer-predisposing_syndrome|Mismatch_repair_cancer_syndrome_3|Hereditary_nonpolyposis_colorectal_neoplasms|not_provided	.|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0030841,MedGen:CN296221,OMIM:619097|MedGen:C0009405|MedGen:CN517202	reviewed_by_expert_panel	Pathogenic	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU132357	ESAD-UK|1|409|0.00244499,LIRI-JP|1|258|0.00387597,GACA-JP|2|585|0.0034188,STAD-US|2|439|0.00455581,BTCA-JP|1|239|0.0041841	0.25	111	366	2	48030639	.	AC	A	111	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=833;VD=8;AF=0.0096;SHIFT3=7;MSI=8;MSILEN=1;SSF=0.52407;SOR=0.87768;LSEQ=TAATTCTGTTGCCGGAAGAT;RSEQ=CCCCCCCTTCTTAGAGCTTA;CSQ=-|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_000179.3|protein_coding|5/10||NM_000179.3:c.3261del|NP_000170.1:p.Phe1088SerfsTer2|3343|3254|1085|T/X|aCc/ac|rs267608078&COSV99029757||1||EntrezGene||YES|||7|2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding||||||||||rs267608078&COSV99029757|3419|-1||EntrezGene||YES||||2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281492.2|protein_coding|3/8||NM_001281492.2:c.2871del|NP_001268421.1:p.Phe958SerfsTer2|2953|2864|955|T/X|aCc/ac|rs267608078&COSV99029757||1||EntrezGene|||||7|2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281493.2|protein_coding|4/9||NM_001281493.2:c.2355del|NP_001268422.1:p.Phe786SerfsTer2|3173|2348|783|T/X|aCc/ac|rs267608078&COSV99029757||1||EntrezGene|||||7|2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281494.2|protein_coding|5/10||NM_001281494.2:c.2355del|NP_001268423.1:p.Phe786SerfsTer2|3141|2348|783|T/X|aCc/ac|rs267608078&COSV99029757||1||EntrezGene|||||7|2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding||||||||||rs267608078&COSV99029757|3419|-1||EntrezGene||||||2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding||||||||||rs267608078&COSV99029757|3419|-1||EntrezGene||||||2:g.48030647del|1.201e-05|6.201e-05|0|9.968e-05|0|0|8.879e-06|0|0|9.968e-05|gnomAD_ASJ|pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:833:8:4,4:442,383:825,8:0.0096:2,2:45.4:1:37:0:1:1.15385:60:16:0.0099:0:0	0/1:366:4:2,2:203,159:362,4:0.0109:2,2:30.5:1:37:1:1:1.27586:60:8:0.0111:0.0027:0
    611. 

  611. 2	48030838	48030838	A	T	intronic	MSH6	.	.	.	0.62	0.3215	0.1746	0.4761	0.37	0.6412	0.3298	0.3606	0.3313	rs2020911	rs2020911	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52273834;OCCURENCE=23(large_intestine),1(lung)	51641	Lynch_syndrome|Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|none_provided	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN235283	reviewed_by_expert_panel	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18078893	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	255	293	2	48030838	.	A	T	255	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=128;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=GAGACAGGTAACTGATTCTT;RSEQ=AAGTTTTGTTATCAGAAAGT;CSQ=T|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_000179.3|protein_coding||5/9|NM_000179.3:c.3438+14A>T|||||||rs2020911&COSV52273834||1||EntrezGene||YES||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding||||||||||rs2020911&COSV52273834|3221|-1||EntrezGene||YES||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281492.2|protein_coding||3/7|NM_001281492.2:c.3048+14A>T|||||||rs2020911&COSV52273834||1||EntrezGene||||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding||4/8|NM_001281493.2:c.2532+14A>T|||||||rs2020911&COSV52273834||1||EntrezGene||||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding||5/9|NM_001281494.2:c.2532+14A>T|||||||rs2020911&COSV52273834||1||EntrezGene||||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding||||||||||rs2020911&COSV52273834|3221|-1||EntrezGene||||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding||||||||||rs2020911&COSV52273834|3221|-1||EntrezGene||||||2:g.48030838A>T|0.4118|0.1685|0.5075|0.3773|0.624|0.3416|0.3819|0.3993|0.4764|0.624|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:128:128:34,94:0,0:0,128:1:0,2:26.1:1:36.5:1:1:0:60:256:1:0:1.1	0/0:293:0:0,0:109,184:293,0:0:2,0:37.6:1:36.8:1:1:0:60:292:1:0:0.1
    612. 

  612. 2	48032123	48032123	T	G	exonic	MSH6	.	nonsynonymous SNV	MSH6:NM_001281492:exon4:c.T3123G:p.D1041E,MSH6:NM_001281493:exon5:c.T2607G:p.D869E,MSH6:NM_000179:exon6:c.T3513G:p.D1171E,MSH6:NM_001281494:exon6:c.T2607G:p.D869E	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	3.01	0.863	M	-2.31	0.878	D	-3.79	0.716	D	0.838	0.937	0.642	0.924	D	0.806	0.935	D	0.445	0.942	D	5.563	0.757	26.4	0.995	0.677	0.834	0.422	D	c	0.155	-0.005	0.087	0.160	0.707	0.730	0	-1.33	0.086	0.359	0.198	-0.882	0.027	0.993	0.376	0.989	0.536	11.516	0.496	DNA mismatch repair protein MutS, C-terminal|P-loop containing nucleoside triphosphate hydrolase;DNA mismatch repair protein MutS, core	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	38	271	2	48032123	.	T	G	38	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=262;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.13072;SOR=0;LSEQ=TGCAGGCTCACACCAATTGA;RSEQ=AGAGTGTTTACTAGACTTGG;CSQ=G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_000179.3|protein_coding|6/10||NM_000179.3:c.3513T>G|NP_000170.1:p.Asp1171Glu|3602|3513|1171|D/E|gaT/gaG|CD040601&CD160998||1||EntrezGene||YES||||2:g.48032123T>G||||||||||||||1&1,G|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding||||||||||CD040601&CD160998|1936|-1||EntrezGene||YES||||2:g.48032123T>G||||||||||||||1&1,G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281492.2|protein_coding|4/8||NM_001281492.2:c.3123T>G|NP_001268421.1:p.Asp1041Glu|3212|3123|1041|D/E|gaT/gaG|CD040601&CD160998||1||EntrezGene||||||2:g.48032123T>G||||||||||||||1&1,G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281493.2|protein_coding|5/9||NM_001281493.2:c.2607T>G|NP_001268422.1:p.Asp869Glu|3432|2607|869|D/E|gaT/gaG|CD040601&CD160998||1||EntrezGene||||||2:g.48032123T>G||||||||||||||1&1,G|missense_variant|MODERATE|MSH6|2956|Transcript|NM_001281494.2|protein_coding|6/10||NM_001281494.2:c.2607T>G|NP_001268423.1:p.Asp869Glu|3400|2607|869|D/E|gaT/gaG|CD040601&CD160998||1||EntrezGene||||||2:g.48032123T>G||||||||||||||1&1,G|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding||||||||||CD040601&CD160998|1936|-1||EntrezGene||||||2:g.48032123T>G||||||||||||||1&1,G|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding||||||||||CD040601&CD160998|1936|-1||EntrezGene||||||2:g.48032123T>G||||||||||||||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:262:0:0,0:98,164:262,0:0:2,0:31.3:1:35.8:1:1:0:60:51.4:1:0:0.1	0/1:271:3:1,2:107,161:268,3:0.0111:2,2:47:1:24.3:1:1:1.32784:60:2:0.0078:0:3.3
    613. 

  613. 2	48032741	48032741	T	-	intronic	MSH6	.	.	.	0.23	0.0373	0.1051	0.0255	0	0.0044	0.0337	0.0032	0.0212	rs267608102	rs56221304	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	94891	Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	43	2	48032740	.	AT	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=4;VD=0;AF=0;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.76109;SOR=0;LSEQ=AAAATGAGTATTCATTTGTG;RSEQ=TTTTTTTTTTTTAAGGTGAA;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_000179.3|protein_coding||6/9|NM_000179.3:c.3557-4del|||||||rs267608102&COSV52289154||1||EntrezGene||YES||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding||||||||||rs267608102&COSV52289154|1318|-1||EntrezGene||YES||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281492.2|protein_coding||4/7|NM_001281492.2:c.3167-4del|||||||rs267608102&COSV52289154||1||EntrezGene||||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281493.2|protein_coding||5/8|NM_001281493.2:c.2651-4del|||||||rs267608102&COSV52289154||1||EntrezGene||||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|MSH6|2956|Transcript|NM_001281494.2|protein_coding||6/9|NM_001281494.2:c.2651-4del|||||||rs267608102&COSV52289154||1||EntrezGene||||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding||||||||||rs267608102&COSV52289154|1318|-1||EntrezGene||||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding||||||||||rs267608102&COSV52289154|1318|-1||EntrezGene||||||2:g.48032753del|0.1059|0.2344|0.1597|0.0793|0.1521|0.08707|0.08148|0.09308|0.08643|0.2344|gnomAD_AFR|uncertain_significance&benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:32.5:1:37:0:1:0:60:8:1:0:0	0/1:43:3:2,1:26,14:40,3:0.0698:2,2:34.3:1:37:1:1:1.08:60:6:0.0698:0.0233:0.3
    614. 

  614. 2	48032909	48032909	T	-	intronic	MSH6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	50	2	48032908	.	AT	A	37	d5;v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATTTGTACAAATAACT;RSEQ=TTTTATAGAAGATTATCTGA;CSQ=-|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_000179.3|protein_coding||7/9|NM_000179.3:c.3646+67del|||||||||1||EntrezGene||YES||||2:g.48032913del||||||||||||||,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding|||||||||||1150|-1||EntrezGene||YES||||2:g.48032913del||||||||||||||,-|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281492.2|protein_coding||5/7|NM_001281492.2:c.3256+67del|||||||||1||EntrezGene||||||2:g.48032913del||||||||||||||,-|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281493.2|protein_coding||6/8|NM_001281493.2:c.2740+67del|||||||||1||EntrezGene||||||2:g.48032913del||||||||||||||,-|intron_variant|MODIFIER|MSH6|2956|Transcript|NM_001281494.2|protein_coding||7/9|NM_001281494.2:c.2740+67del|||||||||1||EntrezGene||||||2:g.48032913del||||||||||||||,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding|||||||||||1150|-1||EntrezGene||||||2:g.48032913del||||||||||||||,-|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding|||||||||||1150|-1||EntrezGene||||||2:g.48032913del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:50:2:1,1:16,32:48,2:0.04:2,2:49.5:1:37:0:1:1.97:60:4:0.04:0:1
    615. 

  615. 2	48033981	48033981	-	TTGA	exonic	MSH6	.	frameshift insertion	MSH6:NM_001281492:exon8:c.3675_3676insTTGA:p.K1228Dfs*2,MSH6:NM_001281493:exon9:c.3159_3160insTTGA:p.K1056Dfs*2,MSH6:NM_000179:exon10:c.4065_4066insTTGA:p.K1358Dfs*2,MSH6:NM_001281494:exon10:c.3159_3160insTTGA:p.K1056Dfs*2	0.039	0.0016	0	0	0	0.0297	0	0	0	rs55740729	rs55740729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	94992	Malignant_tumor_of_sigmoid_colon|Lynch_syndrome|Lynch_syndrome_I|Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms|not_specified|not_provided	MONDO:MONDO:0001464,MedGen:C0153436|MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0007356,MedGen:C2936783,OMIM:120435|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405|MedGen:CN169374|MedGen:CN517202	reviewed_by_expert_panel	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114604822	COCA-CN|1|321|0.00311526	0.5	107	169	2	48033981	.	T	TTTGA	107	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=8;VD=8;AF=1;SHIFT3=6;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=GCTGTCCATAAATTGCTGAC;RSEQ=TTGATTAAGGAATTATAGAC;CSQ=TTGA|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_000179.3|protein_coding|10/10||NM_000179.3:c.4068_4071dup|NP_000170.1:p.Lys1358AspfsTer2|4154-4155|4065-4066|1355-1356|-/LX|-/TTGA|rs55740729||1||EntrezGene||YES|||6|2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001190274.2|protein_coding||||||||||rs55740729|77|-1||EntrezGene||YES||||2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281492.2|protein_coding|8/8||NM_001281492.2:c.3678_3681dup|NP_001268421.1:p.Lys1228AspfsTer2|3764-3765|3675-3676|1225-1226|-/LX|-/TTGA|rs55740729||1||EntrezGene|||||6|2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281493.2|protein_coding|9/9||NM_001281493.2:c.3162_3165dup|NP_001268422.1:p.Lys1056AspfsTer2|3984-3985|3159-3160|1053-1054|-/LX|-/TTGA|rs55740729||1||EntrezGene|||||6|2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|frameshift_variant|HIGH|MSH6|2956|Transcript|NM_001281494.2|protein_coding|10/10||NM_001281494.2:c.3162_3165dup|NP_001268423.1:p.Lys1056AspfsTer2|3952-3953|3159-3160|1053-1054|-/LX|-/TTGA|rs55740729||1||EntrezGene|||||6|2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_001374325.1|protein_coding||||||||||rs55740729|77|-1||EntrezGene||||||2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1,TTGA|downstream_gene_variant|MODIFIER|FBXO11|80204|Transcript|NM_025133.4|protein_coding||||||||||rs55740729|77|-1||EntrezGene||||||2:g.48033984_48033987dup|0.002533|6.155e-05|0.0001159|0|0.03325|0|0|0.0006536|0.0005235|0.0387|EAS|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:8:8:3,5:0,0:0,8:1:0,2:40.6:1:35.8:1:1:0:62:16:1:0:0.4	0/0:169:0:0,0:79,89:168,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    616. 

  616. 2	58387000	58387000	C	T	UTR3	VRK2	NM_001288837:c.*172C>T;NM_001288838:c.*557C>T;NM_001288839:c.*172C>T;NM_001130480:c.*172C>T;NM_006296:c.*172C>T;NM_001288836:c.*172C>T;NM_001130483:c.*557C>T;NM_001130482:c.*172C>T;NM_001130481:c.*172C>T	.	.	0.92	0.4299	0.8180	0.2698	0.2285	0.2503	0.3083	0.2723	0.3070	rs3732136	rs3732136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52078210;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU22950450	LAML-KR|2|205|0.0097561,COCA-CN|4|321|0.0124611	0.25	90	8	2	58387000	.	C	T	90	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATAAAATTGCTTTGTA;RSEQ=TAGAAATAGTGTCATAGAAT;CSQ=T|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001114636.1|protein_coding||13/13|NM_001114636.1:c.1108-65G>A|||||||rs3732136&COSV52078210||-1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding|13/13||NM_001130480.2:c.*172C>T||1884|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding|13/13||NM_001130481.2:c.*172C>T||1726|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding|13/13||NM_001130482.2:c.*172C>T||1830|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding|14/14||NM_001130483.2:c.*557C>T||1933|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding|14/14||NM_001288836.1:c.*172C>T||2021|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding|16/16||NM_001288837.2:c.*172C>T||2503|||||rs3732136&COSV52078210||1||EntrezGene||YES||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding|16/16||NM_001288838.2:c.*557C>T||2434|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding|12/12||NM_001288839.2:c.*172C>T||1697|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001374615.1|protein_coding||14/14|NM_001374615.1:c.1138-65G>A|||||||rs3732136&COSV52078210||-1||EntrezGene||YES||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|3_prime_UTR_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding|13/13||NM_006296.7:c.*172C>T||1767|||||rs3732136&COSV52078210||1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_018062.4|protein_coding||13/13|NM_018062.4:c.1093-65G>A|||||||rs3732136&COSV52078210||-1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA||9/9|NR_156742.1:n.882-65G>A|||||||rs3732136&COSV52078210||-1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA||11/11|NR_164659.1:n.974-65G>A|||||||rs3732136&COSV52078210||-1||EntrezGene||||||2:g.58387000C>T||||||||||0.9213|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:8:6:4,2:1,1:2,6:0.75:2,2:42.3:1:35:1:1:1.83:60:12:0.8571:0:1.3
    617. 

  617. 2	58387289	58387289	C	T	exonic	FANCL	.	nonsynonymous SNV	FANCL:NM_001114636:exon13:c.G1061A:p.R354K,FANCL:NM_018062:exon13:c.G1046A:p.R349K	.	.	.	.	.	.	.	.	.	.	.	0.041	0.473	D	0.993	0.899	D	0.952	0.875	D	0.000	0.843	D	1.000	0.548	D	2.13	0.595	M	-0.2	0.672	T	-2.27	0.506	N	0.709	0.711	-0.171	0.784	T	0.465	0.793	T	0.038	0.579	D	5.852	0.802	27.3	0.996	0.710	0.992	0.924	D	c	0.761	0.761	1.000	0.747	0.707	0.730	0	5.66	0.872	5.460	0.662	0.935	0.490	1.000	0.715	0.973	0.468	19.714	0.961	FANCL C-terminal domain;FANCL C-terminal domain|Zinc finger, RING-type|Zinc finger, RING/FYVE/PHD-type	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	117	2	58387289	.	C	T	37	d5;v3;f0.01;p8;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.96653;SOR=0;LSEQ=ATATGATGTTAAAACTCTGT;RSEQ=TACTAGTTAGTAGTCCTCTC;CSQ=T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001114636.1|protein_coding|13/14||NM_001114636.1:c.1061G>A|NP_001108108.1:p.Arg354Lys|1128|1061|354|R/K|aGa/aAa|COSV99288019||-1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding||||||||||COSV99288019|234|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding||||||||||COSV99288019|234|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding||||||||||COSV99288019|234|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding||||||||||COSV99288019|234|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding||||||||||COSV99288019|234|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding||||||||||COSV99288019|283|1||EntrezGene||YES||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding||||||||||COSV99288019|283|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding||||||||||COSV99288019|283|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001374615.1|protein_coding|14/15||NM_001374615.1:c.1091G>A|NP_001361544.1:p.Arg364Lys|1103|1091|364|R/K|aGa/aAa|COSV99288019||-1||EntrezGene||YES||||2:g.58387289C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding||||||||||COSV99288019|283|1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_018062.4|protein_coding|13/14||NM_018062.4:c.1046G>A|NP_060532.2:p.Arg349Lys|1058|1046|349|R/K|aGa/aAa|COSV99288019||-1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA|9/10||NR_156742.1:n.835G>A||835|||||COSV99288019||-1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|11/12||NR_164659.1:n.927G>A||927|||||COSV99288019||-1||EntrezGene||||||2:g.58387289C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:7:0:37:0:1:0:60:4:1:0:1	0/1:117:2:1,1:55,60:115,2:0.0171:2,2:26:1:37:0:1:1.09:60:4:0.0172:0:1
    618. 

  618. 2	58387344	58387344	G	A	intronic	FANCL	.	.	.	0.0002	3.234e-05	0	0	0	0.0006	0	0	0	rs371524685	rs371524685	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	93	2	58387344	.	G	A	37	pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=2;AF=0.4;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0021;SOR=inf;LSEQ=TTAAAAGATAAAGGAGAAGC;RSEQ=TCAGCATGATTACAAATTAC;CSQ=A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001114636.1|protein_coding||12/13|NM_001114636.1:c.1036-30C>T|||||||rs371524685||-1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding||||||||||rs371524685|289|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding||||||||||rs371524685|289|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding||||||||||rs371524685|289|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding||||||||||rs371524685|289|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding||||||||||rs371524685|289|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding||||||||||rs371524685|338|1||EntrezGene||YES||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding||||||||||rs371524685|338|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding||||||||||rs371524685|338|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001374615.1|protein_coding||13/14|NM_001374615.1:c.1066-30C>T|||||||rs371524685||-1||EntrezGene||YES||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding||||||||||rs371524685|338|1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_018062.4|protein_coding||12/13|NM_018062.4:c.1021-30C>T|||||||rs371524685||-1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA||8/9|NR_156742.1:n.810-30C>T|||||||rs371524685||-1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA||10/11|NR_164659.1:n.902-30C>T|||||||rs371524685||-1||EntrezGene||||||2:g.58387344G>A|4.404e-05|6.206e-05|2.899e-05|0|0.0004356|0|8.887e-06|0|0|0.0004356|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:5:2:1,1:2,1:3,2:0.4:2,2:16:0:37:0:1:1.7321:60:4:0.4:0:1	0/0:93:0:0,0:36,57:93,0:0:2,0:38.7:1:36.1:1:1:0:60:45.5:1:0:0
    619. 

  619. 2	58388696	58388696	A	G	exonic	FANCL	.	synonymous SNV	FANCL:NM_001114636:exon12:c.T996C:p.S332S,FANCL:NM_018062:exon12:c.T981C:p.S327S	0.95	0.6976	0.8947	0.6751	0.5430	0.5789	0.6272	0.6195	0.6442	rs848291	rs848291	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52073421;OCCURENCE=1(stomach),2(haematopoietic_and_lymphoid_tissue)	250750	Fanconi_anemia,_complementation_group_L|Fanconi_anemia|not_specified	MONDO:MONDO:0013566,MedGen:C3469528,OMIM:614083|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU748980	LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763	0.75	174	48	2	58388696	.	A	G	174	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.33143;SOR=inf;LSEQ=TGGAAAGGTTGTCCACACTG;RSEQ=GAATTATCACACACTTGATC;CSQ=G|synonymous_variant|LOW|FANCL|55120|Transcript|NM_001114636.1|protein_coding|12/14||NM_001114636.1:c.996T>C|NP_001108108.1:p.Ser332%3D|1063|996|332|S|tcT/tcC|rs848291&COSV52073421||-1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding||||||||||rs848291&COSV52073421|1641|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding||||||||||rs848291&COSV52073421|1641|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding||||||||||rs848291&COSV52073421|1641|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding||||||||||rs848291&COSV52073421|1641|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding||||||||||rs848291&COSV52073421|1641|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding||||||||||rs848291&COSV52073421|1690|1||EntrezGene||YES||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding||||||||||rs848291&COSV52073421|1690|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding||||||||||rs848291&COSV52073421|1690|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|synonymous_variant|LOW|FANCL|55120|Transcript|NM_001374615.1|protein_coding|13/15||NM_001374615.1:c.1026T>C|NP_001361544.1:p.Ser342%3D|1038|1026|342|S|tcT/tcC|rs848291&COSV52073421||-1||EntrezGene||YES||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding||||||||||rs848291&COSV52073421|1690|1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|synonymous_variant|LOW|FANCL|55120|Transcript|NM_018062.4|protein_coding|12/14||NM_018062.4:c.981T>C|NP_060532.2:p.Ser327%3D|993|981|327|S|tcT/tcC|rs848291&COSV52073421||-1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA|8/10||NR_156742.1:n.770T>C||770|||||rs848291&COSV52073421||-1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|10/12||NR_164659.1:n.862T>C||862|||||rs848291&COSV52073421||-1||EntrezGene||||||2:g.58388696A>G|0.6434|0.9094|0.6799|0.5516|0.5582|0.6568|0.6088|0.6232|0.6654|0.947|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:70.5:1:37:0:1:0:60:4:1:0:1	1/0:48:27:16,11:11,10:21,27:0.5625:2,2:40:1:36.6:1:0.77101:1.31:60:54:0.5625:0:1.2
    620. 

  620. 2	58388730	58388730	T	A	exonic	FANCL	.	nonsynonymous SNV	FANCL:NM_001114636:exon12:c.A962T:p.D321V,FANCL:NM_018062:exon12:c.A947T:p.D316V	.	.	.	.	.	.	.	.	.	.	.	0.009	0.586	D	0.724	0.466	P	0.685	0.518	P	0.000	0.537	D	1	0.810	D	3.015	0.864	M	-0.26	0.677	T	-2.77	0.674	D	0.432	0.493	-0.344	0.738	T	0.358	0.720	T	0.086	0.748	D	6.296	0.870	29.1	0.992	0.559	0.966	0.698	D	c	0.348	0.394	0.995	0.340	0.732	0.924	0	4.73	0.593	4.583	0.604	1.061	0.807	1.000	0.715	0.923	0.397	12.145	0.531	FANCL C-terminal domain;FANCL C-terminal domain|Zinc finger, RING-type|Zinc finger, RING/FYVE/PHD-type	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	48	2	58388730	.	T	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.92082;SOR=0;LSEQ=CTTGATCAGGAATGGTACCG;RSEQ=CAAGTTGATAAGCATAACAA;CSQ=A|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001114636.1|protein_coding|12/14||NM_001114636.1:c.962A>T|NP_001108108.1:p.Asp321Val|1029|962|321|D/V|gAc/gTc|||-1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding|||||||||||1675|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding|||||||||||1675|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding|||||||||||1675|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding|||||||||||1675|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding|||||||||||1675|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding|||||||||||1724|1||EntrezGene||YES||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding|||||||||||1724|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding|||||||||||1724|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001374615.1|protein_coding|13/15||NM_001374615.1:c.992A>T|NP_001361544.1:p.Asp331Val|1004|992|331|D/V|gAc/gTc|||-1||EntrezGene||YES||||2:g.58388730T>A||||||||||||||,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding|||||||||||1724|1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|missense_variant|MODERATE|FANCL|55120|Transcript|NM_018062.4|protein_coding|12/14||NM_018062.4:c.947A>T|NP_060532.2:p.Asp316Val|959|947|316|D/V|gAc/gTc|||-1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA|8/10||NR_156742.1:n.736A>T||736|||||||-1||EntrezGene||||||2:g.58388730T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|10/12||NR_164659.1:n.828A>T||828|||||||-1||EntrezGene||||||2:g.58388730T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:38:1:31:1:1:0:60:4:1:0:1	0/1:48:2:1,1:24,22:46,2:0.0417:2,2:39:1:37:0:1:1.08892:60:4:0.0435:0:1
    621. 

  621. 2	58390218	58390218	-	A	intronic	FANCL	.	.	.	0.19	0.0544	0.1703	0.0169	0	0	0.0053	0.0008	0.0132	rs770095807	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	290414	Fanconi_anemia|not_specified	MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	39	58	2	58390218	.	T	TA	39	d5;v3;f0.01;MSI12;MSI12	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2;VD=0;AF=0;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.9339;SOR=0;LSEQ=GGGGTTTTACCACTTCAGAT;RSEQ=AAAAAAAAAAAATTTAATAA;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_001114636.1|protein_coding||9/13|NM_001114636.1:c.791-10dup|||||||rs374236117||-1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130480.2|protein_coding||||||||||rs374236117|3163|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130481.2|protein_coding||||||||||rs374236117|3163|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130482.2|protein_coding||||||||||rs374236117|3163|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001130483.2|protein_coding||||||||||rs374236117|3163|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288836.1|protein_coding||||||||||rs374236117|3163|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288837.2|protein_coding||||||||||rs374236117|3212|1||EntrezGene||YES||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288838.2|protein_coding||||||||||rs374236117|3212|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_001288839.2|protein_coding||||||||||rs374236117|3212|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_001374615.1|protein_coding||10/14|NM_001374615.1:c.821-10dup|||||||rs374236117||-1||EntrezGene||YES||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|downstream_gene_variant|MODIFIER|VRK2|7444|Transcript|NM_006296.7|protein_coding||||||||||rs374236117|3212|1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_018062.4|protein_coding||9/13|NM_018062.4:c.776-10dup|||||||rs374236117||-1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FANCL|55120|Transcript|NR_156742.1|misc_RNA||5/9|NR_156742.1:n.565-10dup|||||||rs374236117||-1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1,A|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA||9/11|NR_164659.1:n.784+350dup|||||||rs374236117||-1||EntrezGene||||||2:g.58390230dup|0.02972|0.22|0.03045|0.02218|0.006668|0.01491|0.008284|0.02404|0.01029|0.22|gnomAD_AFR|uncertain_significance&benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:46.5:1:37:0:1:0:60:4:1:0:0.5	0/1:58:2:1,1:16,37:53,2:0.0345:2,2:23.6:1:39.7:0:0.5266:2.27:64.4:4:0.037:0:0
    622. 

  622. 2	58393014	58393014	G	T	intronic	FANCL	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	172	2	58393014	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=0;MSI=7;MSILEN=1;SSF=0.88308;SOR=0;LSEQ=TGCTTATTAAGGAGCTCTGT;RSEQ=AAAAAAATGAAAGTTGAATA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_001114636.1|protein_coding||7/13|NM_001114636.1:c.556-5C>A|||||||||-1||EntrezGene||||||2:g.58393014G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_001374615.1|protein_coding||8/14|NM_001374615.1:c.586-5C>A|||||||||-1||EntrezGene||YES||||2:g.58393014G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_018062.4|protein_coding||7/13|NM_018062.4:c.541-5C>A|||||||||-1||EntrezGene||||||2:g.58393014G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FANCL|55120|Transcript|NR_156742.1|misc_RNA||3/9|NR_156742.1:n.330-5C>A|||||||||-1||EntrezGene||||||2:g.58393014G>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FANCL|55120|Transcript|NR_164659.1|misc_RNA||7/11|NR_164659.1:n.550-5C>A|||||||||-1||EntrezGene||||||2:g.58393014G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:3,8:11,0:0:2,0:30.5:1:34.8:1:1:0:60:22:1:0:0.5	0/1:172:2:1,1:45,125:170,2:0.0116:2,2:46.5:1:37:0:0.4645:2.76:60:4:0.0119:0:1
    623. 

  623. 2	58425721	58425721	G	T	exonic	FANCL	.	nonsynonymous SNV	FANCL:NM_001114636:exon7:c.C548A:p.S183Y	.	.	.	.	.	.	.	.	.	.	.	0.028	0.531	D	0.131	0.256	B	0.056	0.247	B	.	.	.	1	0.090	N	.	.	.	0.77	0.510	T	-0.42	0.142	N	0.098	0.140	-1.029	0.208	T	0.058	0.244	T	0.011	0.277	T	2.792	0.396	21.3	0.984	0.407	0.031	0.079	N	c	-0.914	-0.853	0.000	0.050	0.651	0.465	0	0.637	0.168	0.070	0.143	0.584	0.286	0.001	0.137	0.996	0.625	3.885	0.085	Fanconi anemia complex, subunit FancL, WD-repeat containing domain	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	37	159	2	58425721	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.90621;SOR=0;LSEQ=TTTAAGAATTTACCTGAGGA;RSEQ=AATTTACCTGAGGTGTCCAG;CSQ=T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001114636.1|protein_coding|7/14||NM_001114636.1:c.548C>A|NP_001108108.1:p.Ser183Tyr|615|548|183|S/Y|tCt/tAt|||-1||EntrezGene||||||2:g.58425721G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_001374615.1|protein_coding||7/14|NM_001374615.1:c.540+8C>A|||||||||-1||EntrezGene||YES||||2:g.58425721G>T||||||||||||||,T|splice_region_variant&intron_variant|LOW|FANCL|55120|Transcript|NM_018062.4|protein_coding||7/13|NM_018062.4:c.540+8C>A|||||||||-1||EntrezGene||||||2:g.58425721G>T||||||||||||||,T|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FANCL|55120|Transcript|NR_156742.1|misc_RNA||3/9|NR_156742.1:n.329+8C>A|||||||||-1||EntrezGene||||||2:g.58425721G>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|7/12||NR_164659.1:n.542C>A||542|||||||-1||EntrezGene||||||2:g.58425721G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:51.2:1:37:0:1:0:60:16:1:0:0.1	0/1:159:2:1,1:85,72:157,2:0.0126:2,2:53.5:1:37:0:1:1.17932:60:4:0.0128:0:1
    624. 

  624. 2	58431279	58431279	T	C	exonic	FANCL	.	nonsynonymous SNV	FANCL:NM_001114636:exon6:c.A457G:p.K153E,FANCL:NM_018062:exon6:c.A457G:p.K153E	.	.	.	.	.	.	.	.	.	.	.	0.027	0.465	D	0.586	0.493	P	0.18	0.497	B	0.000	0.629	D	0.999	0.810	D	2.82	0.824	M	0.86	0.468	T	-1.11	0.287	N	0.368	0.711	-0.661	0.623	T	0.265	0.636	T	0.020	0.431	T	4.005	0.538	23.6	0.998	0.870	0.818	0.408	D	c	0.233	0.267	1.000	0.747	0.732	0.924	0	4.03	0.459	3.871	0.555	0.114	0.208	1.000	0.715	0.995	0.604	11.229	0.479	Fanconi anemia complex, subunit FancL, WD-repeat containing domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	52	158	2	58431279	.	T	C	52	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.59179;SOR=0;LSEQ=ACATACCTTTGCCTTCAACT;RSEQ=GAGAGTGATTAAATGCTCTC;CSQ=C|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001114636.1|protein_coding|6/14||NM_001114636.1:c.457A>G|NP_001108108.1:p.Lys153Glu|524|457|153|K/E|Aag/Gag|||-1||EntrezGene||||||2:g.58431279T>C||||||||||||||,C|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001374615.1|protein_coding|6/15||NM_001374615.1:c.457A>G|NP_001361544.1:p.Lys153Glu|469|457|153|K/E|Aag/Gag|||-1||EntrezGene||YES||||2:g.58431279T>C||||||||||||||,C|missense_variant|MODERATE|FANCL|55120|Transcript|NM_018062.4|protein_coding|6/14||NM_018062.4:c.457A>G|NP_060532.2:p.Lys153Glu|469|457|153|K/E|Aag/Gag|||-1||EntrezGene||||||2:g.58431279T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA|2/10||NR_156742.1:n.246A>G||246|||||||-1||EntrezGene||||||2:g.58431279T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|6/12||NR_164659.1:n.451A>G||451|||||||-1||EntrezGene||||||2:g.58431279T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:19,11:30,0:0:2,0:33.6:1:37:0:1:0:60:60:1:0:0.1	0/1:158:3:2,1:101,54:155,3:0.019:2,2:28.7:1:33:1:1:1.07:60:6:0.0192:0:1.7
    625. 

  625. 2	58431303	58431303	C	T	exonic	FANCL	.	nonsynonymous SNV	FANCL:NM_001114636:exon6:c.G433A:p.G145S,FANCL:NM_018062:exon6:c.G433A:p.G145S	.	.	.	.	.	.	.	.	.	.	.	0.045	0.481	D	0.862	0.899	P	0.461	0.971	P	0.000	0.843	D	1	0.810	D	2.985	0.859	M	0.9	0.468	T	-2.69	0.582	D	0.368	0.797	-0.336	0.740	T	0.411	0.760	T	0.025	0.483	D	5.805	0.794	27.1	0.998	0.846	0.807	0.400	D	c	0.463	0.538	1.000	0.747	0.732	0.924	0	6.03	0.978	2.911	0.482	0.935	0.490	1.000	0.715	1.000	0.888	18.747	0.917	Fanconi anemia complex, subunit FancL, WD-repeat containing domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	175	2	58431303	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.69378;SOR=0;LSEQ=AGTGATTAAATGCTCTCTAC;RSEQ=AGAAGCATCTTCTGCTTTTA;CSQ=T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001114636.1|protein_coding|6/14||NM_001114636.1:c.433G>A|NP_001108108.1:p.Gly145Ser|500|433|145|G/S|Ggt/Agt|||-1||EntrezGene||||||2:g.58431303C>T||||||||||||||,T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_001374615.1|protein_coding|6/15||NM_001374615.1:c.433G>A|NP_001361544.1:p.Gly145Ser|445|433|145|G/S|Ggt/Agt|||-1||EntrezGene||YES||||2:g.58431303C>T||||||||||||||,T|missense_variant|MODERATE|FANCL|55120|Transcript|NM_018062.4|protein_coding|6/14||NM_018062.4:c.433G>A|NP_060532.2:p.Gly145Ser|445|433|145|G/S|Ggt/Agt|||-1||EntrezGene||||||2:g.58431303C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA|2/10||NR_156742.1:n.222G>A||222|||||||-1||EntrezGene||||||2:g.58431303C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA|6/12||NR_164659.1:n.427G>A||427|||||||-1||EntrezGene||||||2:g.58431303C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:35:0:0,0:21,14:35,0:0:2,0:49.1:1:36.3:1:1:0:60:70:1:0:0.3	0/1:175:2:1,1:99,73:172,2:0.0114:2,2:12.5:1:37:0:1:1.35374:60:4:0.0116:0:1.5
    626. 

  626. 2	58453843	58453843	-	A	intronic	FANCL	.	.	.	0.35	0.2920	0.0835	0.4194	0.3333	0.3209	0.4288	0.3730	0.3878	rs372101290	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112120040	BTCA-SG|3|71|0.0422535	0.5	79	72	2	58453843	.	G	GA	79	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=6;VD=4;AF=0.6667;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.00034;SOR=39.5956;LSEQ=GCAGTATGGTAACAGTGTCA;RSEQ=AAAAAAAAAAAATTCTTACC;CSQ=A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001114636.1|protein_coding||4/13|NM_001114636.1:c.273+19dup|||||||rs372101290||-1||EntrezGene||||||2:g.58453855dup|0.4155|0.2046|0.4441|0.4109|0.4031|0.4124|0.4174|0.4177|0.4512|0.4512|gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_001374615.1|protein_coding||4/14|NM_001374615.1:c.273+19dup|||||||rs372101290||-1||EntrezGene||YES||||2:g.58453855dup|0.4155|0.2046|0.4441|0.4109|0.4031|0.4124|0.4174|0.4177|0.4512|0.4512|gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCL|55120|Transcript|NM_018062.4|protein_coding||4/13|NM_018062.4:c.273+19dup|||||||rs372101290||-1||EntrezGene||||||2:g.58453855dup|0.4155|0.2046|0.4441|0.4109|0.4031|0.4124|0.4174|0.4177|0.4512|0.4512|gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_156742.1|misc_RNA||1/9|NR_156742.1:n.163+14509dup|||||||rs372101290||-1||EntrezGene||||||2:g.58453855dup|0.4155|0.2046|0.4441|0.4109|0.4031|0.4124|0.4174|0.4177|0.4512|0.4512|gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FANCL|55120|Transcript|NR_164659.1|misc_RNA||4/11|NR_164659.1:n.267+19dup|||||||rs372101290||-1||EntrezGene||||||2:g.58453855dup|0.4155|0.2046|0.4441|0.4109|0.4031|0.4124|0.4174|0.4177|0.4512|0.4512|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:6:4:4,0:1,1:2,4:0.6667:2,0:44.8:1:39.7:0:0.33333:0:64.4:8:0.6667:0:0	0/1:72:3:2,1:37,28:65,3:0.0417:2,2:49.4:1:39.7:0:1:1.5:64.4:6:0.05:0:0
    627. 

  627. 2	61108996	61108996	A	T	intronic	REL	.	.	.	0.2	0.0863	0.1195	0.1038	0.1788	0.0993	0.0610	0.0685	0.0888	rs842650	rs842650	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV104400085;OCCURENCE=1(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81733188	LICA-CN|1|402|0.00248756,COCA-CN|1|321|0.00311526	0.25	192	71	2	61108996	.	A	T	192	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=411;VD=54;AF=0.1314;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.0001;SOR=inf;LSEQ=ATGGCCTCCGGTGAGTGTTC;RSEQ=TGGGGCGCGGGCCTGGGCCG;CSQ=T|intron_variant|MODIFIER|REL|5966|Transcript|NM_001291746.2|protein_coding||1/9|NM_001291746.2:c.10+11A>T|||||||rs842650&COSV104400085||1||EntrezGene||||||2:g.61108996A>T|0.1073|0.1337|0.1147|0.1405|0.1125|0.07064|0.08082|0.1204|0.1448|0.1448|gnomAD_SAS||0&1|0&1,T|intron_variant|MODIFIER|REL|5966|Transcript|NM_002908.4|protein_coding||1/10|NM_002908.4:c.10+11A>T|||||||rs842650&COSV104400085||1||EntrezGene||YES||||2:g.61108996A>T|0.1073|0.1337|0.1147|0.1405|0.1125|0.07064|0.08082|0.1204|0.1448|0.1448|gnomAD_SAS||0&1|0&1,T|upstream_gene_variant|MODIFIER|LINC01185|400957|Transcript|NR_033980.1|lncRNA||||||||||rs842650&COSV104400085|547|-1||EntrezGene||YES||||2:g.61108996A>T|0.1073|0.1337|0.1147|0.1405|0.1125|0.07064|0.08082|0.1204|0.1448|0.1448|gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:411:54:24,30:166,191:357,54:0.1314:2,2:45.8:1:33.5:1:0.88374:1.08614:60:9.8:0.1256:0:1.1	0/0:71:0:0,0:30,41:71,0:0:2,0:40.7:1:34.9:1:1:0:60:34.5:1:0:0.1
    628. 

  628. 2	61118786	61118786	C	A	intronic	REL	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	175	2	61118786	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=38;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.67433;SOR=0;LSEQ=ATTAATTGCTATATTAATCT;RSEQ=ACTGACCTCCTCCTTTTTAA;CSQ=A|intron_variant|MODIFIER|REL|5966|Transcript|NM_001291746.2|protein_coding||1/9|NM_001291746.2:c.11-32C>A|||||||||1||EntrezGene||||||2:g.61118786C>A||||||||||||||,A|intron_variant|MODIFIER|REL|5966|Transcript|NM_002908.4|protein_coding||1/10|NM_002908.4:c.11-32C>A|||||||||1||EntrezGene||YES||||2:g.61118786C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:38:0:0,0:31,7:38,0:0:2,0:31.2:1:36.7:1:1:0:60:76:1:0:0.1	0/1:175:2:1,1:125,48:173,2:0.0114:2,2:38.5:1:37:0:0.48276:2.58775:60:4:0.0118:0:1
    629. 

  629. 2	61118821	61118821	C	T	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon2:c.C14T:p.A5V,REL:NM_002908:exon2:c.C14T:p.A5V	0.0001	3.231e-05	0	0	0	0	0.0003	0	0	rs146326268	rs146326268	0.068	0.357	T	0.003	0.209	B	0.0	0.063	B	0.121	0.190	N	1.000	0.198	N	-0.41	0.029	N	0.84	0.475	T	-0.59	0.176	N	0.035	0.016	-1.048	0.150	T	0.068	0.280	T	0.012	0.295	T	4.190	0.562	23.8	0.972	0.325	0.411	0.263	N	c	-0.592	-0.410	1.000	0.467	0.660	0.490	0	3.66	0.409	1.541	0.355	-0.401	0.062	0.955	0.331	0.906	0.385	9.642	0.388	Rel homology domain (RHD), DNA-binding domain	.	.	ID=COSV54368077;OCCURENCE=1(large_intestine),1(stomach)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	253	2	61118821	.	C	T	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=2;AF=0.0213;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1796;SOR=5.44627;LSEQ=TTTTAAAAACTTTTCAGGTG;RSEQ=GTATAACCCGTATATAGAGA;CSQ=T|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|2/10||NM_001291746.2:c.14C>T|NP_001278675.1:p.Ala5Val|281|14|5|A/V|gCg/gTg|rs146326268&COSV54368077||1||EntrezGene||||||2:g.61118821C>T|2.035e-05|0|0|0|5.556e-05|0|3.583e-05|0|0|0.0001163|EA||0&1|0&1,T|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|2/11||NM_002908.4:c.14C>T|NP_002899.1:p.Ala5Val|281|14|5|A/V|gCg/gTg|rs146326268&COSV54368077||1||EntrezGene||YES||||2:g.61118821C>T|2.035e-05|0|0|0|5.556e-05|0|3.583e-05|0|0|0.0001163|EA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:94:2:1,1:54,37:91,2:0.0213:2,2:26.5:1:37:0:1:1.45337:60:4:0.0213:0:1	0/0:253:1:1,0:156,96:252,1:0.004:2,0:16:0:37:0:1:0:60:2:0.004:0:1
    630. 

  630. 2	61118847	61118847	-	AACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC	exonic	REL	.	frameshift insertion	REL:NM_001291746:exon2:c.40_41insAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC:p.R45Pfs*38,REL:NM_002908:exon2:c.40_41insAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC:p.R45Pfs*38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	61	297	2	61118847	.	G	GAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC	61	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=150;VD=3;AF=0.02;SHIFT3=70;MSI=1;MSILEN=1;SSF=0.03729;SOR=inf;LSEQ=ACCCGTATATAGAGATAATT;RSEQ=AACAACCCAGGCAGAGGGGA;CSQ=AACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC|frameshift_variant|HIGH|REL|5966|Transcript|NM_001291746.2|protein_coding|2/10||NM_001291746.2:c.48_133dup|NP_001278675.1:p.Arg45ProfsTer38|307-308|40-41|14|E/EQPRQRGMRFRYKCEGRSAGSIPGEHSTDX|gaa/gAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGACaa|||1||EntrezGene|||||93|2:g.61118898_61118899insCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGACAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGAT||||||||||||||,AACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGAC|frameshift_variant|HIGH|REL|5966|Transcript|NM_002908.4|protein_coding|2/11||NM_002908.4:c.48_133dup|NP_002899.1:p.Arg45ProfsTer38|307-308|40-41|14|E/EQPRQRGMRFRYKCEGRSAGSIPGEHSTDX|gaa/gAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGATCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGACaa|||1||EntrezGene||YES|||93|2:g.61118898_61118899insCAGCAGGCAGCATTCCAGGGGAGCACAGCACAGACAACAACCCAGGCAGAGGGGAATGCGTTTTAGATACAAATGTGAAGGGCGAT||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:150:3:1,1:28,23:51,3:0.02:2,2:19.4:1:39:1:1:1.21285:64.5:6:0.0556:0.0133:0	0/0:297:0:0,0:161,136:297,0:0:2,0:37.9:1:35.5:1:1:0:60:48.5:1:0:0.1
    631. 

  631. 2	61118866	61118866	G	T	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon2:c.G59T:p.G20V,REL:NM_002908:exon2:c.G59T:p.G20V	.	.	.	.	.	.	.	.	.	.	.	0.006	0.784	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	2.795	0.818	M	0.57	0.544	T	-7.94	0.963	D	0.944	0.944	-0.095	0.802	T	0.423	0.767	T	0.048	0.634	D	6.602	0.907	31	0.998	0.911	0.982	0.799	D	c	1.000	0.962	1.0	0.983	0.660	0.490	0	5.62	0.857	9.996	0.993	0.946	0.533	1.000	0.715	1.000	0.888	19.653	0.958	Rel homology domain (RHD), DNA-binding domain|p53-like transcription factor, DNA-binding	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	320	2	61118866	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=149;VD=2;AF=0.0134;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.10047;SOR=inf;LSEQ=TGAACAACCCAGGCAGAGGG;RSEQ=AATGCGTTTTAGATACAAAT;CSQ=T|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|2/10||NM_001291746.2:c.59G>T|NP_001278675.1:p.Gly20Val|326|59|20|G/V|gGa/gTa|||1||EntrezGene||||||2:g.61118866G>T||||||||||||||,T|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|2/11||NM_002908.4:c.59G>T|NP_002899.1:p.Gly20Val|326|59|20|G/V|gGa/gTa|||1||EntrezGene||YES||||2:g.61118866G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:149:2:1,1:75,72:147,2:0.0134:2,2:62:1:37:0:1:1.04139:60:4:0.0135:0:1	0/0:320:0:0,0:162,158:320,0:0:2,0:39.2:1:36.6:1:1:0:60:319:1:0:0.1
    632. 

  632. 2	61121492	61121492	G	A	intronic	REL	.	.	.	1.	0.9602	0.9878	0.9187	0.9801	0.9994	0.9444	0.9459	0.9532	rs842644	rs842644	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81733201	COCA-CN|5|321|0.0155763	1	208	56	2	61121492	.	G	A	208	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGATCAGTTTATAATGCA;RSEQ=TCTATTTGGATCATGTATTT;CSQ=A|intron_variant|MODIFIER|REL|5966|Transcript|NM_001291746.2|protein_coding||2/9|NM_001291746.2:c.154-40G>A|||||||rs842644||1||EntrezGene||||||2:g.61121492G>A|0.9492|0.9883|0.9028|0.9723|0.999|0.944|0.9438|0.9506|0.9557|1|EAS|||,A|intron_variant|MODIFIER|REL|5966|Transcript|NM_002908.4|protein_coding||2/10|NM_002908.4:c.154-40G>A|||||||rs842644||1||EntrezGene||YES||||2:g.61121492G>A|0.9492|0.9883|0.9028|0.9723|0.999|0.944|0.9438|0.9506|0.9557|1|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:56.5:1:37:0:1:0:60:4:1:0:1.5	1/1:56:56:45,11:0,0:0,56:1:0,2:31.9:1:35.9:1:1:0:60:112:1:0:1.2
    633. 

  633. 2	61121650	61121650	C	T	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon3:c.C272T:p.A91V,REL:NM_002908:exon3:c.C272T:p.A91V	.	.	.	.	.	.	.	.	.	.	.	0.37	0.115	T	1.0	0.899	D	0.969	0.703	D	0.000	0.629	D	1.000	0.508	D	0.535	0.137	N	1.18	0.377	T	-2.04	0.468	N	0.459	0.575	-1.045	0.158	T	0.106	0.387	T	0.015	0.351	T	5.064	0.682	25.2	0.999	0.949	0.953	0.639	D	c	0.375	0.429	0.988	0.313	0.707	0.730	0	5.14	0.699	5.016	0.636	0.935	0.490	1.000	0.715	0.997	0.653	12.342	0.542	Rel homology domain (RHD), DNA-binding domain|p53-like transcription factor, DNA-binding	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	239	2	61121650	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=2;AF=0.1429;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.00285;SOR=inf;LSEQ=CAGAGACGGCTACTATGAAG;RSEQ=AGAATTTGGACAAGAACGCA;CSQ=T|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|3/10||NM_001291746.2:c.272C>T|NP_001278675.1:p.Ala91Val|539|272|91|A/V|gCa/gTa|||1||EntrezGene||||||2:g.61121650C>T||||||||||||||,T|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|3/11||NM_002908.4:c.272C>T|NP_002899.1:p.Ala91Val|539|272|91|A/V|gCa/gTa|||1||EntrezGene||YES||||2:g.61121650C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:14:2:1,1:7,5:12,2:0.1429:2,2:13:0:37:0:1:1.36624:60:4:0.1429:0:1	0/0:239:0:0,0:112,127:239,0:0:2,0:40.6:1:36.1:1:1:0:60:118.5:1:0:0.1
    634. 

  634. 2	61143994	61143994	T	-	intronic	REL	.	.	.	0.0066	9.855e-05	0	0	0	0	0.0003	0.0001	0	rs771754683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU43898185	COCA-CN|1|321|0.00311526,BTCA-JP|1|239|0.0041841	0.5	37	105	2	61143993	.	AT	A	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=10;VD=2;AF=0.2;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.03739;SOR=12.2362;LSEQ=GTGACTATTACATTTAAAAA;RSEQ=TTTTTTTTTCTATTCAGTCC;CSQ=-|intron_variant|MODIFIER|REL|5966|Transcript|NM_001291746.2|protein_coding||4/9|NM_001291746.2:c.395-9del|||||||rs527378932&COSV54364557||1||EntrezGene||||||2:g.61144003del|0.0007699|0.0005345|0.0005977|0.001622|0.0005036|0.000901|0.0008945|0.0002254|0.0005283|0.005394|AA||0&1|0&1,-|intron_variant|MODIFIER|REL|5966|Transcript|NM_002908.4|protein_coding||4/10|NM_002908.4:c.395-9del|||||||rs527378932&COSV54364557||1||EntrezGene||YES||||2:g.61144003del|0.0007699|0.0005345|0.0005977|0.001622|0.0005036|0.000901|0.0008945|0.0002254|0.0005283|0.005394|AA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:10:2:1,1:6,2:8,2:0.2:2,2:50.5:1:37:0:1:2.64575:60:4:0.2:0:0	0/1:105:2:1,1:79,24:103,2:0.019:2,2:31.5:1:37:0:0.42125:3.24549:60:4:0.0194:0:0
    635. 

  635. 2	61145423	61145423	T	C	exonic	REL	.	synonymous SNV	REL:NM_001291746:exon6:c.T633C:p.V211V,REL:NM_002908:exon6:c.T633C:p.V211V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	157	2	61145423	.	T	C	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.96274;SOR=0;LSEQ=TTTCTACTTTGTGACAAAGT;RSEQ=CAGAAAGGTATTTATTTATT;CSQ=C|synonymous_variant|LOW|REL|5966|Transcript|NM_001291746.2|protein_coding|6/10||NM_001291746.2:c.633T>C|NP_001278675.1:p.Val211%3D|900|633|211|V|gtT/gtC|||1||EntrezGene||||||2:g.61145423T>C||||||||||||||,C|synonymous_variant|LOW|REL|5966|Transcript|NM_002908.4|protein_coding|6/11||NM_002908.4:c.633T>C|NP_002899.1:p.Val211%3D|900|633|211|V|gtT/gtC|||1||EntrezGene||YES||||2:g.61145423T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:28.7:1:37:0:1:0:60:6:1:0:0	0/1:157:2:1,1:67,88:155,2:0.0127:2,2:65.5:1:37:0:1:1.31:60:4:0.0129:0:1
    636. 

  636. 2	61145709	61145709	C	T	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon7:c.C821T:p.S274F,REL:NM_002908:exon7:c.C821T:p.S274F	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.909	0.663	D	0.000	0.629	D	0.998	0.448	D	1.665	0.427	L	0.94	0.437	T	-3.71	0.718	D	0.598	0.639	-0.307	0.748	T	0.330	0.698	T	0.036	0.568	D	6.677	0.914	32	0.999	0.933	0.960	0.670	D	c	0.880	0.838	1.000	0.747	0.732	0.924	0	5.78	0.914	6.081	0.707	0.852	0.362	0.910	0.314	0.998	0.697	20.020	0.975	IPT domain|Immunoglobulin E-set|Immunoglobulin-like fold|Rel homology dimerisation domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	222	2	61145709	.	C	T	37	v3;p8	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=2;AF=0.0227;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07992;SOR=inf;LSEQ=TGACCAGGAAGTTAGTGAAT;RSEQ=TATGGATTTTAGATATCTGC;CSQ=T|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|7/10||NM_001291746.2:c.821C>T|NP_001278675.1:p.Ser274Phe|1088|821|274|S/F|tCt/tTt|||1||EntrezGene||||||2:g.61145709C>T||||||||||||||,T|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|7/11||NM_002908.4:c.821C>T|NP_002899.1:p.Ser274Phe|1088|821|274|S/F|tCt/tTt|||1||EntrezGene||YES||||2:g.61145709C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:88:2:1,1:24,62:86,2:0.0227:2,2:6:1:37:0:0.48981:2.55:60:4:0.0233:0:1	0/0:222:0:0,0:76,146:222,0:0:2,0:35.4:1:36.2:1:1:0:60:110:1:0:0.1
    637. 

  637. 2	61145727	61145727	T	C	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon7:c.T839C:p.L280P,REL:NM_002908:exon7:c.T839C:p.L280P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	1.0	0.899	D	0.925	0.668	D	0.000	0.843	D	1	0.810	D	2.925	0.847	M	0.19	0.603	T	-5.94	0.897	D	0.912	0.906	-0.454	0.703	T	0.306	0.677	T	0.063	0.688	D	6.341	0.876	29.3	0.999	0.980	0.994	0.951	D	c	0.665	0.688	1.000	0.747	0.732	0.924	0	5.78	0.914	6.174	0.717	0.964	0.580	1.000	0.715	1.000	0.888	16.120	0.811	IPT domain|Immunoglobulin E-set|Immunoglobulin-like fold|Rel homology dimerisation domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	187	2	61145727	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.66038;SOR=0;LSEQ=ATCTATGGATTTTAGATATC;RSEQ=GCCAGATGAAAAAGGTATGA;CSQ=C|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|7/10||NM_001291746.2:c.839T>C|NP_001278675.1:p.Leu280Pro|1106|839|280|L/P|cTg/cCg|||1||EntrezGene||||||2:g.61145727T>C||||||||||||||,C|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|7/11||NM_002908.4:c.839T>C|NP_002899.1:p.Leu280Pro|1106|839|280|L/P|cTg/cCg|||1||EntrezGene||YES||||2:g.61145727T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:43:0:0,0:10,32:42,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:187:2:1,1:60,125:185,2:0.0107:2,2:17.5:1:37:0:0.54718:2.07:60:4:0.0108:0:1.5
    638. 

  638. 2	61145728	61145728	G	T	exonic	REL	.	synonymous SNV	REL:NM_001291746:exon7:c.G840T:p.L280L,REL:NM_002908:exon7:c.G840T:p.L280L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	183	2	61145728	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.65499;SOR=0;LSEQ=TCTATGGATTTTAGATATCT;RSEQ=CCAGATGAAAAAGGTATGAC;CSQ=T|synonymous_variant|LOW|REL|5966|Transcript|NM_001291746.2|protein_coding|7/10||NM_001291746.2:c.840G>T|NP_001278675.1:p.Leu280%3D|1107|840|280|L|ctG/ctT|||1||EntrezGene||||||2:g.61145728G>T||||||||||||||,T|synonymous_variant|LOW|REL|5966|Transcript|NM_002908.4|protein_coding|7/11||NM_002908.4:c.840G>T|NP_002899.1:p.Leu280%3D|1107|840|280|L|ctG/ctT|||1||EntrezGene||YES||||2:g.61145728G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:43:0:0,0:10,33:43,0:0:2,0:29.1:1:37:0:1:0:60:86:1:0:0	0/1:183:2:1,1:58,123:181,2:0.0109:2,2:42.5:1:37:0:0.54206:2.11:60:4:0.0109:0:1
    639. 

  639. 2	61147234	61147234	C	T	exonic	REL	.	synonymous SNV	REL:NM_001291746:exon8:c.C912T:p.C304C,REL:NM_002908:exon8:c.C912T:p.C304C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.5	31	79	2	61147234	.	C	T	31	v3;q22.5;SN1.5	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=2;AF=0.0571;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.36006;SOR=2.31407;LSEQ=CTGCTTTTCCAGAAACTGTG;RSEQ=CAGGATCACGGTAAGAATAG;CSQ=T|synonymous_variant|LOW|REL|5966|Transcript|NM_001291746.2|protein_coding|8/10||NM_001291746.2:c.912C>T|NP_001278675.1:p.Cys304%3D|1179|912|304|C|tgC/tgT|||1||EntrezGene||||||2:g.61147234C>T||||||||||||||,T|synonymous_variant|LOW|REL|5966|Transcript|NM_002908.4|protein_coding|8/11||NM_002908.4:c.912C>T|NP_002899.1:p.Cys304%3D|1179|912|304|C|tgC/tgT|||1||EntrezGene||YES||||2:g.61147234C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:35:2:1,1:15,18:33,2:0.0571:2,2:34:1:11:0:1:1.19:60:0:0:0:1	0/1:79:2:1,1:29,48:77,2:0.0253:2,2:29:1:31:1:1:1.64:60:4:0.0253:0:1
    640. 

  640. 2	61149615	61149615	G	A	exonic	REL	.	nonsynonymous SNV	REL:NM_001291746:exon10:c.G1709A:p.S570N,REL:NM_002908:exon11:c.G1805A:p.S602N	0.0023	0.0003	0.0010	0	0	0	0	0	0	rs149938178	rs149938178	0.35	0.127	T	0.0	0.026	B	0.0	0.013	B	0.901	0.073	N	1	0.090	N	-1.355	0.007	N	1.05	0.453	T	-0.19	0.127	N	0.03	0.011	-1.025	0.220	T	0.049	0.210	T	0.006	0.166	T	0.304	0.123	5.736	0.827	0.138	0.036	0.088	N	c	-1.049	-0.983	0.047	0.147	0.672	0.522	0	-0.896	0.100	0.088	0.147	0.018	0.143	0.026	0.200	0.991	0.552	4.562	0.115	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	168	2	61149615	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=72;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.48912;SOR=0;LSEQ=TCAGTATTCAGGTATTGGCA;RSEQ=TATGCAAAATGAGCAATTGA;CSQ=A|missense_variant|MODERATE|REL|5966|Transcript|NM_001291746.2|protein_coding|10/10||NM_001291746.2:c.1709G>A|NP_001278675.1:p.Ser570Asn|1976|1709|570|S/N|aGt/aAt|rs149938178||1||EntrezGene||||||2:g.61149615G>A|8.048e-05|0.001175|0|0|0|0|0|0.0001653|0|0.0023|AFR|||,A|missense_variant|MODERATE|REL|5966|Transcript|NM_002908.4|protein_coding|11/11||NM_002908.4:c.1805G>A|NP_002899.1:p.Ser602Asn|2072|1805|602|S/N|aGt/aAt|rs149938178||1||EntrezGene||YES||||2:g.61149615G>A|8.048e-05|0.001175|0|0|0|0|0|0.0001653|0|0.0023|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:72:0:0,0:23,49:72,0:0:2,0:33.2:1:36.3:1:1:0:60:144:1:0:0.1	0/1:168:2:1,1:67,99:166,2:0.0119:2,2:34:1:37:0:1:1.47:60:4:0.0127:0:1
    641. 

  641. 2	61706094	61706094	G	A	exonic	XPO1	.	nonsynonymous SNV	XPO1:NM_003400:exon25:c.C3077T:p.A1026V	.	.	.	.	.	.	.	.	.	rs865910927	.	0.103	0.301	T	0.033	0.239	B	0.009	0.133	B	0.000	0.843	D	1	0.810	D	2.045	0.562	M	-0.29	0.677	T	-2.05	0.470	N	0.733	0.746	-0.698	0.606	T	0.274	0.646	T	0.034	0.555	D	3.167	0.440	22.7	0.995	0.660	0.987	0.854	D	c	0.303	0.481	1.000	0.747	0.672	0.522	0	5.72	0.893	9.957	0.990	0.953	0.551	1.000	0.715	1.000	0.888	19.873	0.968	Armadillo-like helical|Armadillo-type fold|CRM1 C-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	2	61706094	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=108;VD=2;AF=0.0185;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.15115;SOR=inf;LSEQ=AATCAGAAGTGTCTTCACCT;RSEQ=CAAATTCCTGTGAAAACAGA;CSQ=A|missense_variant|MODERATE|XPO1|7514|Transcript|NM_003400.4|protein_coding|25/25||NM_003400.4:c.3077C>T|NP_003391.1:p.Ala1026Val|3878|3077|1026|A/V|gCa/gTa|rs865910927||-1||EntrezGene||YES||||2:g.61706094G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:108:2:1,1:35,71:106,2:0.0185:2,2:19.5:1:37:0:1:2.01:60:4:0.0189:0:1	0/0:169:0:0,0:64,105:169,0:0:2,0:38.9:1:35.2:1:1:0:60:23.143:1:0:0
    642. 

  642. 2	61708365	61708365	A	G	exonic	XPO1	.	synonymous SNV	XPO1:NM_003400:exon24:c.T3024C:p.I1008I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	79	2	61708365	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.55364;SOR=0;LSEQ=AAATGTTCCTTGAAAGCAGG;RSEQ=ATATCTTGATTTAAGCTGAA;CSQ=G|synonymous_variant|LOW|XPO1|7514|Transcript|NM_003400.4|protein_coding|24/25||NM_003400.4:c.3024T>C|NP_003391.1:p.Ile1008%3D|3825|3024|1008|I|atT/atC|rs1362926712||-1||EntrezGene||YES||||2:g.61708365A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:27:0:0,0:17,10:27,0:0:2,0:33.3:1:37:0:1:0:60:54:1:0:0	0/1:79:2:1,1:43,34:77,2:0.0253:2,2:27.5:1:37:0:1:1.26091:60:4:0.0253:0:1
    643. 

  643. 2	61709603	61709603	A	G	exonic	XPO1	.	synonymous SNV	XPO1:NM_003400:exon23:c.T2884C:p.L962L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	74	2	61709603	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=31;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.49469;SOR=0;LSEQ=AACTGGATTTCCAGGATTTA;RSEQ=TGATGTACTTATTTTTCCTT;CSQ=G|synonymous_variant|LOW|XPO1|7514|Transcript|NM_003400.4|protein_coding|23/25||NM_003400.4:c.2884T>C|NP_003391.1:p.Leu962%3D|3685|2884|962|L|Tta/Cta|||-1||EntrezGene||YES||||2:g.61709603A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:31:0:0,0:7,24:31,0:0:2,0:28.1:1:37:0:1:0:60:62:1:0:0	0/1:74:2:1,1:27,45:72,2:0.027:2,2:62:1:37:0:1:1.65:60:4:0.0278:0:1
    644. 

  644. 2	61711222	61711222	C	T	exonic	XPO1	.	nonsynonymous SNV	XPO1:NM_003400:exon21:c.G2527A:p.E843K	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.871	0.541	P	0.893	0.616	P	0.000	0.843	D	1	0.810	D	3.685	0.946	H	-0.45	0.699	T	-3.7	0.705	D	0.942	0.945	0.286	0.873	D	0.576	0.847	D	0.105	0.781	D	7.677	0.954	35	0.999	0.956	0.992	0.928	D	c	0.909	0.878	1.000	0.747	0.672	0.522	0	5.62	0.857	7.840	0.850	0.852	0.362	1.000	0.715	1.000	0.888	20.036	0.975	Armadillo-like helical|Armadillo-type fold|CRM1 C-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	154	2	61711222	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=2;AF=0.0769;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.02017;SOR=inf;LSEQ=GAAAAAGTTCGTTCTATGTT;RSEQ=AGGATATTCTTCAAAGTCCT;CSQ=T|missense_variant|MODERATE|XPO1|7514|Transcript|NM_003400.4|protein_coding|21/25||NM_003400.4:c.2527G>A|NP_003391.1:p.Glu843Lys|3328|2527|843|E/K|Gaa/Aaa|||-1||EntrezGene||YES||||2:g.61711222C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:26:2:1,1:10,14:24,2:0.0769:2,2:57:1:37:0:1:1.38:60:4:0.08:0:1	0/0:154:0:0,0:56,98:154,0:0:2,0:36.7:1:36.7:1:1:0:60:153:1:0:0
    645. 

  645. 2	61721144	61721144	G	A	exonic	XPO1	.	nonsynonymous SNV	XPO1:NM_003400:exon12:c.C1130T:p.A377V	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.039	0.197	B	0.008	0.127	B	0.000	0.843	D	1	0.810	D	0.29	0.101	N	-0.16	0.654	T	0.32	0.040	N	0.673	0.707	-0.917	0.460	T	0.133	0.445	T	0.019	0.420	T	2.356	0.344	18.53	0.910	0.197	0.995	0.972	D	c	-0.038	0.240	1.0	0.983	0.722	0.854	0	6.08	0.990	9.990	0.992	0.998	0.613	1.000	0.715	0.999	0.750	20.672	0.997	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	176	2	61721144	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=21;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.79768;SOR=0;LSEQ=TCTCTCTATAGAGTTCAGCA;RSEQ=CCAAATGATTCCAGTATTCA;CSQ=A|missense_variant|MODERATE|XPO1|7514|Transcript|NM_003400.4|protein_coding|12/25||NM_003400.4:c.1130C>T|NP_003391.1:p.Ala377Val|1931|1130|377|A/V|gCt/gTt|||-1||EntrezGene||YES||||2:g.61721144G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:21:0:0,0:8,13:21,0:0:2,0:25.8:1:36.4:1:1:0:60:42:1:0:0	0/1:176:2:1,1:77,96:173,2:0.0114:2,2:42:1:37:0:1:1.25:60:4:0.0116:0:1
    646. 

  646. 2	61722702	61722702	T	C	exonic	XPO1	.	nonsynonymous SNV	XPO1:NM_003400:exon11:c.A935G:p.K312R	.	.	.	.	.	.	.	.	.	.	.	0.138	0.258	T	0.0	0.026	B	0.0	0.013	B	0.000	0.843	D	1.000	0.524	D	-0.145	0.044	N	.	.	.	-0.67	0.193	N	0.57	0.602	-1.006	0.281	T	0.114	0.405	T	0.004	0.101	T	2.662	0.381	20.6	0.997	0.831	0.988	0.864	D	c	-0.086	0.163	1.000	0.747	0.707	0.730	0	5.77	0.910	7.981	0.876	1.011	0.635	1.000	0.715	0.998	0.697	16.085	0.808	Armadillo-like helical	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	137	2	61722702	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.88011;SOR=0;LSEQ=TGAAGTTCTGTTCATCATCT;RSEQ=TTCCATTTGAGTACGCAAGT;CSQ=C|missense_variant|MODERATE|XPO1|7514|Transcript|NM_003400.4|protein_coding|11/25||NM_003400.4:c.935A>G|NP_003391.1:p.Lys312Arg|1736|935|312|K/R|aAa/aGa|rs1287180593||-1||EntrezGene||YES||||2:g.61722702T>C|4.086e-06|0|0|0|0|0|8.932e-06|0|0|8.932e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:5,4:9,0:0:2,0:33.8:1:37:0:1:0:60:18:1:0:0	0/1:137:2:1,1:61,74:135,2:0.0146:2,2:33.5:1:37:0:1:1.21:58.5:4:0.0146:0:1
    647. 

  647. 2	61726050	61726050	-	A	splicing	XPO1	NM_003400:exon8:c.591-2->T	.	.	0.19	0.0028	0.0014	0.0019	0.0040	0.0096	0.0204	0.0007	0.0054	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29370340	BTCA-SG|3|71|0.0422535	0.25	39	30	2	61726050	.	T	TA	39	d5;v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=Insertion;DP=0;VD=0;AF=0;SHIFT3=11;MSI=12;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATTCATTGCACATGC;RSEQ=AAAAAAAAAAACACACAAAA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|XPO1|7514|Transcript|NM_003400.4|protein_coding||7/24|NM_003400.4:c.591-3dup|||||||rs372688892||-1||EntrezGene||YES||||2:g.61726061dup|0.1018|0.08901|0.1438|0.1367|0.1233|0.05566|0.08988|0.1298|0.1289|0.1438|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:30:2:1,1:4,23:27,2:0.0667:2,2:57.1:1:39.5:0:0.3202:5.25:64:4:0.069:0:0
    648. 

  648. 2	96919642	96919642	C	T	exonic	TMEM127	.	synonymous SNV	TMEM127:NM_001193304:exon4:c.G621A:p.A207A,TMEM127:NM_017849:exon4:c.G621A:p.A207A	0.28	0.1365	0.0642	0.1539	0.1556	0.0772	0.1472	0.1795	0.1622	rs3852673	rs3852673	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51497428;OCCURENCE=1(stomach),2(lung)	54989	Pheochromocytoma|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU585120	LUSC-KR|2|170|0.0117647,COCA-CN|1|321|0.00311526	0.5	357	193	2	96919642	.	C	T	357	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2139;VD=1006;AF=0.4703;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00138;SOR=0.62874;LSEQ=ATCTCTGAGAGCAGCTCCAG;RSEQ=GCCTGCTCCTCTTCCTCTGT;CSQ=T|synonymous_variant|LOW|TMEM127|55654|Transcript|NM_001193304.3|protein_coding|4/4||NM_001193304.3:c.621G>A|NP_001180233.1:p.Ala207%3D|858|621|207|A|gcG/gcA|rs3852673&COSV51497428||-1||EntrezGene||||||2:g.96919642C>T|0.1631|0.06012|0.1223|0.1748|0.07578|0.1519|0.1741|0.1936|0.2731|0.2781|SAS|benign|0&1|1&1,T|synonymous_variant|LOW|TMEM127|55654|Transcript|NM_017849.4|protein_coding|4/4||NM_017849.4:c.621G>A|NP_060319.1:p.Ala207%3D|881|621|207|A|gcG/gcA|rs3852673&COSV51497428||-1||EntrezGene||YES||||2:g.96919642C>T|0.1631|0.06012|0.1223|0.1748|0.07578|0.1519|0.1741|0.1936|0.2731|0.2781|SAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2139:1006:578,428:646,478:1124,1006:0.4703:2,2:35.9:1:35.8:1:1:1.00074:60:40.917:0.4665:0:1.1	1/0:193:113:67,46:50,30:80,113:0.5855:2,2:33.7:1:36:1:0.76502:1.14348:60:55.5:0.5873:0:1.1
    649. 

  649. 2	96919781	96919783	TGC	-	exonic	TMEM127	.	nonframeshift deletion	TMEM127:NM_001193304:exon4:c.480_482del:p.Q160del,TMEM127:NM_017849:exon4:c.480_482del:p.Q160del	0.0002	.	.	.	.	.	.	.	.	rs777748763	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU4754441	GACA-JP|1|585|0.0017094	0.5	186	284	2	96919780	.	ATGC	A	186	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=3284;VD=34;AF=0.0104;SHIFT3=11;MSI=4;MSILEN=3;SSF=0.35833;SOR=0.73238;LSEQ=TGGGATCCATGGTACTTCTT;RSEQ=TGCTGCTGCTGGGCCAAGAT;CSQ=-|inframe_deletion|MODERATE|TMEM127|55654|Transcript|NM_001193304.3|protein_coding|4/4||NM_001193304.3:c.480_482del|NP_001180233.1:p.Gln160del|717-719|480-482|160-161|QH/H|caGCAt/cat|rs777748763||-1||EntrezGene||||||2:g.96919792_96919794del|3.979e-06|0|0|0|0|4.628e-05|0|0|0|4.628e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|TMEM127|55654|Transcript|NM_017849.4|protein_coding|4/4||NM_017849.4:c.480_482del|NP_060319.1:p.Gln160del|740-742|480-482|160-161|QH/H|caGCAt/cat|rs777748763||-1||EntrezGene||YES||||2:g.96919792_96919794del|3.979e-06|0|0|0|0|4.628e-05|0|0|0|4.628e-05|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3284:34:17,17:1655,1592:3247,34:0.0104:2,2:33.2:1:36.7:1:1:1.03957:60:68:0.0105:0.0021:0.1	0/1:284:4:2,2:141,139:280,4:0.0141:2,2:37.5:1:37:0:1:1.01434:60:8:0.0142:0:0
    650. 

  650. 2	96930889	96930889	C	T	exonic	TMEM127	.	synonymous SNV	TMEM127:NM_001193304:exon2:c.G231A:p.P77P,TMEM127:NM_017849:exon2:c.G231A:p.P77P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1041737	Hereditary_Paraganglioma-Pheochromocytoma_Syndromes	MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072	criteria_provided,_single_submitter	Uncertain_significance	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	188	2	96930889	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1401;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.01393;SOR=0;LSEQ=CCCTCACCTTTCAGCAGGTC;RSEQ=GGGTGCACATAGCCCAACAC;CSQ=T|synonymous_variant|LOW|TMEM127|55654|Transcript|NM_001193304.3|protein_coding|2/4||NM_001193304.3:c.231G>A|NP_001180233.1:p.Pro77%3D|468|231|77|P|ccG/ccA|||-1||EntrezGene||||||2:g.96930889C>T||||||||||||||,T|upstream_gene_variant|MODIFIER|CIAO1|9391|Transcript|NM_004804.3|protein_coding|||||||||||1074|1||EntrezGene||YES||||2:g.96930889C>T||||||||||||||,T|synonymous_variant|LOW|TMEM127|55654|Transcript|NM_017849.4|protein_coding|2/4||NM_017849.4:c.231G>A|NP_060319.1:p.Pro77%3D|491|231|77|P|ccG/ccA|||-1||EntrezGene||YES||||2:g.96930889C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1401:0:0,0:758,640:1398,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:188:2:1,1:114,72:186,2:0.0106:2,2:36.5:1:37:0:1:1.57928:60:4:0.0107:0:1
    651. 

  651. 2	96931067	96931067	G	A	exonic	TMEM127	.	nonsynonymous SNV	TMEM127:NM_001193304:exon2:c.C53T:p.P18L,TMEM127:NM_017849:exon2:c.C53T:p.P18L	0.026	0.0006	0.0005	0	0	0.0086	0	6.681e-05	0	rs377740271	rs377740271	0.17	0.228	T	0.073	0.226	B	0.007	0.121	B	0.001	0.405	N	1.000	0.511	D	0.69	0.170	N	-1.29	0.795	T	-1.84	0.431	N	0.236	0.289	-0.693	0.608	T	0.263	0.635	T	.	.	.	3.267	0.452	22.8	0.988	0.460	0.354	0.251	N	c	-0.132	0.080	1.000	0.747	0.726	0.872	0	4.67	0.579	1.438	0.344	1.044	0.665	0.980	0.350	0.998	0.697	11.352	0.486	.	.	.	ID=COSV99302534;OCCURENCE=1(stomach)	239028	Pheochromocytoma|Hereditary_cancer-predisposing_syndrome|Hereditary_Paraganglioma-Pheochromocytoma_Syndromes	Human_Phenotype_Ontology:HP:0002666,MONDO:MONDO:0008233,MedGen:C0031511,OMIM:171300|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0017366,MedGen:C1708353,Orphanet:ORPHA29072	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	MU121209839	GACA-JP|1|585|0.0017094	0.25	254	63	2	96931067	.	G	A	254	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=335;VD=147;AF=0.4388;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGGGCAGAGCGCTGCCTCCC;RSEQ=GGCTCCTCCGCCGGCGCCCG;CSQ=A|missense_variant|MODERATE|TMEM127|55654|Transcript|NM_001193304.3|protein_coding|2/4||NM_001193304.3:c.53C>T|NP_001180233.1:p.Pro18Leu|290|53|18|P/L|cCg/cTg|rs377740271&COSV99302534||-1||EntrezGene||||||2:g.96931067G>A|0.000911|0|0|0|0.01026|0|2.162e-05|0.0005308|0.0003251|0.01026|gnomAD_EAS|likely_benign&benign|0&1|1&1,A|upstream_gene_variant|MODIFIER|CIAO1|9391|Transcript|NM_004804.3|protein_coding||||||||||rs377740271&COSV99302534|896|1||EntrezGene||YES||||2:g.96931067G>A|0.000911|0|0|0|0.01026|0|2.162e-05|0.0005308|0.0003251|0.01026|gnomAD_EAS|likely_benign&benign|0&1|1&1,A|missense_variant|MODERATE|TMEM127|55654|Transcript|NM_017849.4|protein_coding|2/4||NM_017849.4:c.53C>T|NP_060319.1:p.Pro18Leu|313|53|18|P/L|cCg/cTg|rs377740271&COSV99302534||-1||EntrezGene||YES||||2:g.96931067G>A|0.000911|0|0|0|0.01026|0|2.162e-05|0.0005308|0.0003251|0.01026|gnomAD_EAS|likely_benign&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:335:147:37,110:51,136:187,147:0.4388:2,2:32.6:1:35.3:1:0.7083:1.1145:60:28.4:0.4316:0:1.1	0/0:63:0:0,0:10,53:63,0:0:2,0:38.7:1:36.6:1:1:0:60:62:1:0:0
    652. 

  652. 2	96931124	96931124	G	T	UTR5	TMEM127	NM_017849:c.-5C>A;NM_001193304:c.-5C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	41	2	96931124	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=2;AF=0.0148;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.58734;SOR=inf;LSEQ=CTCCGGGGGCGTACATGCCC;RSEQ=GGGCCGCCCGCCGTCGCTCC;CSQ=T|5_prime_UTR_variant|MODIFIER|TMEM127|55654|Transcript|NM_001193304.3|protein_coding|2/4||NM_001193304.3:c.-5C>A||233|||||||-1||EntrezGene||||||2:g.96931124G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|CIAO1|9391|Transcript|NM_004804.3|protein_coding|||||||||||839|1||EntrezGene||YES||||2:g.96931124G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|TMEM127|55654|Transcript|NM_017849.4|protein_coding|2/4||NM_017849.4:c.-5C>A||256|||||||-1||EntrezGene||YES||||2:g.96931124G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:135:2:1,1:23,110:133,2:0.0148:2,2:66.5:1:37:0:0.32504:4.7:60:4:0.0148:0:1	0/0:41:0:0,0:3,38:41,0:0:2,0:30.7:1:36.4:1:1:0:60:82:1:0:0
    653. 

  653. 2	99172244	99172244	A	G	exonic	INPP4A	.	nonsynonymous SNV	INPP4A:NM_001134225:exon16:c.A1795G:p.T599A,INPP4A:NM_001134224:exon17:c.A1810G:p.T604A	0.42	0.2493	0.2557	0.2983	0.2914	0.3160	0.1966	0.2477	0.2418	rs2278206	rs2278206	0.658	0.047	T	0.0	0.026	B	0.0	0.013	B	0.110	0.194	N	1	0.414	P	-0.345	0.033	N	2.4	0.156	T	0.08	0.060	N	0.021	0.014	-0.910	0.468	T	0.000	0.000	T	.	.	.	-0.484	0.056	0.241	0.307	0.017	0.036	0.088	N	c	-1.250	-1.130	0.998	0.360	0.722	0.854	0	2.4	0.284	-0.004	0.127	-1.427	0.011	0.002	0.151	0.578	0.284	1.352	0.020	.	ENSG00000040933.11|ENSG00000040933.11|ENSG00000040933.11|ENSG00000115446.7|ENSG00000040933.11|ENSG00000115446.7	Adipose_Subcutaneous|Adipose_Visceral_Omentum|Cells_Transformed_fibroblasts|Liver|Nerve_Tibial|Testis	ID=COSV50818983;OCCURENCE=1(skin)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU19580158	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,COCA-CN|2|321|0.00623053	0.25	58	0	2	99172244	.	A	G	58	d5	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=3;AF=0.75;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTCCACCATGCCCTCC;RSEQ=CTGCATGCCATCCTCATCTG;CSQ=G|missense_variant|MODERATE|INPP4A|3631|Transcript|NM_001134224.2|protein_coding|17/26||NM_001134224.2:c.1810A>G|NP_001127696.1:p.Thr604Ala|2203|1810|604|T/A|Act/Gct|rs2278206&CM084964&COSV50818983||1||EntrezGene||YES||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|missense_variant|MODERATE|INPP4A|3631|Transcript|NM_001134225.2|protein_coding|16/25||NM_001134225.2:c.1795A>G|NP_001127697.1:p.Thr599Ala|2188|1795|599|T/A|Act/Gct|rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351424.1|protein_coding||17/25|NM_001351424.1:c.1723+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351425.2|protein_coding||17/25|NM_001351425.2:c.1723+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351426.2|protein_coding||17/25|NM_001351426.2:c.1723+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351427.2|protein_coding||17/25|NM_001351427.2:c.1720+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351428.2|protein_coding||16/24|NM_001351428.2:c.1705+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001351429.2|protein_coding||16/23|NM_001351429.2:c.1705+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_001566.2|protein_coding||17/25|NM_001566.2:c.1720+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1,G|intron_variant|MODIFIER|INPP4A|3631|Transcript|NM_004027.3|protein_coding||17/25|NM_004027.3:c.1720+90A>G|||||||rs2278206&CM084964&COSV50818983||1||EntrezGene||||||2:g.99172244A>G|0.2664|0.2539|0.2998|0.3257|0.3049|0.2052|0.2507|0.2936|0.2818|0.3257|gnomAD_ASJ||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:3:1,2:1,0:1,3:0.75:0,2:57.3:1:37:0:1:0:60:6:0.75:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    654. 

  654. 2	99193496	99193496	C	T	exonic	INPP4A	.	synonymous SNV	INPP4A:NM_001351429:exon23:c.C2526T:p.S842S,INPP4A:NM_001134225:exon24:c.C2676T:p.S892S,INPP4A:NM_001351428:exon24:c.C2559T:p.S853S,INPP4A:NM_001134224:exon25:c.C2691T:p.S897S,INPP4A:NM_001351424:exon25:c.C2577T:p.S859S,INPP4A:NM_001351425:exon25:c.C2577T:p.S859S,INPP4A:NM_001351426:exon25:c.C2577T:p.S859S,INPP4A:NM_001351427:exon25:c.C2574T:p.S858S,INPP4A:NM_001566:exon25:c.C2574T:p.S858S,INPP4A:NM_004027:exon25:c.C2574T:p.S858S	0.31	0.2294	0.1729	0.2854	0.2933	0.3079	0.2106	0.2530	0.2418	rs2230388	rs2230388	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV50785142;OCCURENCE=1(breast),1(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4557178	ESAD-UK|2|409|0.00488998,LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053,PBCA-DE|1|499|0.00200401	0.5	37	0	2	99193496	.	C	T	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTTCACCAGCTGCAAGAG;RSEQ=GCTAAGGACCGTACAGCCAT;CSQ=T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001134224.2|protein_coding|25/26||NM_001134224.2:c.2691C>T|NP_001127696.1:p.Ser897%3D|3084|2691|897|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||YES||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001134225.2|protein_coding|24/25||NM_001134225.2:c.2676C>T|NP_001127697.1:p.Ser892%3D|3069|2676|892|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351424.1|protein_coding|25/26||NM_001351424.1:c.2577C>T|NP_001338353.1:p.Ser859%3D|2811|2577|859|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351425.2|protein_coding|25/26||NM_001351425.2:c.2577C>T|NP_001338354.1:p.Ser859%3D|2970|2577|859|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351426.2|protein_coding|25/26||NM_001351426.2:c.2577C>T|NP_001338355.1:p.Ser859%3D|2883|2577|859|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351427.2|protein_coding|25/26||NM_001351427.2:c.2574C>T|NP_001338356.1:p.Ser858%3D|2880|2574|858|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351428.2|protein_coding|24/25||NM_001351428.2:c.2559C>T|NP_001338357.1:p.Ser853%3D|2865|2559|853|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001351429.2|protein_coding|23/24||NM_001351429.2:c.2526C>T|NP_001338358.1:p.Ser842%3D|2832|2526|842|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_001566.2|protein_coding|25/26||NM_001566.2:c.2574C>T|NP_001557.1:p.Ser858%3D|2967|2574|858|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1,T|synonymous_variant|LOW|INPP4A|3631|Transcript|NM_004027.3|protein_coding|25/26||NM_004027.3:c.2574C>T|NP_004018.1:p.Ser858%3D|2967|2574|858|S|agC/agT|rs2230388&COSV50785142||1||EntrezGene||||||2:g.99193496C>T|0.2599|0.1707|0.2949|0.3212|0.2927|0.2147|0.2536|0.2843|0.2758|0.3212|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:51.5:1:37:0:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    655. 

  655. 2	109347326	109347326	C	A	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon3:c.C237A:p.A79A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	132	2	109347326	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.92808;SOR=0;LSEQ=GAAGAAAACACAGACAAAGC;RSEQ=GTTGAATGTTACAGGGTAAG;CSQ=A|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|3/29||NM_006267.5:c.237C>A|NP_006258.3:p.Ala79%3D|362|237|79|A|gcC/gcA|||1||EntrezGene||YES||||2:g.109347326C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:2,3:5,0:0:2,0:55.2:1:37:0:1:0:57:10:1:0:0	0/1:132:2:1,1:56,74:130,2:0.0152:2,2:23:1:37:0:1:1.32:52.5:4:0.0152:0:2
    656. 

  656. 2	109352037	109352037	A	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon5:c.A455T:p.D152V	.	.	.	.	.	.	.	.	.	.	.	0.005	0.632	D	1.0	0.899	D	0.998	0.875	D	.	.	.	1.000	0.588	D	2.71	0.795	M	1.44	0.327	T	-5.75	0.877	D	0.825	0.813	-0.835	0.530	T	0.165	0.503	T	0.064	0.693	D	3.830	0.517	23.4	0.994	0.620	0.986	0.845	D	c	0.718	0.701	1.000	0.747	0.732	0.924	0	4.98	0.655	8.557	0.904	1.177	0.903	1.000	0.715	1.000	0.888	14.962	0.707	Tetratricopeptide-like helical domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	279	2	109352037	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=99;VD=2;AF=0.0202;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06808;SOR=inf;LSEQ=TGGATGGAATAAACTTTTTG;RSEQ=CTTGATTCAGTCAGAACTTT;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|5/29||NM_006267.5:c.455A>T|NP_006258.3:p.Asp152Val|580|455|152|D/V|gAc/gTc|||1||EntrezGene||YES||||2:g.109352037A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:99:2:2,0:69,27:96,2:0.0202:2,0:18.5:1:37:0:1:0:45:4:0.0206:0:1	0/0:279:0:0,0:167,112:279,0:0:2,0:38.6:1:35.9:1:1:0:36.9:45.5:1:0:0.1
    657. 

  657. 2	109365364	109365364	T	-	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	76	2	109365363	.	AT	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=65;VD=2;AF=0.0308;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.21074;SOR=inf;LSEQ=AAGTGATGGAAATAACTTAA;RSEQ=TTTTTTTTCAGGGCACATGT;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding||8/28|NM_006267.5:c.1064-4del|||||||||1||EntrezGene||YES||||2:g.109365372del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:65:2:1,1:44,19:63,2:0.0308:2,2:14:0:37:0:0.52404:2.28269:60:4:0.0308:0:0	0/0:76:0:0,0:55,21:76,0:0:2,0:35.5:1:36.4:1:1:0:59.2:152:1:0:0.1
    658. 

  658. 2	109365442	109365442	C	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon9:c.C1130T:p.A377V	0.0002	.	.	.	.	.	.	.	.	rs747201977	.	0.027	0.465	D	0.999	0.764	D	0.994	0.807	D	.	.	.	0.916	0.365	D	2.005	0.547	M	1.42	0.332	T	-2.64	0.566	D	0.722	0.722	-0.750	0.579	T	0.189	0.540	T	0.029	0.517	D	3.839	0.518	23.4	0.999	0.949	0.930	0.568	D	c	0.650	0.613	1.000	0.747	0.732	0.924	0	5.53	0.825	4.453	0.596	0.931	0.441	1.000	0.715	0.979	0.486	19.814	0.965	.	.	.	ID=COSV51696475;OCCURENCE=1(thyroid),1(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU1951365	UCEC-US|1|531|0.00188324	0.25	37	153	2	109365442	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=165;VD=2;AF=0.0121;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.26844;SOR=inf;LSEQ=AGAGATTGTTGAAACTTTTG;RSEQ=CAACAAAAGCGGGCAGTCTG;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|9/29||NM_006267.5:c.1130C>T|NP_006258.3:p.Ala377Val|1255|1130|377|A/V|gCc/gTc|rs747201977&COSV51696475||1||EntrezGene||YES||||2:g.109365442C>T|3.983e-06|0|0|0|0|4.619e-05|0|0|0|4.619e-05|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:165:2:1,1:90,73:163,2:0.0121:2,2:39.5:1:37:0:1:1.2313:60:4:0.0127:0:1	0/0:153:0:0,0:89,64:153,0:0:2,0:35.6:1:35.5:1:1:0:57.7:306:1:0:0.1
    659. 

  659. 2	109365456	109365456	C	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon9:c.C1144A:p.Q382K	.	.	.	.	.	.	.	.	.	.	.	0.338	0.128	T	0.842	0.446	P	0.237	0.368	B	.	.	.	1.000	0.253	N	2.005	0.547	M	1.61	0.284	T	-1.3	0.326	N	0.774	0.766	-1.028	0.212	T	0.067	0.276	T	0.008	0.218	T	0.949	0.185	10.37	0.980	0.371	0.925	0.555	D	c	0.305	0.390	0.999	0.392	0.732	0.924	0	5.53	0.825	4.526	0.600	0.931	0.441	1.000	0.715	0.998	0.697	13.547	0.610	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	162	2	109365456	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=194;VD=2;AF=0.0103;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.29627;SOR=inf;LSEQ=CTTTTGCCAACAAAAGCGGG;RSEQ=AGTCTGCATTATATGATGCT;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|9/29||NM_006267.5:c.1144C>A|NP_006258.3:p.Gln382Lys|1269|1144|382|Q/K|Cag/Aag|||1||EntrezGene||YES||||2:g.109365456C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:194:2:1,1:102,90:192,2:0.0103:2,2:39:1:37:0:1:1.1326:60:4:0.0104:0:1	0/0:162:0:0,0:90,72:162,0:0:2,0:35.5:1:36.6:1:1:0:57:161:1:0:0.2
    660. 

  660. 2	109365467	109365467	A	G	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon9:c.A1155G:p.L385L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	164	2	109365467	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.20343;SOR=0;LSEQ=AAAAGCGGGCAGTCTGCATT;RSEQ=TATGATGCTCTGTTTTCTAG;CSQ=G|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|9/29||NM_006267.5:c.1155A>G|NP_006258.3:p.Leu385%3D|1280|1155|385|L|ttA/ttG|||1||EntrezGene||YES||||2:g.109365467A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:199:0:0,0:105,94:199,0:0:2,0:33.5:1:36:1:1:0:53.1:48.75:1:0:0.1	0/1:164:2:1,1:88,74:162,2:0.0122:2,2:36.5:1:37:0:1:1.18792:60:4:0.0127:0:1
    661. 

  661. 2	109365535	109365535	A	G	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon9:c.A1223G:p.N408S	.	.	.	.	.	.	.	.	.	.	.	0.327	0.132	T	0.008	0.135	B	0.003	0.080	B	.	.	.	1.000	0.240	N	0.785	0.196	N	-1.68	0.829	D	-1.73	0.410	N	0.017	0.007	-0.795	0.555	T	0.315	0.685	T	0.022	0.448	T	-0.043	0.090	2.195	0.974	0.335	0.605	0.310	D	c	-0.509	-0.365	0.795	0.241	0.732	0.924	0	3.14	0.350	1.543	0.355	1.193	0.911	0.834	0.299	0.992	0.562	9.956	0.406	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	156	2	109365535	.	A	G	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=156;VD=2;AF=0.0128;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.2492;SOR=inf;LSEQ=TGGTAGCGATGATATTGGAA;RSEQ=CATTGATGTACGAGAACCAG;CSQ=G|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|9/29||NM_006267.5:c.1223A>G|NP_006258.3:p.Asn408Ser|1348|1223|408|N/S|aAc/aGc|||1||EntrezGene||YES||||2:g.109365535A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:156:2:1,1:70,84:154,2:0.0128:2,2:58:1:31:1:1:1.2:60:4:0.0132:0:1	0/0:156:0:0,0:66,90:156,0:0:2,0:40.4:1:36.2:1:1:0:54.3:77:1:0:0.2
    662. 

  662. 2	109367705	109367705	T	C	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	85	2	109367705	.	T	C	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=2;AF=0.0357;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.15603;SOR=inf;LSEQ=CAAACCCTTAAGCCAATTTT;RSEQ=TAATTTTATTTCAGGTGCTA;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding||9/28|NM_006267.5:c.1274-15T>C|||||||||1||EntrezGene||YES||||2:g.109367705T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:56:2:1,1:43,11:54,2:0.0357:2,2:33.5:1:25:0:0.38571:3.78594:46:4:0.0357:0:1	0/0:85:0:0,0:64,21:85,0:0:2,0:38.8:1:35.7:1:1:0:47:84:1:0:0
    663. 

  663. 2	109367754	109367754	C	T	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon10:c.C1308T:p.H436H	0.001	.	.	.	.	.	.	.	.	rs2912843	rs2912843	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51708452;OCCURENCE=1(liver)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	MU113223402	LICA-FR|1|252|0.00396825	0.25	74	141	2	109367754	.	C	T	74	p8	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=155;VD=4;AF=0.0258;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.21635;SOR=3.69424;LSEQ=CATAATGGTAGTCTTCAGCA;RSEQ=CTTACTTGGCTTGGCTTACA;CSQ=T|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1308C>T|NP_006258.3:p.His436%3D|1433|1308|436|H|caC/caT|rs2912843&COSV51708452||1||EntrezGene||YES||||2:g.109367754C>T|1.613e-05|0|0|0|5.443e-05|0|2.676e-05|0|0|0.001|EUR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:155:4:2,2:80,71:151,4:0.0258:2,2:5.5:1:37:0:1:1.12589:19.5:8:0.026:0:1.2	0/0:141:1:1,0:90,49:139,1:0.0071:2,0:28:0:37:0:1:0:0:2:0.0074:0:1
    664. 

  664. 2	109367788	109367788	C	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon10:c.C1342A:p.P448T	.	.	.	.	.	.	.	.	.	.	.	0.044	0.410	D	0.049	0.208	B	0.024	0.190	B	.	.	.	1	0.090	N	2.08	0.576	M	1.05	0.400	T	-1.3	0.326	N	0.159	0.191	-1.026	0.216	T	0.071	0.290	T	0.012	0.300	T	0.800	0.170	9.463	0.995	0.690	0.435	0.269	N	c	-0.449	-0.354	0.256	0.187	0.732	0.924	0	0.567	0.164	0.578	0.233	-0.178	0.104	0.909	0.314	0.968	0.456	5.502	0.160	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	163	2	109367788	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=179;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.22642;SOR=0;LSEQ=GCTTACAGTGGAATTCATTG;RSEQ=CTGCTTTACCTGGAATCCGA;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1342C>A|NP_006258.3:p.Pro448Thr|1467|1342|448|P/T|Cct/Act|||1||EntrezGene||YES||||2:g.109367788C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:179:0:0,0:88,91:179,0:0:2,0:43.3:1:36.4:1:1:0:39.3:88.5:1:0:0.1	0/1:163:2:1,1:90,71:161,2:0.0123:2,2:31:0:37:0:1:1.26574:45:4:0.0125:0:1
    665. 

  665. 2	109367827	109367827	T	C	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon10:c.T1381C:p.F461L	.	.	.	.	.	.	.	.	.	.	.	0.017	0.512	D	0.997	0.689	D	0.985	0.749	D	.	.	.	0.943	0.374	D	2.72	0.798	M	0.87	0.464	T	-4.38	0.771	D	0.772	0.764	-0.601	0.648	T	0.238	0.606	T	0.018	0.401	T	3.622	0.493	23.2	0.997	0.780	0.980	0.783	D	c	0.713	0.690	1.000	0.747	0.732	0.924	0	5.15	0.702	7.305	0.780	1.051	0.754	1.000	0.715	0.997	0.653	15.252	0.731	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	25	174	2	109367827	.	T	C	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=161;VD=2;AF=0.0124;SHIFT3=2;MSI=4;MSILEN=1;SSF=0.23023;SOR=inf;LSEQ=GAAAATGGCTAAAACAGCTT;RSEQ=TCCATCATTTGCCCCATGAA;CSQ=C|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1381T>C|NP_006258.3:p.Phe461Leu|1506|1381|461|F/L|Ttc/Ctc|||1||EntrezGene||YES||||2:g.109367827T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:161:2:1,1:71,88:159,2:0.0124:2,2:31:1:25:0:1:1.24:44:4:0.0127:0:1	0/0:174:0:0,0:89,84:173,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    666. 

  666. 2	109367841	109367841	C	T	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon10:c.C1395T:p.P465P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	172	2	109367841	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=140;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.30312;SOR=0;LSEQ=CAGCTTTTCCATCATTTGCC;RSEQ=CATGAAACCTCAAGGCTTGA;CSQ=T|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1395C>T|NP_006258.3:p.Pro465%3D|1520|1395|465|P|ccC/ccT|||1||EntrezGene||YES||||2:g.109367841C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:140:0:0,0:58,82:140,0:0:2,0:33.2:1:36.4:1:1:0:43:69:1:0:0.1	0/1:172:2:1,1:85,85:170,2:0.0116:2,2:30:1:37:0:1:1:45:4:0.0119:0:1
    667. 

  667. 2	109367844	109367844	T	G	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon10:c.T1398G:p.H466Q	0.0006	6.475e-05	0	0	0	0.0006	0	6.7e-05	0	rs746894026	rs2693126	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	.	.	.	0.998	0.226	N	-2.19	0.001	N	-1.62	0.824	D	1.81	0.005	N	0.145	0.171	-0.887	0.492	T	0.125	0.430	T	0.041	0.598	D	0.037	0.097	2.951	0.599	0.062	0.129	0.173	N	c	-0.942	-0.648	0.951	0.279	0.732	0.924	0	2.44	0.287	2.412	0.440	0.129	0.215	1.000	0.715	0.999	0.750	5.496	0.160	.	.	.	ID=COSV51696167;OCCURENCE=3(endometrium)	516283	Encephalopathy,_acute,_infection-induced,_3,_suceptibility_to	MONDO:MONDO:0011953,MedGen:C2675556,OMIM:608033,Orphanet:ORPHA88619	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	174	2	109367844	.	T	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=131;VD=2;AF=0.0153;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.18367;SOR=inf;LSEQ=CTTTTCCATCATTTGCCCCA;RSEQ=GAAACCTCAAGGCTTGAAAC;CSQ=G|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1398T>G|NP_006258.3:p.His466Gln|1523|1398|466|H/Q|caT/caG|rs746894026&COSV51696167||1||EntrezGene||YES||||2:g.109367844T>G|9.59e-05|6.324e-05|0.0001157|0|0.0003809|0|8.841e-05|0.0003286|0|0.0003809|gnomAD_EAS|uncertain_significance|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:131:2:0,2:53,76:129,2:0.0153:2,0:16:1:37:0:0.5145:0:12.5:4:0.0154:0:1	0/0:174:0:0,0:85,89:174,0:0:2,0:37.3:1:35.9:1:1:0:46:173:1:0:0.1
    668. 

  668. 2	109367851	109367851	T	C	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon10:c.T1405C:p.S469P	.	.	.	.	.	.	.	.	.	.	.	0.107	0.295	T	0.999	0.764	D	0.996	0.832	D	.	.	.	0.970	0.388	D	2.695	0.791	M	-1.88	0.845	D	-3.58	0.691	D	0.762	0.756	0.607	0.920	D	0.717	0.903	D	0.108	0.785	D	3.463	0.474	23.0	0.998	0.872	0.972	0.733	D	c	0.700	0.676	1.000	0.747	0.732	0.924	0	5.25	0.731	5.597	0.670	1.051	0.754	1.000	0.715	0.999	0.750	15.450	0.749	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	176	2	109367851	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=124;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.34337;SOR=0;LSEQ=ATCATTTGCCCCATGAAACC;RSEQ=CAAGGCTTGAAACAAATGCA;CSQ=C|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1405T>C|NP_006258.3:p.Ser469Pro|1530|1405|469|S/P|Tca/Cca|||1||EntrezGene||YES||||2:g.109367851T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:124:0:0,0:48,76:124,0:0:2,0:29.8:1:35.6:1:1:0:45:30:1:0:0.1	0/1:176:2:1,1:82,92:174,2:0.0114:2,2:64.5:1:37:0:1:1.12:44:4:0.0117:0:1
    669. 

  669. 2	109367871	109367871	A	G	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon10:c.A1425G:p.A475A	0.0003	3.241e-05	0	0	0	0	0	6.69e-05	0	rs745596658	rs2949978	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51696038;OCCURENCE=1(breast),1(liver),1(meninges),2(prostate)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU83764132	LICA-CN|1|402|0.00248756,PRAD-FR|2|25|0.08	0.25	37	144	2	109367871	.	A	G	37	v3;pSTD	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.29066;SOR=3.64426;LSEQ=TCAAGGCTTGAAACAAATGC;RSEQ=CCTGAATCAATATGTATTTT;CSQ=G|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|10/29||NM_006267.5:c.1425A>G|NP_006258.3:p.Ala475%3D|1550|1425|475|A|gcA/gcG|rs745596658&COSV51696038||1||EntrezGene||YES||||2:g.109367871A>G|6.415e-05|0.0001298|2.899e-05|0|0.0005984|0|1.773e-05|0|0|0.0005984|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:27,51:78,2:0.025:2,2:12:0:37:0:1:1.87:44:4:0.025:0:1	0/0:144:1:0,1:62,81:143,1:0.0069:2,0:59:0:37:0:1:0:0:2:0.007:0:1
    670. 

  670. 2	109368129	109368129	C	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon11:c.C1601T:p.A534V	0.0001	.	.	.	.	.	.	.	.	rs763321558	.	0.006	0.614	D	1.0	0.899	D	0.996	0.832	D	.	.	.	0.860	0.431	D	2.72	0.798	M	0.53	0.551	T	-3.18	0.644	D	0.601	0.626	-0.439	0.708	T	0.350	0.714	T	0.022	0.446	T	4.781	0.641	24.7	0.999	0.992	0.979	0.775	D	c	0.774	0.749	1.000	0.747	0.732	0.924	0	5.25	0.731	7.008	0.759	0.927	0.437	1.000	0.715	0.998	0.697	19.212	0.937	.	.	.	.	628378	Encephalopathy,_acute,_infection-induced,_3,_suceptibility_to	MONDO:MONDO:0011953,MedGen:C2675556,OMIM:608033,Orphanet:ORPHA88619	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129570176	UCEC-US|1|531|0.00188324	0.25	37	155	2	109368129	.	C	T	37	v3;Q0	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=87;VD=2;AF=0.023;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.29399;SOR=3.60328;LSEQ=ACAAAAATCTTGGTGGGATG;RSEQ=GGTTTGTACTCTGATTCACA;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|11/29||NM_006267.5:c.1601C>T|NP_006258.3:p.Ala534Val|1726|1601|534|A/V|gCg/gTg|rs763321558||1||EntrezGene||YES||||2:g.109368129C>T|2.509e-05|0|0|0|0|0|5.57e-05|0|0|5.57e-05|gnomAD_NFE|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:87:2:1,1:41,43:84,2:0.023:2,2:37.5:1:37:0:1:1.05:0:4:0.0238:0:1	0/0:155:1:1,0:60,93:153,1:0.0065:2,0:67:0:37:0:0.3961:0:40:2:0.0066:0:1
    671. 

  671. 2	109368130	109368130	G	A	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon11:c.G1602A:p.A534A	0.0001	6.496e-05	0	0	0	0	0	0.0001	0	rs764385067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	987863	Encephalopathy,_acute,_infection-induced,_3,_suceptibility_to	MONDO:MONDO:0011953,MedGen:C2675556,OMIM:608033,Orphanet:ORPHA88619	criteria_provided,_single_submitter	Uncertain_significance	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	153	2	109368130	.	G	A	37	v3;Q0	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=87;VD=2;AF=0.023;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.13044;SOR=inf;LSEQ=CAAAAATCTTGGTGGGATGC;RSEQ=GTTTGTACTCTGATTCACAG;CSQ=A|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|11/29||NM_006267.5:c.1602G>A|NP_006258.3:p.Ala534%3D|1727|1602|534|A|gcG/gcA|rs764385067||1||EntrezGene||YES||||2:g.109368130G>A|4.589e-05|0|3.004e-05|0|0|0|9.264e-05|0|0|9.264e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:87:2:1,1:41,44:85,2:0.023:2,2:44.5:1:37:0:1:1.07:0:4:0.0233:0:1	0/0:153:0:0,0:63,90:153,0:0:2,0:36.9:1:35.5:1:1:0:22.9:37.25:1:0:0.1
    672. 

  672. 2	109368145	109368145	T	A	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon11:c.T1617A:p.I539I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	140	2	109368145	.	T	A	37	v3;Q0	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.13117;SOR=inf;LSEQ=GATGCGGTTTGTACTCTGAT;RSEQ=CACAGAAAAGCAGTGTAAGT;CSQ=A|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|11/29||NM_006267.5:c.1617T>A|NP_006258.3:p.Ile539%3D|1742|1617|539|I|atT/atA|||1||EntrezGene||YES||||2:g.109368145T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:37,41:78,2:0.025:2,2:13:1:37:0:1:1.11:0:4:0.025:0:1	0/0:140:0:0,0:53,87:140,0:0:2,0:36.7:1:36.7:1:1:0:24.9:280:1:0:0.1
    673. 

  673. 2	109368155	109368155	G	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon11:c.G1627T:p.A543S	.	.	.	.	.	.	.	.	.	.	.	0.836	0.028	T	0.045	0.204	B	0.007	0.121	B	.	.	.	0.999	0.254	N	1.935	0.520	L	-1.71	0.832	D	-0.46	0.150	N	0.236	0.289	-0.819	0.540	T	0.320	0.689	T	0.012	0.312	T	1.068	0.197	11.04	0.995	0.681	0.922	0.549	D	c	-0.299	-0.121	0.918	0.265	0.732	0.924	0	4.59	0.561	2.560	0.453	0.128	0.215	1.000	0.715	0.589	0.286	6.144	0.194	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	127	2	109368155	.	G	T	37	v3;Q0	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=2;AF=0.0282;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12742;SOR=inf;LSEQ=GTACTCTGATTCACAGAAAA;RSEQ=CAGTGTAAGTAGTAAAACAA;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|11/29||NM_006267.5:c.1627G>T|NP_006258.3:p.Ala543Ser|1752|1627|543|A/S|Gca/Tca|||1||EntrezGene||YES||||2:g.109368155G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:71:2:1,1:31,38:69,2:0.0282:2,2:55:1:37:0:1:1.22:0:4:0.0282:0:1	0/0:127:0:0,0:47,80:127,0:0:2,0:56:0:11:0:1:0:42:0:0:0:1
    674. 

  674. 2	109368324	109368324	T	C	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	138	2	109368324	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.65036;SOR=0;LSEQ=TAGTAAATTGAACTATTTTT;RSEQ=AGACCTGGAAACGTAGCAAA;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding||11/28|NM_006267.5:c.1632-3T>C|||||||||1||EntrezGene||YES||||2:g.109368324T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:33:0:0,0:19,14:33,0:0:2,0:37.5:1:36.2:1:1:0:60:32:1:0:0	0/1:138:2:1,1:78,58:136,2:0.0145:2,2:62:1:31:1:1:1.34189:60:4:0.0147:0:1
    675. 

  675. 2	109368344	109368344	A	G	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon12:c.A1649G:p.K550R	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	0.996	0.670	D	0.877	0.604	P	.	.	.	0.685	0.333	D	2.695	0.791	M	0.45	0.565	T	-1.89	0.441	N	0.589	0.617	-0.221	0.771	T	0.287	0.659	T	0.013	0.330	T	3.497	0.478	23.1	0.998	0.885	0.956	0.652	D	c	0.665	0.655	1.000	0.747	0.732	0.924	0	5.32	0.753	5.938	0.697	1.187	0.908	1.000	0.715	1.000	0.888	15.562	0.759	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	2	109368344	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=38;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.6458;SOR=0;LSEQ=TAGACCTGGAAACGTAGCAA;RSEQ=ATTGAGACTTCTAGTTCAGC;CSQ=G|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|12/29||NM_006267.5:c.1649A>G|NP_006258.3:p.Lys550Arg|1774|1649|550|K/R|aAa/aGa|||1||EntrezGene||YES||||2:g.109368344A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:38:0:0,0:21,17:38,0:0:2,0:38.7:1:34.7:1:1:0:60:18:1:0:0	0/1:156:2:1,1:81,73:154,2:0.0128:2,2:48:1:37:0:1:1.10885:60:4:0.0131:0:1
    676. 

  676. 2	109368445	109368445	A	-	exonic	RANBP2	.	frameshift deletion	RANBP2:NM_006267:exon12:c.1750delA:p.T585Rfs*15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	130	2	109368444	.	GA	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=34;VD=2;AF=0.0588;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.04197;SOR=inf;LSEQ=CATTGGGCAGAATGCCTTCA;RSEQ=AAACGGTGAGTTTTAAAGTA;CSQ=-|frameshift_variant|HIGH|RANBP2|5903|Transcript|NM_006267.5|protein_coding|12/29||NM_006267.5:c.1753del|NP_006258.3:p.Thr585ArgfsTer15|1875|1750|584|K/X|Aaa/aa|||1||EntrezGene||YES|||3|2:g.109368448del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:2:1,1:10,22:32,2:0.0588:2,2:39:0:37:0:1:2.14:60:4:0.0588:0:0	0/0:130:0:0,0:43,87:130,0:0:2,0:36.8:1:36.2:1:1:0:59.9:42.333:1:0:0.1
    677. 

  677. 2	109370032	109370032	A	T	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	71	2	109370032	.	A	T	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.92003;SOR=0;LSEQ=TTGCACTGGTAAGTAGATGC;RSEQ=GTACTTGAGCTAAAAGTTTT;CSQ=T|intron_variant|MODIFIER|RANBP2|5903|Transcript|NM_006267.5|protein_coding||14/28|NM_006267.5:c.2055+13A>T|||||||||1||EntrezGene||YES||||2:g.109370032A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:2,1:3,0:0:2,0:48.3:1:37:0:1:0:56:6:1:0:0	0/1:71:2:1,1:18,51:69,2:0.0282:2,2:34.5:1:37:0:0.4664:2.78:60:4:0.0282:0:1
    678. 

  678. 2	109371471	109371471	A	G	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon16:c.A2313G:p.A771A	0.16	.	.	.	.	.	.	.	.	rs76482726	rs201686966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51697993;OCCURENCE=2(liver),2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	MU44465532	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805	0.5	74	166	2	109371471	.	A	G	74	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=4;AF=0.1429;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01637;SOR=6.64016;LSEQ=AATGGTTCTTTGCGAAATGC;RSEQ=GATTCAGAAATAAAACATTC;CSQ=G|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|16/29||NM_006267.5:c.2313A>G|NP_006258.3:p.Ala771%3D|2438|2313|771|A|gcA/gcG|rs76482726&COSV51697993||1||EntrezGene||YES||||2:g.109371471A>G|0.001856|0.001582|0.0007345|0|0.02296|0.0002328|0.000231|0.0004985|9.917e-05|0.02296|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:28:4:2,2:10,14:24,4:0.1429:2,2:48.8:1:37:0:1:1.38:31.5:8:0.1429:0:1.5	0/1:166:4:2,2:74,88:162,4:0.0241:2,2:58.8:1:37:0:1:1.19:11.5:8:0.0242:0:1.8
    679. 

  679. 2	109371620	109371620	-	T	intronic	RANBP2	.	.	.	0.012	0.0053	0.0183	0	0	0	0	6.72e-05	0.0010	rs542446071	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	39	80	2	109371620	.	A	AT	39	v3;pSTD	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=49;VD=2;AF=0.0408;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.3219;SOR=3.32915;LSEQ=AATGCTGTTTTGTTATTTTT;RSEQ=TTTTTTTTTAGTATTCTCCC;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding||16/28|NM_006267.5:c.2383-3dup|||||||rs542446071||1||EntrezGene||YES||||2:g.109371629dup|0.000585|0.008437|0.0002925|0|5.491e-05|0|3.556e-05|0.0003324|0|0.0121|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:49:2:1,1:30,16:46,2:0.0408:2,2:39:0:39:0:1:1.84915:63.2:4:0.0435:0:0	0/1:80:1:1,0:38,37:75,1:0.0125:2,0:12.6:0:39:0:1:0:54.8:2:0.0137:0:0
    680. 

  680. 2	109371693	109371693	G	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon17:c.G2444A:p.C815Y	.	.	.	.	.	.	.	.	.	.	.	0.013	0.538	D	1.0	0.899	D	0.997	0.850	D	.	.	.	0.961	0.460	D	1.445	0.365	L	1.85	0.245	T	-5.72	0.875	D	0.853	0.840	-0.991	0.322	T	0.129	0.438	T	0.027	0.499	D	3.965	0.534	23.6	0.992	0.556	0.987	0.857	D	c	0.762	0.800	1.000	0.747	0.732	0.924	0	5.8	0.921	8.674	0.909	1.033	0.654	1.000	0.715	1.000	0.888	20.061	0.977	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	82	2	109371693	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.29226;SOR=inf;LSEQ=TTCTTTACTGAAAATGATTT;RSEQ=CCAACAAGTAGAGGCCATTA;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|17/29||NM_006267.5:c.2444G>A|NP_006258.3:p.Cys815Tyr|2569|2444|815|C/Y|tGc/tAc|||1||EntrezGene||YES||||2:g.109371693G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:53,42:95,2:0.0206:2,2:17:0:37:0:1:1.25885:60:4:0.022:0:1	0/0:82:0:0,0:29,53:82,0:0:2,0:36.5:1:36.1:1:1:0:59:81:1:0:0.2
    681. 

  681. 2	109374849	109374849	-	T	intronic	RANBP2	.	.	.	0.0001	0.0003	0.0008	0	0	0	0	6.7e-05	0	rs769154262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	39	153	2	109374849	.	A	AT	39	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=50;VD=2;AF=0.04;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.2544;SOR=3.1242;LSEQ=TAAATGTTTAAAATTATTTG;RSEQ=TTTTTTTTTCTTCCAATAGA;CSQ=T|intron_variant|MODIFIER|RANBP2|5903|Transcript|NM_006267.5|protein_coding||17/28|NM_006267.5:c.2467-11dup|||||||rs747860271||1||EntrezGene||YES||||2:g.109374858dup|0.0001602|0.0001923|0.0004061|0.0002989|0|4.621e-05|6.199e-05|0.0003298|0.0003272|0.0004061|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:50:2:2,0:39,7:46,2:0.04:2,0:34.8:1:39:0:1:0:63.2:4:0.0426:0:2.6	0/1:153:2:1,1:109,34:143,2:0.0131:2,2:19:1:39:1:0.42577:3.17421:63.2:4:0.015:0.0065:0.5
    682. 

  682. 2	109375003	109375003	A	G	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon18:c.A2601G:p.T867T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	74	292	2	109375003	.	A	G	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=211;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.11259;SOR=0;LSEQ=TTTCATGGGGCTCCACTAAC;RSEQ=GGTGAGCTGGCAAGTGGATA;CSQ=G|splice_region_variant&synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|18/29||NM_006267.5:c.2601A>G|NP_006258.3:p.Thr867%3D|2726|2601|867|T|acA/acG|||1||EntrezGene||YES||||2:g.109375003A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:211:0:0,0:89,122:211,0:0:2,0:34.9:1:36.4:1:1:0:51:69.333:1:0:0	0/1:292:4:2,2:108,180:288,4:0.0137:2,2:41.2:1:37:0:0.63364:1.66:41:8:0.014:0:1
    683. 

  683. 2	109375019	109375019	G	A	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	254	2	109375019	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=180;VD=2;AF=0.0111;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.17145;SOR=inf;LSEQ=TAACAGGTGAGCTGGCAAGT;RSEQ=GATAATCGCATATTTTAGTA;CSQ=A|intron_variant|MODIFIER|RANBP2|5903|Transcript|NM_006267.5|protein_coding||18/28|NM_006267.5:c.2602+15G>A|||||||||1||EntrezGene||YES||||2:g.109375019G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:180:2:1,1:73,105:178,2:0.0111:2,2:45.5:1:37:0:1:1.44:51:4:0.0112:0:1	0/0:254:0:0,0:86,165:251,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    684. 

  684. 2	109382170	109382170	A	G	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon20:c.A5175G:p.E1725E	0.0014	0.0180	0.0155	0.0110	0.0248	0.0138	0.0119	0.0211	0.0227	rs535428027	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51697758;OCCURENCE=2(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(stomach),3(prostate)	508772	Encephalopathy,_acute,_infection-induced,_3,_suceptibility_to	MONDO:MONDO:0011953,MedGen:C2675556,OMIM:608033,Orphanet:ORPHA88619	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	MU67785042	PBCA-US|2|186|0.0107527,MALY-DE|1|241|0.00414938,LAML-KR|1|205|0.00487805,GACA-CN|1|123|0.00813008,COCA-CN|1|321|0.00311526	0.25	137	621	2	109382170	.	A	G	137	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2362;VD=23;AF=0.0097;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00013;SOR=0.29562;LSEQ=GGAATGTTCACTAAGAAGGA;RSEQ=GGACAGTGGGATTGCAGTGT;CSQ=G|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.5175A>G|NP_006258.3:p.Glu1725%3D|5300|5175|1725|E|gaA/gaG|rs535428027&COSV51697758||1||EntrezGene||YES||||2:g.109382170A>G|1.592e-05|0.0001231|5.792e-05|0|0|0|0|0|0|0.0014|AMR|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2362:23:15,8:1150,1170:2320,23:0.0097:2,2:35.1:1:30.3:1:0.14753:1.91:24.2:3.6:0.0085:0:1.7	0/1:621:20:9,11:299,293:592,20:0.0322:2,2:36:1:33.8:1:0.65649:1.2468:36.6:9:0.034:0:1.4
    685. 

  685. 2	109382706	109382706	A	G	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon20:c.A5711G:p.E1904G	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.999	0.764	D	0.895	0.617	P	.	.	.	0.987	0.405	D	2.34	0.674	M	1.57	0.293	T	-3.68	0.703	D	0.516	0.559	-0.894	0.486	T	0.156	0.488	T	0.018	0.404	T	1.610	0.255	13.91	0.992	0.552	0.998	0.998	D	c	0.620	0.589	1.000	0.747	0.707	0.730	0	5.45	0.796	8.863	0.918	1.082	0.851	1.000	0.715	0.736	0.318	15.817	0.783	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	195	2	109382706	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=373;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.11746;SOR=0;LSEQ=ATTTAAATTTGGCATTTCGG;RSEQ=ACCAGGAAATCAAGAAAAGA;CSQ=G|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.5711A>G|NP_006258.3:p.Glu1904Gly|5836|5711|1904|E/G|gAa/gGa|||1||EntrezGene||YES||||2:g.109382706A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:373:0:0,0:207,166:373,0:0:2,0:39.1:1:36.2:1:1:0:51.4:123.333:1:0:0.1	0/1:195:2:1,1:93,100:193,2:0.0103:2,2:51:0:31:1:1:1.07:60:4:0.0104:0:1
    686. 

  686. 2	109382902	109382902	G	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon20:c.G5907T:p.K1969N	.	.	.	.	.	.	.	.	.	.	.	0.046	0.405	D	0.993	0.637	D	0.738	0.538	P	.	.	.	0.904	0.276	N	2.47	0.719	M	1.57	0.293	T	-2.93	0.612	D	0.182	0.222	-1.017	0.248	T	0.115	0.408	T	0.018	0.401	T	3.036	0.425	22.3	0.996	0.738	0.858	0.447	D	c	0.282	0.231	0.990	0.320	0.732	0.924	0	1.45	0.216	1.393	0.339	-0.358	0.068	1.000	0.715	0.993	0.574	8.048	0.295	.	.	.	ID=COSV51700417;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	44	249	2	109382902	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=873;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.01083;SOR=0;LSEQ=AAAAAAGACCCCAATTTCAA;RSEQ=GGATTTTCAGGTGCTGGAGA;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.5907G>T|NP_006258.3:p.Lys1969Asn|6032|5907|1969|K/N|aaG/aaT|COSV51700417||1||EntrezGene||YES||||2:g.109382902G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:873:0:0,0:408,465:873,0:0:2,0:35.5:1:35.7:1:1:0:47.1:42.65:1:0:0.2	0/1:249:3:1,2:126,120:246,3:0.012:2,2:55.7:1:28.3:1:0.61602:2.09395:53.3:2:0.0083:0:3.3
    687. 

  687. 2	109383878	109383878	G	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon20:c.G6883A:p.E2295K	.	.	.	.	.	.	.	.	.	.	.	0.028	0.461	D	0.996	0.670	D	0.877	0.604	P	.	.	.	1.000	0.492	D	1.935	0.520	L	1.62	0.282	T	-2.76	0.585	D	0.529	0.569	-1.099	0.043	T	0.122	0.425	T	0.012	0.307	T	4.818	0.647	24.8	0.999	0.941	0.992	0.924	D	c	0.662	0.728	1.000	0.747	0.732	0.924	0	5.8	0.921	10.003	0.997	1.048	0.713	1.000	0.715	1.000	0.888	20.059	0.977	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	303	2	109383878	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.15762;SOR=inf;LSEQ=GGACTTCAGTTGGCACTGAT;RSEQ=AAGAATCTGATGTTACTCAA;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.6883G>A|NP_006258.3:p.Glu2295Lys|7008|6883|2295|E/K|Gaa/Aaa|||1||EntrezGene||YES||||2:g.109383878G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:68,130:198,2:0.01:2,2:8:0:37:0:1:1.91:60:4:0.0101:0:1	0/0:303:0:0,0:163,140:303,0:0:2,0:39.1:1:36.4:1:1:0:32.3:74.75:1:0:0.1
    688. 

  688. 2	109384046	109384046	G	T	exonic	RANBP2	.	stopgain	RANBP2:NM_006267:exon20:c.G7051T:p.E2351X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.869	0.998	48	0.997	0.815	0.994	0.956	D	c	1.233	1.100	1.0	0.983	0.732	0.924	0	5.6	0.849	9.917	0.987	1.048	0.713	1.000	0.715	1.000	0.888	19.978	0.973	PH domain-like|Ran binding domain	.	.	ID=COSV99313140;OCCURENCE=1(endometrium)	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129599355	UCEC-US|1|531|0.00188324	0.25	44	249	2	109384046	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.6589;SOR=0;LSEQ=AAGATGTTGGTCAATGGAAA;RSEQ=AAAGGGGCATTGGTGATATA;CSQ=T|stop_gained|HIGH|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.7051G>T|NP_006258.3:p.Glu2351Ter|7176|7051|2351|E/*|Gaa/Taa|COSV99313140||1||EntrezGene||YES||||2:g.109384046G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:37:0:0,0:20,17:37,0:0:2,0:29.4:1:35.6:1:1:0:44.5:36:1:0:0.1	0/1:249:3:1,2:122,124:246,3:0.012:2,2:26.3:1:28.3:1:1:1.96259:44.7:2:0.0082:0:1
    689. 

  689. 2	109384147	109384147	C	T	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon20:c.C7152T:p.H2384H	0.0001	.	.	.	.	.	.	.	.	rs774033010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	276	2	109384147	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=2;AF=0.0256;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.04806;SOR=inf;LSEQ=TTAAAACTTTGTGCCAATCA;RSEQ=AGAATAACTCCAGACATGAC;CSQ=T|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.7152C>T|NP_006258.3:p.His2384%3D|7277|7152|2384|H|caC/caT|rs774033010||1||EntrezGene||YES||||2:g.109384147C>T|4.028e-06|0|2.892e-05|0|0|0|0|0|0|2.892e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:78:2:1,1:51,25:76,2:0.0256:2,2:36:1:37:0:1:2.01996:46:4:0.0256:0:1	0/0:276:0:0,0:136,140:276,0:0:2,0:36:1:36.4:1:1:0:49.7:137:1:0:0.1
    690. 

  690. 2	109384647	109384647	C	T	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon20:c.C7652T:p.A2551V	.	.	.	.	.	.	.	.	.	.	.	0.015	0.524	D	0.062	0.218	B	0.014	0.158	B	.	.	.	0.944	0.267	N	2.175	0.612	M	1.53	0.304	T	-1.45	0.356	N	0.259	0.315	-1.028	0.212	T	0.075	0.303	T	0.008	0.225	T	3.301	0.455	22.9	0.993	0.567	0.959	0.664	D	c	-0.129	0.030	1.000	0.747	0.737	0.974	0	4.7	0.586	2.290	0.430	0.036	0.152	0.998	0.411	0.997	0.653	13.989	0.637	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	228	2	109384647	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=143;VD=2;AF=0.014;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.14793;SOR=inf;LSEQ=GTTTGGATTTAGTTTTAATG;RSEQ=ACCTTTGAAAAGTAACAATA;CSQ=T|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|20/29||NM_006267.5:c.7652C>T|NP_006258.3:p.Ala2551Val|7777|7652|2551|A/V|gCa/gTa|||1||EntrezGene||YES||||2:g.109384647C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:143:2:1,1:55,86:141,2:0.014:2,2:32:1:37:0:1:1.56:29.5:4:0.0141:0:1	0/0:228:0:0,0:105,123:228,0:0:2,0:40:1:35.9:1:1:0:51.8:56:1:0:0.1
    691. 

  691. 2	109388231	109388231	G	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon21:c.G7924A:p.A2642T	0.0001	.	.	.	.	.	.	.	.	rs756532502	.	0.478	0.083	T	0.016	0.161	B	0.008	0.127	B	.	.	.	0.996	0.260	N	0.46	0.130	N	1.36	0.344	T	0.29	0.042	N	0.121	0.137	-1.016	0.249	T	0.043	0.183	T	0.011	0.275	T	4.883	0.656	24.9	0.894	0.182	0.390	0.259	N	c	-0.675	-0.495	0.996	0.346	0.732	0.924	0	3.42	0.381	0.901	0.279	-0.849	0.029	0.445	0.263	0.821	0.343	10.667	0.447	Nup358/RanBP2 E3 ligase domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	183	2	109388231	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.92749;SOR=0;LSEQ=TATATGAACTAACTCCAACC;RSEQ=CTGAGCAGAAAGCCCTTGCA;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|21/29||NM_006267.5:c.7924G>A|NP_006258.3:p.Ala2642Thr|8049|7924|2642|A/T|Gct/Act|rs756532502&COSV51700553||1||EntrezGene||YES||||2:g.109388231G>A|2.388e-05|0|2.891e-05|0|0.0001087|0|1.76e-05|0|3.266e-05|0.0001087|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:5,2:7,0:0:2,0:27.7:1:35.3:1:1:0:60:14:1:0:0	0/1:183:2:1,1:89,91:180,2:0.0109:2,2:67:1:31:1:1:1.02:60:4:0.0111:0:1
    692. 

  692. 2	109389012	109389012	T	C	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon22:c.T8088C:p.C2696C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	91	2	109389012	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.82727;SOR=0;LSEQ=TTGGATGGCTCAGAAAAATG;RSEQ=AGACCCTTGGAAGAAAATAC;CSQ=C|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|22/29||NM_006267.5:c.8088T>C|NP_006258.3:p.Cys2696%3D|8213|8088|2696|C|tgT/tgC|||1||EntrezGene||YES||||2:g.109389012T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:4,5:9,0:0:2,0:37:1:35.7:1:1:0:60:18:1:0:0.4	0/1:91:2:1,1:45,44:89,2:0.022:2,2:36.5:1:31:1:1:1.02248:60:4:0.022:0:1
    693. 

  693. 2	109389045	109389045	A	G	intronic	RANBP2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	83	2	109389045	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.869;SOR=0;LSEQ=GAAAATACAGCAGGTATGTT;RSEQ=AGTGTAAAGGACATTTATAA;CSQ=G|splice_region_variant&intron_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding||22/28|NM_006267.5:c.8113+8A>G|||||||||1||EntrezGene||YES||||2:g.109389045A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:2,4:6,0:0:2,0:29.7:1:32.7:1:1:0:60:5:1:0:0.7	0/1:83:2:1,1:37,44:81,2:0.0241:2,2:27:1:37:0:1:1.19:60:4:0.0241:0:1
    694. 

  694. 2	109389463	109389463	G	A	exonic	RANBP2	.	synonymous SNV	RANBP2:NM_006267:exon23:c.G8253A:p.E2751E	1.	0.9884	0.9595	0.9976	1	1	1	0.9999	0.9980	rs826580	rs826580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU81738486	COCA-CN|5|321|0.0155763	1	266	189	2	109389463	.	G	A	266	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGACAATGGAAATGGGGA;RSEQ=GACTTTCAATCAGAGCTTCA;CSQ=A|synonymous_variant|LOW|RANBP2|5903|Transcript|NM_006267.5|protein_coding|23/29||NM_006267.5:c.8253G>A|NP_006258.3:p.Glu2751%3D|8378|8253|2751|E|gaG/gaA|rs826580||1||EntrezGene||YES||||2:g.109389463G>A|0.9968|0.9572|0.9977|1|1|1|0.9998|0.9985|1|1|EAS&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_SAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:8:8:4,4:0,0:0,8:1:0,2:36.9:1:37:0:1:0:60:16:1:0:1	1/1:189:189:74,115:0,0:0,189:1:0,2:39.2:1:35.3:1:1:0:60:26:1:0:1.1
    695. 

  695. 2	109397724	109397724	G	T	splicing	RANBP2	NM_006267:exon26:c.8600-1G>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.079	0.684	25.3	0.995	0.686	0.997	0.991	D	c	1.206	1.062	1.000	0.747	0.295	0.044	0	5.87	0.942	9.015	0.931	0.985	0.599	1.000	0.715	1.000	0.888	20.194	0.982	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	189	2	109397724	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=119;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.37578;SOR=0;LSEQ=ATATCCTGATTTATTCATCA;RSEQ=ATAAAAATTTCCAATGGGCA;CSQ=T|splice_acceptor_variant|HIGH|RANBP2|5903|Transcript|NM_006267.5|protein_coding||25/28|NM_006267.5:c.8600-1G>T|||||||||1||EntrezGene||YES||||2:g.109397724G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:119:0:0,0:63,56:119,0:0:2,0:30.6:1:36.7:1:1:0:60:118:1:0:0.1	0/1:189:2:1,1:124,63:187,2:0.0106:2,2:22.5:1:31:1:1:1.96074:60:4:0.0108:0:1.5
    696. 

  696. 2	109397725	109397725	A	G	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon26:c.A8600G:p.D2867G	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	1.0	0.899	D	0.994	0.807	D	.	.	.	0.987	0.405	D	2.46	0.717	M	1.56	0.296	T	-5.4	0.851	D	0.647	0.662	-0.649	0.628	T	0.222	0.585	T	0.050	0.644	D	5.753	0.786	27.0	0.999	0.936	0.997	0.984	D	c	0.828	0.788	1.000	0.747	0.732	0.924	0	5.87	0.942	8.403	0.900	1.126	0.882	1.000	0.715	1.000	0.888	16.257	0.823	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	190	2	109397725	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=119;VD=2;AF=0.0168;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.14754;SOR=inf;LSEQ=TATCCTGATTTATTCATCAG;RSEQ=TAAAAATTTCCAATGGGCAA;CSQ=G|missense_variant&splice_region_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|26/29||NM_006267.5:c.8600A>G|NP_006258.3:p.Asp2867Gly|8725|8600|2867|D/G|gAt/gGt|||1||EntrezGene||YES||||2:g.109397725A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:119:2:1,1:62,55:117,2:0.0168:2,2:39:0:37:0:1:1.12613:60:4:0.0169:0:1	0/0:190:0:0,0:126,64:190,0:0:2,0:36.6:1:36.4:1:1:0:60:62.333:1:0:0.1
    697. 

  697. 2	109397820	109397820	G	A	exonic	RANBP2	.	nonsynonymous SNV	RANBP2:NM_006267:exon26:c.G8695A:p.G2899S	.	.	.	.	.	.	.	.	.	.	.	0.125	0.273	T	0.912	0.484	P	0.251	0.373	B	.	.	.	0.654	0.305	N	2.43	0.707	M	1.4	0.336	T	-3.38	0.667	D	0.268	0.329	-0.860	0.513	T	0.101	0.374	T	0.015	0.360	T	5.046	0.679	25.2	0.990	0.505	0.975	0.753	D	c	0.408	0.460	1.000	0.747	0.707	0.730	0	4.99	0.658	5.983	0.700	0.985	0.599	1.000	0.715	0.987	0.523	16.432	0.836	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	235	2	109397820	.	G	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=2;AF=0.0187;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.09725;SOR=inf;LSEQ=AAGTTGGTGAAGATGAAGAT;RSEQ=GTAGTGATGAAGAAGTAGTT;CSQ=A|missense_variant|MODERATE|RANBP2|5903|Transcript|NM_006267.5|protein_coding|26/29||NM_006267.5:c.8695G>A|NP_006258.3:p.Gly2899Ser|8820|8695|2899|G/S|Ggt/Agt|||1||EntrezGene||YES||||2:g.109397820G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:47,58:105,2:0.0187:2,2:24.5:1:31:1:1:1.23:60:4:0.019:0:1	0/0:235:0:0,0:101,134:235,0:0:2,0:40.1:1:36.1:1:1:0:60:77.333:1:0:0.1
    698. 

  698. 2	109397829	109397829	G	T	exonic	RANBP2	.	stopgain	RANBP2:NM_006267:exon26:c.G8704T:p.E2902X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.711	1.000	56	0.997	0.824	0.991	0.908	D	c	1.208	1.086	1.000	0.747	0.707	0.730	0	5.87	0.942	9.015	0.931	0.985	0.599	1.000	0.715	1.000	0.888	20.194	0.982	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	222	2	109397829	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=2;AF=0.0227;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.07992;SOR=inf;LSEQ=AAGATGAAGATGGTAGTGAT;RSEQ=AAGAAGTAGTTCATAATGAA;CSQ=T|stop_gained|HIGH|RANBP2|5903|Transcript|NM_006267.5|protein_coding|26/29||NM_006267.5:c.8704G>T|NP_006258.3:p.Glu2902Ter|8829|8704|2902|E/*|Gaa/Taa|COSV51704404||1||EntrezGene||YES||||2:g.109397829G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:88:2:1,1:36,50:86,2:0.0227:2,2:18.5:1:37:0:1:1.38:60:4:0.0227:0:1	0/0:222:0:0,0:91,131:222,0:0:2,0:39:1:36.2:1:1:0:60:54.5:1:0:0.1
    699. 

  699. 2	128015286	128015286	G	A	exonic	ERCC3	.	synonymous SNV	ERCC3:NM_000122:exon15:c.C2235T:p.G745G,ERCC3:NM_001303416:exon15:c.C2043T:p.G681G,ERCC3:NM_001303418:exon15:c.C2043T:p.G681G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	157	2	128015286	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=502;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05648;SOR=0;LSEQ=CCAGACATAGAACTCATGGT;RSEQ=CCAAAGCGCCGAGATGCCTG;CSQ=A|synonymous_variant|LOW|ERCC3|2071|Transcript|NM_000122.2|protein_coding|15/15||NM_000122.2:c.2235C>T|NP_000113.1:p.Gly745%3D|2298|2235|745|G|ggC/ggT|||-1||EntrezGene||YES||||2:g.128015286G>A||||||||||||||,A|synonymous_variant|LOW|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|15/15||NM_001303416.2:c.2043C>T|NP_001290345.1:p.Gly681%3D|2495|2043|681|G|ggC/ggT|||-1||EntrezGene||||||2:g.128015286G>A||||||||||||||,A|synonymous_variant|LOW|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|15/15||NM_001303418.2:c.2043C>T|NP_001290347.1:p.Gly681%3D|2557|2043|681|G|ggC/ggT|||-1||EntrezGene||||||2:g.128015286G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:502:0:0,0:147,355:502,0:0:2,0:36.2:1:36.7:1:1:0:60:250:1:0:0.2	0/1:157:2:1,1:64,91:155,2:0.0127:2,2:50:1:37:0:1:1.42:60:4:0.0127:0:1.5
    700. 

  700. 2	128016931	128016931	T	A	exonic	ERCC3	.	nonsynonymous SNV	ERCC3:NM_000122:exon14:c.A2158T:p.T720S,ERCC3:NM_001303416:exon14:c.A1966T:p.T656S,ERCC3:NM_001303418:exon14:c.A1966T:p.T656S	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.000	0.477	N	0.601	0.325	D	-2.015	0.002	N	0.1	0.614	T	1.41	0.008	N	0.038	0.018	-1.002	0.293	T	0.045	0.194	T	0.010	0.270	T	0.774	0.168	9.302	0.584	0.058	0.802	0.396	D	c	-0.724	-0.464	0.934	0.271	0.707	0.730	0	1.5	0.219	3.588	0.535	1.061	0.807	1.000	0.715	0.997	0.653	10.775	0.454	ERCC3/RAD25/XPB helicase, C-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	160	2	128016931	.	T	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1745;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00701;SOR=0;LSEQ=CTCCTCGGCATCCAGGTCAG;RSEQ=GGCTGCCAGGACTTTCTGTA;CSQ=A|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_000122.2|protein_coding|14/15||NM_000122.2:c.2158A>T|NP_000113.1:p.Thr720Ser|2221|2158|720|T/S|Act/Tct|||-1||EntrezGene||YES||||2:g.128016931T>A||||||||||||||,A|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|14/15||NM_001303416.2:c.1966A>T|NP_001290345.1:p.Thr656Ser|2418|1966|656|T/S|Act/Tct|||-1||EntrezGene||||||2:g.128016931T>A||||||||||||||,A|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|14/15||NM_001303418.2:c.1966A>T|NP_001290347.1:p.Thr656Ser|2480|1966|656|T/S|Act/Tct|||-1||EntrezGene||||||2:g.128016931T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1745:0:0,0:914,830:1744,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:160:2:1,1:80,78:158,2:0.0125:2,2:33:1:37:0:1:1.02548:60:4:0.0132:0:1
    701. 

  701. 2	128017027	128017027	G	A	intronic	ERCC3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	122	2	128017027	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1867;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00373;SOR=0;LSEQ=AGCGAGTTTCGTGATCACCT;RSEQ=CAAAGCCCAAGCCAGCAGAC;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERCC3|2071|Transcript|NM_000122.2|protein_coding||13/14|NM_000122.2:c.2065-3C>T|||||||rs1395572182||-1||EntrezGene||YES||||2:g.128017027G>A|3.979e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERCC3|2071|Transcript|NM_001303416.2|protein_coding||13/14|NM_001303416.2:c.1873-3C>T|||||||rs1395572182||-1||EntrezGene||||||2:g.128017027G>A|3.979e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERCC3|2071|Transcript|NM_001303418.2|protein_coding||13/14|NM_001303418.2:c.1873-3C>T|||||||rs1395572182||-1||EntrezGene||||||2:g.128017027G>A|3.979e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1867:0:0,0:824,1043:1867,0:0:2,0:36.7:1:36.6:1:1:0:60:123.467:1:0:0.1	0/1:122:2:1,1:51,69:120,2:0.0164:2,2:33.5:1:37:0:1:1.35:60:4:0.0168:0:1
    702. 

  702. 2	128038139	128038139	C	T	exonic	ERCC3	.	nonsynonymous SNV	ERCC3:NM_000122:exon9:c.G1411A:p.V471I,ERCC3:NM_001303416:exon9:c.G1219A:p.V407I,ERCC3:NM_001303418:exon9:c.G1219A:p.V407I	0.0069	0.0001	0.0002	0	0	0.0012	0	0	0	rs371627165	rs371627165	0.005	0.632	D	0.965	0.541	D	0.74	0.539	P	0.000	0.843	D	1	0.810	D	1.98	0.539	M	1.43	0.330	T	-0.65	0.189	N	0.348	0.435	-0.825	0.537	T	0.150	0.477	T	0.042	0.604	D	5.990	0.823	27.8	0.997	0.839	0.981	0.794	D	c	0.436	0.407	1.000	0.747	0.707	0.730	0	4.73	0.593	7.896	0.858	0.930	0.439	1.000	0.715	0.993	0.574	14.484	0.670	Helicase superfamily 1/2, ATP-binding domain|P-loop containing nucleoside triphosphate hydrolase	.	.	ID=COSV53426190;OCCURENCE=2(breast),1(large_intestine),1(upper_aerodigestive_tract),1(endometrium)	881017	Xeroderma_pigmentosum,_complementation_group_b|not_provided	MONDO:MONDO:0012531,MedGen:C0268136,OMIM:610651|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129569302	UCEC-US|1|531|0.00188324,BRCA-US|1|1020|0.000980392	0.25	364	344	2	128038139	.	C	T	364	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2449;VD=1142;AF=0.4663;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=AATTTTGTCATCTTCGCGGA;RSEQ=GAGGGTCGCAGTCAAACCCA;CSQ=T|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_000122.2|protein_coding|9/15||NM_000122.2:c.1411G>A|NP_000113.1:p.Val471Ile|1474|1411|471|V/I|Gtc/Atc|rs371627165&COSV53426190||-1||EntrezGene||YES||||2:g.128038139C>T|0.0002149|0.0002462|0|9.927e-05|0.001577|0|1.76e-05|0.000163|0.0005553|0.0069|EAS|uncertain_significance|0&1|1&1,T|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|9/15||NM_001303416.2:c.1219G>A|NP_001290345.1:p.Val407Ile|1671|1219|407|V/I|Gtc/Atc|rs371627165&COSV53426190||-1||EntrezGene||||||2:g.128038139C>T|0.0002149|0.0002462|0|9.927e-05|0.001577|0|1.76e-05|0.000163|0.0005553|0.0069|EAS|uncertain_significance|0&1|1&1,T|missense_variant|MODERATE|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|9/15||NM_001303418.2:c.1219G>A|NP_001290347.1:p.Val407Ile|1733|1219|407|V/I|Gtc/Atc|rs371627165&COSV53426190||-1||EntrezGene||||||2:g.128038139C>T|0.0002149|0.0002462|0|9.927e-05|0.001577|0|1.76e-05|0.000163|0.0005553|0.0069|EAS|uncertain_significance|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2449:1142:521,621:622,682:1304,1142:0.4663:2,2:39.3:1:35.9:1:0.31012:1.08704:60:50.909:0.4626:0:1.1	0/0:344:0:0,0:172,172:344,0:0:2,0:36:1:36.3:1:1:0:60:85:1:0:0.1
    703. 

  703. 2	128046944	128046946	TCT	-	exonic	ERCC3	.	nonframeshift deletion	ERCC3:NM_000122:exon6:c.789_791del:p.E264del,ERCC3:NM_001303416:exon6:c.597_599del:p.E200del,ERCC3:NM_001303418:exon6:c.597_599del:p.E200del	0.0052	0	0	0	0	0	0	0	0	rs761456808	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	162	218	2	128046943	.	CTCT	C	162	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1702;VD=21;AF=0.0123;SHIFT3=14;MSI=5;MSILEN=3;SSF=0.3137;SOR=0.66852;LSEQ=TCAAAAGACACTGTCTGTGT;RSEQ=TCTTCTTCTTCTTCATCCTT;CSQ=-|inframe_deletion|MODERATE|ERCC3|2071|Transcript|NM_000122.2|protein_coding|6/15||NM_000122.2:c.789_791del|NP_000113.1:p.Glu264del|852-854|789-791|263-264|EE/E|gaAGAg/gag|rs761456808||-1||EntrezGene||YES||||2:g.128046958_128046960del|7.613e-05|6.186e-05|5.811e-05|9.962e-05|5.46e-05|0|0.0001066|0|6.568e-05|0.00521|EA|||,-|inframe_deletion|MODERATE|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|6/15||NM_001303416.2:c.597_599del|NP_001290345.1:p.Glu200del|1049-1051|597-599|199-200|EE/E|gaAGAg/gag|rs761456808||-1||EntrezGene||||||2:g.128046958_128046960del|7.613e-05|6.186e-05|5.811e-05|9.962e-05|5.46e-05|0|0.0001066|0|6.568e-05|0.00521|EA|||,-|inframe_deletion|MODERATE|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|6/15||NM_001303418.2:c.597_599del|NP_001290347.1:p.Glu200del|1111-1113|597-599|199-200|EE/E|gaAGAg/gag|rs761456808||-1||EntrezGene||||||2:g.128046958_128046960del|7.613e-05|6.186e-05|5.811e-05|9.962e-05|5.46e-05|0|0.0001066|0|6.568e-05|0.00521|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1702:21:11,10:971,709:1680,21:0.0123:2,2:34.4:1:37:1:0.66049:1.24486:60:42:0.0124:0.0006:0	0/1:218:4:2,2:134,80:214,4:0.0183:2,2:33.2:1:37:0:0.63268:1.6708:60:8:0.0185:0:0.5
    704. 

  704. 2	128051272	128051272	C	T	exonic	ERCC3	.	synonymous SNV	ERCC3:NM_000122:exon2:c.G51A:p.R17R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53428051;OCCURENCE=1(endometrium)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU1841471	UCEC-US|1|531|0.00188324	0.25	37	48	2	128051272	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=450;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00911;SOR=0;LSEQ=TCCTCTTCATCCTCATAGTG;RSEQ=CGCTTCCTGGATTTCTTCTT;CSQ=T|synonymous_variant|LOW|ERCC3|2071|Transcript|NM_000122.2|protein_coding|2/15||NM_000122.2:c.51G>A|NP_000113.1:p.Arg17%3D|114|51|17|R|cgG/cgA|COSV53428051||-1||EntrezGene||YES||||2:g.128051272C>T|||||||||||||1|1,T|5_prime_UTR_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|2/15||NM_001303416.2:c.-142G>A||311|||||COSV53428051||-1||EntrezGene||||||2:g.128051272C>T|||||||||||||1|1,T|5_prime_UTR_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|2/15||NM_001303418.2:c.-142G>A||373|||||COSV53428051||-1||EntrezGene||||||2:g.128051272C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371910.2|protein_coding||||||||||COSV53428051|4972|-1||EntrezGene||YES||||2:g.128051272C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371911.1|protein_coding||||||||||COSV53428051|4972|-1||EntrezGene||||||2:g.128051272C>T|||||||||||||1|1,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_006609.5|protein_coding||||||||||COSV53428051|4972|-1||EntrezGene||||||2:g.128051272C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:450:0:0,0:155,295:450,0:0:2,0:34.1:1:36.4:1:1:0:60:111.5:1:0:0.2	0/1:48:2:1,1:13,33:46,2:0.0417:2,2:12.5:1:37:0:0.50266:2.48:60:4:0.0417:0:2
    705. 

  705. 2	128051360	128051360	C	T	intronic	ERCC3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	23	2	128051360	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=2;AF=0.0136;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.74702;SOR=inf;LSEQ=GTTCCCTCCGCACCGCTTGG;RSEQ=AGCATTTCACCTGCGCCGCC;CSQ=T|intron_variant|MODIFIER|ERCC3|2071|Transcript|NM_000122.2|protein_coding||1/14|NM_000122.2:c.29-66G>A|||||||||-1||EntrezGene||YES||||2:g.128051360C>T||||||||||||||,T|intron_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303416.2|protein_coding||1/14|NM_001303416.2:c.-164-66G>A|||||||||-1||EntrezGene||||||2:g.128051360C>T||||||||||||||,T|intron_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303418.2|protein_coding||1/14|NM_001303418.2:c.-165+11G>A|||||||||-1||EntrezGene||||||2:g.128051360C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371910.2|protein_coding|||||||||||4884|-1||EntrezGene||YES||||2:g.128051360C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371911.1|protein_coding|||||||||||4884|-1||EntrezGene||||||2:g.128051360C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_006609.5|protein_coding|||||||||||4884|-1||EntrezGene||||||2:g.128051360C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:147:2:1,1:54,91:145,2:0.0136:2,2:35.5:1:37:0:1:1.68:60:4:0.0136:0:1	0/0:23:0:0,0:11,12:23,0:0:2,0:34.3:1:36:1:1:0:60:46:1:0:0.1
    706. 

  706. 2	128051613	128051613	C	T	UTR5	ERCC3	NM_001303418:c.-483G>A;NM_001303416:c.-483G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	41	2	128051613	.	C	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=255;VD=3;AF=0.0118;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.63831;SOR=inf;LSEQ=GGCAGTCGTGGCTGAGCGTG;RSEQ=CCGCGCAACGTCTCACCGCG;CSQ=T|intron_variant|MODIFIER|ERCC3|2071|Transcript|NM_000122.2|protein_coding||1/14|NM_000122.2:c.28+17G>A|||||||rs1452916741||-1||EntrezGene||YES||||2:g.128051613C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303416.2|protein_coding|1/15||NM_001303416.2:c.-345G>A||108|||||rs1452916741||-1||EntrezGene||||||2:g.128051613C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|ERCC3|2071|Transcript|NM_001303418.2|protein_coding|1/15||NM_001303418.2:c.-407G>A||108|||||rs1452916741||-1||EntrezGene||||||2:g.128051613C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371910.2|protein_coding||||||||||rs1452916741|4631|-1||EntrezGene||YES||||2:g.128051613C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_001371911.1|protein_coding||||||||||rs1452916741|4631|-1||EntrezGene||||||2:g.128051613C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|MAP3K2|10746|Transcript|NM_006609.5|protein_coding||||||||||rs1452916741|4631|-1||EntrezGene||||||2:g.128051613C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:255:3:1,2:109,143:252,3:0.0118:2,2:58:1:37:0:1:1.52206:60:6:0.012:0:1.3	0/0:41:0:0,0:16,25:41,0:0:2,0:41:1:36.7:1:1:0:60:82:1:0:0
    707. 

  707. 2	136873084	136873084	G	A	exonic	CXCR4	.	synonymous SNV	CXCR4:NM_001008540:exon1:c.C426T:p.I142I,CXCR4:NM_001348060:exon2:c.C369T:p.I123I,CXCR4:NM_003467:exon2:c.C414T:p.I138I,CXCR4:NM_001348056:exon3:c.C627T:p.I209I,CXCR4:NM_001348059:exon3:c.C513T:p.I171I	0.15	0.0353	0.0157	0.0215	0.1026	0.1222	0.0083	0.0426	0.0407	rs2228014	rs2228014	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV54010972;OCCURENCE=1(breast),1(large_intestine),2(stomach),2(haematopoietic_and_lymphoid_tissue),3(pituitary)	250163	Warts,_hypogammaglobulinemia,_infections,_and_myelokathexis|not_specified	MONDO:MONDO:0008674,MedGen:C0472817,OMIM:193670,Orphanet:ORPHA51636,SNOMED_CT:234571003|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU134858	LAML-KR|2|205|0.0097561,COCA-CN|1|321|0.00311526,BRCA-KR|1|50|0.02	0.25	396	524	2	136873084	.	G	A	396	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=5193;VD=2597;AF=0.5001;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGACTGTTGGTGGCGTGGAC;RSEQ=ATGGCCAGGTAGCGGTCCAG;CSQ=A|synonymous_variant|LOW|CXCR4|7852|Transcript|NM_001008540.2|protein_coding|1/1||NM_001008540.2:c.426C>T|NP_001008540.1:p.Ile142%3D|722|426|142|I|atC/atT|rs2228014&COSV54010972||-1||EntrezGene||||||2:g.136873084G>A|0.04572|0.01839|0.02015|0.07204|0.1259|0.01104|0.03943|0.04268|0.08074|0.1508|EAS|benign|0&1|1&1,A|synonymous_variant|LOW|CXCR4|7852|Transcript|NM_001348056.2|protein_coding|3/3||NM_001348056.2:c.627C>T|NP_001334985.1:p.Ile209%3D|716|627|209|I|atC/atT|rs2228014&COSV54010972||-1||EntrezGene||YES||||2:g.136873084G>A|0.04572|0.01839|0.02015|0.07204|0.1259|0.01104|0.03943|0.04268|0.08074|0.1508|EAS|benign|0&1|1&1,A|synonymous_variant|LOW|CXCR4|7852|Transcript|NM_001348059.2|protein_coding|3/3||NM_001348059.2:c.513C>T|NP_001334988.1:p.Ile171%3D|602|513|171|I|atC/atT|rs2228014&COSV54010972||-1||EntrezGene||||||2:g.136873084G>A|0.04572|0.01839|0.02015|0.07204|0.1259|0.01104|0.03943|0.04268|0.08074|0.1508|EAS|benign|0&1|1&1,A|synonymous_variant|LOW|CXCR4|7852|Transcript|NM_001348060.2|protein_coding|2/2||NM_001348060.2:c.369C>T|NP_001334989.1:p.Ile123%3D|740|369|123|I|atC/atT|rs2228014&COSV54010972||-1||EntrezGene||||||2:g.136873084G>A|0.04572|0.01839|0.02015|0.07204|0.1259|0.01104|0.03943|0.04268|0.08074|0.1508|EAS|benign|0&1|1&1,A|synonymous_variant|LOW|CXCR4|7852|Transcript|NM_003467.3|protein_coding|2/2||NM_003467.3:c.414C>T|NP_003458.1:p.Ile138%3D|503|414|138|I|atC/atT|rs2228014&COSV54010972||-1||EntrezGene||||||2:g.136873084G>A|0.04572|0.01839|0.02015|0.07204|0.1259|0.01104|0.03943|0.04268|0.08074|0.1508|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:5193:2597:1282,1315:1289,1287:2576,2597:0.5001:2,2:37.9:1:35:1:0.63645:1.02734:60:22.826:0.4919:0:1.1	0/0:524:0:0,0:272,252:524,0:0:2,0:38.3:1:36.6:1:1:0:60:130:1:0:0.1
    708. 

  708. 2	136873564	136873564	-	A	UTR5	CXCR4	NM_001008540:c.-56_-55insT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	114	2	136873564	.	T	TA	38	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=143;VD=2;AF=0.014;SHIFT3=6;MSI=7;MSILEN=1;SSF=0.30864;SOR=inf;LSEQ=AAAAAATTTTTAAAGCAATT;RSEQ=AAAAAACCAATTCAGGCTTG;CSQ=A|5_prime_UTR_variant|MODIFIER|CXCR4|7852|Transcript|NM_001008540.2|protein_coding|1/1||NM_001008540.2:c.-56dup||241-242|||||||-1||EntrezGene||||||2:g.136873570dup||||||||||||||,A|intron_variant|MODIFIER|CXCR4|7852|Transcript|NM_001348056.2|protein_coding||2/2|NM_001348056.2:c.229-83dup|||||||||-1||EntrezGene||YES||||2:g.136873570dup||||||||||||||,A|intron_variant|MODIFIER|CXCR4|7852|Transcript|NM_001348059.2|protein_coding||2/2|NM_001348059.2:c.115-83dup|||||||||-1||EntrezGene||||||2:g.136873570dup||||||||||||||,A|intron_variant|MODIFIER|CXCR4|7852|Transcript|NM_001348060.2|protein_coding||1/1|NM_001348060.2:c.-30-83dup|||||||||-1||EntrezGene||||||2:g.136873570dup||||||||||||||,A|intron_variant|MODIFIER|CXCR4|7852|Transcript|NM_003467.3|protein_coding||1/1|NM_003467.3:c.16-83dup|||||||||-1||EntrezGene||||||2:g.136873570dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:143:2:1,1:32,105:137,2:0.014:2,2:14.5:0:38.2:0:0.41977:3.25:62:4:0.0145:0:0	0/0:114:0:0,0:26,88:114,0:0:2,0:30:1:35.9:1:1:0:60:56:1:0:0.1
    709. 

  709. 2	140997040	140997040	A	G	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon88:c.T13386C:p.I4462I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	138	2	140997040	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTACAAAGCACTAAACC;RSEQ=ATTACTAAGGTGGTTATCAA;CSQ=G|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|88/91||NM_018557.3:c.13386T>C|NP_061027.2:p.Ile4462%3D|13673|13386|4462|I|atT/atC|||-1||EntrezGene||YES||||2:g.140997040A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:138:2:1,1:73,63:136,2:0.0145:2,2:30:1:37:0:1:1.15749:60:4:0.0147:0:1.5
    710. 

  710. 2	141032042	141032042	G	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon85:c.C13093A:p.H4365N	.	.	.	.	.	.	.	.	.	.	.	0.406	0.103	T	0.421	0.336	B	0.156	0.328	B	0.000	0.843	U	0.999	0.468	D	0.155	0.089	N	-2.46	0.889	D	0.62	0.024	N	0.467	0.518	-0.310	0.747	T	0.405	0.755	T	0.042	0.606	D	3.000	0.421	22.2	0.935	0.227	0.993	0.942	D	c	0.100	0.315	1.000	0.517	0.554	0.246	0	5.36	0.765	10.003	0.997	1.048	0.713	1.000	0.715	1.000	0.888	17.254	0.869	EGF-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	183	2	141032042	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=40;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.67277;SOR=0;LSEQ=TATAATGCAGTGCCCCCCAT;RSEQ=GCACCTTACACACTTGTCAA;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|85/91||NM_018557.3:c.13093C>A|NP_061027.2:p.His4365Asn|13380|13093|4365|H/N|Cat/Aat|||-1||EntrezGene||YES||||2:g.141032042G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:40:0:0,0:23,17:40,0:0:2,0:36.5:1:36.7:1:1:0:60:80:1:0:1	0/1:183:2:1,1:99,82:181,2:0.0109:2,2:37:1:37:0:1:1.20606:60:4:0.0111:0:1
    711. 

  711. 2	141032088	141032088	C	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon85:c.G13047A:p.T4349T	0.69	0.5412	0.2389	0.5469	0.4967	0.7081	0.6794	0.6628	0.6222	rs1386356	rs1386356	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67186048;OCCURENCE=109(meninges),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU26066624	COCA-CN|5|321|0.0155763	0.75	232	182	2	141032088	.	C	T	232	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=53;VD=53;AF=1;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=CATTTTGGTCCTTCATAGCG;RSEQ=GTTGGACAGACACATTCAAC;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|85/91||NM_018557.3:c.13047G>A|NP_061027.2:p.Thr4349%3D|13334|13047|4349|T|acG/acA|rs1386356&COSV67186048||-1||EntrezGene||YES||||2:g.141032088C>T|0.6084|0.2321|0.5345|0.5176|0.6852|0.6891|0.6733|0.614|0.5766|0.6891|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:53:53:26,27:0,0:0,53:1:0,2:38.9:1:37:0:1:0:60:106:1:0:1	0/1:182:85:40,45:43,54:97,85:0.467:2,2:39.2:1:36.3:1:0.76626:1.12:60:84:0.4719:0:1.1
    712. 

  712. 2	141083409	141083409	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon80:c.G12262A:p.A4088T	.	.	.	.	.	.	.	.	.	.	.	0.063	0.367	T	0.993	0.637	D	0.984	0.745	D	0.001	0.390	U	1.000	0.516	D	2.03	0.557	M	-2.9	0.917	D	-1.93	0.448	N	0.661	0.673	0.691	0.931	D	0.826	0.941	D	0.134	0.817	D	6.891	0.931	33	0.999	0.934	0.979	0.779	D	c	0.635	0.632	1.000	0.517	0.487	0.133	0	5.13	0.696	5.624	0.672	0.892	0.403	1.000	0.715	0.999	0.750	18.583	0.911	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV101254546;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129787404	SKCM-US|1|466|0.00214592	0.25	68	237	2	141083409	.	C	T	68	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.59181;SOR=0;LSEQ=GATGGAGAGCTCAAAGTCAG;RSEQ=CCAATATATGCGTTCACTAA;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|80/91||NM_018557.3:c.12262G>A|NP_061027.2:p.Ala4088Thr|12549|12262|4088|A/T|Gct/Act|COSV101254546||-1||EntrezGene||YES||||2:g.141083409C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:33:0:0,0:15,18:33,0:0:2,0:40.5:1:36.6:1:1:0:60:66:1:0:0	0/1:237:4:2,2:98,135:233,4:0.0169:2,2:38.2:1:34:1:1:1.38:60:8:0.0169:0:1
    713. 

  713. 2	141093264	141093264	C	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon78:c.G12036A:p.Q4012Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	369	2	141093264	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=96;VD=2;AF=0.0208;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04227;SOR=inf;LSEQ=GTGCAGTTGGGGCCATTCAG;RSEQ=TGCCCTACGTTGATAGAGTA;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|78/91||NM_018557.3:c.12036G>A|NP_061027.2:p.Gln4012%3D|12323|12036|4012|Q|caG/caA|||-1||EntrezGene||YES||||2:g.141093264C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:96:2:1,1:59,35:94,2:0.0208:2,2:19:1:37:0:1:1.67609:60:4:0.0213:0:1	0/0:369:0:0,0:208,161:369,0:0:2,0:38.8:1:36.9:1:1:0:60:368:1:0:0.1
    714. 

  714. 2	141108596	141108596	G	A	exonic	LRP1B	.	stopgain	LRP1B:NM_018557:exon77:c.C11662T:p.Q3888X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.452	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.501	0.999	51	0.993	0.593	0.976	0.759	D	c	0.863	0.734	0.922	0.266	0.487	0.133	0	4.83	0.617	6.301	0.726	1.042	0.661	1.000	0.715	1.000	0.888	16.713	0.852	Growth factor receptor cysteine-rich domain|Six-bladed beta-propeller, TolB-like;Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	114	2	141108596	.	G	A	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGCAATGTAGAGAACTT;RSEQ=ATCTTCAGAGCCTGGAGATT;CSQ=A|stop_gained|HIGH|LRP1B|53353|Transcript|NM_018557.3|protein_coding|77/91||NM_018557.3:c.11662C>T|NP_061027.2:p.Gln3888Ter|11949|11662|3888|Q/*|Caa/Taa|||-1||EntrezGene||YES||||2:g.141108596G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:114:2:1,1:44,68:112,2:0.0175:2,2:28:1:37:0:1:1.54:60:4:0.0177:0:1
    715. 

  715. 2	141110697	141110697	C	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	76	2	141110697	.	C	T	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAATTCAGACTCCTATT;RSEQ=TTACCACGTTTCAAAAAAGC;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||75/90|NM_018557.3:c.11531-56G>A|||||||||-1||EntrezGene||YES||||2:g.141110697C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:76:2:1,1:21,53:74,2:0.0263:2,2:8:0:37:0:0.49789:2.49:60:4:0.027:0:1
    716. 

  716. 2	141116499	141116499	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon73:c.A11148G:p.P3716P	0.	.	.	.	.	.	.	.	.	rs776654126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	167	2	141116499	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.88989;SOR=0;LSEQ=CATCTGTGAGGTCTCGTGGA;RSEQ=GGACAAAGAAATTTGACTGA;CSQ=C|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|73/91||NM_018557.3:c.11148A>G|NP_061027.2:p.Pro3716%3D|11435|11148|3716|P|ccA/ccG|rs776654126||-1||EntrezGene||YES||||2:g.141116499T>C|8.037e-06|0|2.909e-05|0|0|0|8.931e-06|0|0|2.909e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:4,6:10,0:0:2,0:36.9:1:37:0:1:0:60:20:1:0:0	0/1:167:2:1,1:67,97:164,2:0.012:2,2:54.5:1:37:0:1:1.44:60:4:0.0121:0:1.5
    717. 

  717. 2	141122246	141122246	T	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon72:c.A11115T:p.E3705D	.	.	.	.	.	.	.	.	.	.	.	0.031	0.450	D	0.999	0.764	D	0.994	0.807	D	0.000	0.843	D	0.960	0.382	D	3.82	0.957	H	-5.13	0.987	D	-2.3	0.511	N	0.518	0.560	1.054	0.982	D	0.980	0.994	D	0.826	0.987	D	5.357	0.725	25.9	0.997	0.834	0.922	0.550	D	c	0.515	0.368	0.000	0.071	0.487	0.133	0	3.1	0.346	0.862	0.274	0.153	0.239	0.791	0.294	1.000	0.888	8.572	0.326	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	126	2	141122246	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.80935;SOR=0;LSEQ=ATACCACACATATCAGGGGC;RSEQ=TCATCAGAGTTGTCTCCACA;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|72/91||NM_018557.3:c.11115A>T|NP_061027.2:p.Glu3705Asp|11402|11115|3705|E/D|gaA/gaT|||-1||EntrezGene||YES||||2:g.141122246T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:14:0:0,0:5,9:14,0:0:2,0:41.8:1:37:0:1:0:60:28:1:0:0	0/1:126:2:1,1:73,51:124,2:0.0159:2,2:24.5:1:37:0:1:1.42719:60:4:0.016:0:1.5
    718. 

  718. 2	141122319	141122319	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon72:c.G11042T:p.C3681F	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	4.575	0.992	H	-6.74	0.998	D	-7.99	0.964	D	0.98	0.982	0.919	0.959	D	0.995	0.999	D	0.754	0.980	D	7.126	0.943	34	0.991	0.513	0.987	0.851	D	c	1.117	1.011	1.000	0.747	0.487	0.133	0	5.58	0.843	7.530	0.807	0.935	0.490	1.000	0.715	1.000	0.888	19.931	0.971	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	2	141122319	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.92708;SOR=0;LSEQ=GTTTGCAGAGAGAATTATTG;RSEQ=AAAGGAACTCATCAGCTCTA;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|72/91||NM_018557.3:c.11042G>T|NP_061027.2:p.Cys3681Phe|11329|11042|3681|C/F|tGc/tTc|COSV67275487||-1||EntrezGene||YES||||2:g.141122319C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:3,3:6,0:0:2,0:17.5:1:37:0:1:0:60:12:1:0:0	0/1:156:2:1,1:74,80:154,2:0.0128:2,2:42:1:37:0:1:1.08:60:4:0.0131:0:1
    719. 

  719. 2	141122327	141122327	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon72:c.G11034T:p.E3678D	.	.	.	.	.	.	.	.	.	.	.	0.041	0.419	D	0.999	0.764	D	0.994	0.807	D	0.000	0.843	D	0.970	0.388	D	1.87	0.498	L	-3.89	0.960	D	-1.29	0.324	N	0.543	0.580	0.855	0.951	D	0.887	0.963	D	0.159	0.840	D	5.035	0.678	25.2	0.995	0.675	0.893	0.494	D	c	0.344	0.269	0.000	0.065	0.487	0.133	0	1.77	0.237	0.244	0.178	0.935	0.490	0.978	0.348	1.000	0.888	10.598	0.444	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	160	2	141122327	.	C	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.95167;SOR=0;LSEQ=AGAGAATTATTGCAAAGGAA;RSEQ=TCATCAGCTCTACATATATT;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|72/91||NM_018557.3:c.11034G>T|NP_061027.2:p.Glu3678Asp|11321|11034|3678|E/D|gaG/gaT|||-1||EntrezGene||YES||||2:g.141122327C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:16.5:1:37:0:1:0:60:8:1:0:0	0/1:160:2:1,1:71,87:158,2:0.0125:2,2:37.5:1:37:0:1:1.22:60:4:0.0127:0:1
    720. 

  720. 2	141130565	141130565	C	T	intronic	LRP1B	.	.	.	0.0001	3.234e-05	0	0	0	0	0	6.668e-05	0	rs376163255	rs376163255	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU44016812	MELA-AU|1|183|0.00546448	0.25	37	103	2	141130565	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00579;SOR=inf;LSEQ=AACTAAATGATATATTACTT;RSEQ=AATCCTTTTACCTGGCTCAC;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||69/90|NM_018557.3:c.10768+12G>A|||||||rs376163255||-1||EntrezGene||YES||||2:g.141130565C>T|7.988e-06|0|5.805e-05|0|0|0|0|0|0|0.0001163|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:9:2:1,1:4,3:7,2:0.2222:2,2:34:0:37:0:1:1.29098:60:4:0.2222:0:1	0/0:103:0:0,0:78,25:103,0:0:2,0:36.2:1:36.3:1:1:0:60:206:1:0:0.1
    721. 

  721. 2	141135855	141135855	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon68:c.A10532G:p.K3511R	.	.	.	.	.	.	.	.	.	.	.	0.454	0.089	T	0.877	0.462	P	0.411	0.430	B	0.000	0.843	D	1	0.810	D	0.295	0.102	N	-2.79	0.910	D	-0.83	0.227	N	0.375	0.436	-0.175	0.783	T	0.480	0.801	T	.	.	.	1.976	0.298	16.06	0.992	0.552	0.977	0.766	D	c	0.134	0.268	0.150	0.174	0.487	0.133	0	5.6	0.849	3.873	0.556	1.011	0.635	1.000	0.715	0.986	0.517	11.735	0.508	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	195	2	141135855	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.52086;SOR=0;LSEQ=TCAATGTACATGTCTGTGGC;RSEQ=CTGGGGATAAAAAAACAGCA;CSQ=C|missense_variant&splice_region_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|68/91||NM_018557.3:c.10532A>G|NP_061027.2:p.Lys3511Arg|10819|10532|3511|K/R|aAg/aGg|||-1||EntrezGene||YES||||2:g.141135855T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:75:0:0,0:24,51:75,0:0:2,0:32.7:1:36.5:1:1:0:60:150:1:0:0.1	0/1:195:2:1,1:89,104:193,2:0.0103:2,2:8:1:37:0:1:1.17:60:4:0.0103:0:1
    722. 

  722. 2	141200032	141200032	T	C	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	207	2	141200032	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=2;AF=0.0244;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0798;SOR=inf;LSEQ=TGGTTGTCGCAGATGATGAC;RSEQ=CAAATACGGAGAGATAAGAC;CSQ=C|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||66/90|NM_018557.3:c.10414+41A>G|||||||||-1||EntrezGene||YES||||2:g.141200032T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:82:2:1,1:49,31:80,2:0.0244:2,2:53.5:1:37:0:1:1.57149:60:4:0.0244:0:1	0/0:207:0:0,0:132,75:207,0:0:2,0:36.3:1:36.7:1:1:0:60:414:1:0:0.1
    723. 

  723. 2	141200116	141200116	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon66:c.C10371T:p.D3457D	.	3.23e-05	0	0	0	0	0	6.662e-05	0	rs953684582	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV101256233;OCCURENCE=1(pancreas)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129044934	PAAD-US|1|177|0.00564972	0.25	31	298	2	141200116	.	G	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=131;VD=2;AF=0.0153;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09275;SOR=inf;LSEQ=TCTGCACAGTCTGGATCCTC;RSEQ=TCACAAACCCACAGCTTGGA;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|66/91||NM_018557.3:c.10371C>T|NP_061027.2:p.Asp3457%3D|10658|10371|3457|D|gaC/gaT|rs953684582&COSV101256233&COSV67244539||-1||EntrezGene||YES||||2:g.141200116G>A|3.982e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:131:2:1,1:62,67:129,2:0.0153:2,2:55:1:31:1:1:1.08:60:4:0.0155:0:1	0/0:298:0:0,0:141,157:298,0:0:2,0:39:1:36.3:1:1:0:60:41.571:1:0:0.1
    724. 

  724. 2	141202033	141202034	GA	-	intronic	LRP1B	.	.	.	0.0019	.	.	.	.	.	.	.	.	rs749802189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	95	292	2	141202032	.	GGA	G	95	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=8;VD=0;AF=0;SHIFT3=12;MSI=7;MSILEN=2;SSF=0.84912;SOR=0;LSEQ=TGTGTGTCTAGAACATAGAA;RSEQ=GAGAGAGAGAGAAAATTTGT;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||64/90|NM_018557.3:c.10175-16_10175-15del|||||||rs749802189||-1||EntrezGene||YES||||2:g.141202045_141202046del|5.262e-05|0|2.955e-05|0.0001018|0.0002763|4.681e-05|1.789e-05|0|9.993e-05|0.0002763|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:3,5:8,0:0:2,0:43.5:1:37:0:1:0:60:16:1:0:0	0/1:292:6:4,2:123,163:286,6:0.0205:2,2:41.7:1:37:0:0.40886:2.64:60:12:0.0208:0:0
    725. 

  725. 2	141202075	141202075	G	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	251	2	141202075	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.94232;SOR=0;LSEQ=GTCTGAATTAAAATCACACA;RSEQ=ACATAATCAGTTGAAAATTA;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||64/90|NM_018557.3:c.10174+57C>A|||||||||-1||EntrezGene||YES||||2:g.141202075G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:2,3:5,0:0:2,0:23.8:1:37:0:1:0:60:10:1:0:0	0/1:251:3:1,2:113,134:247,3:0.012:2,2:48:1:28.3:1:1:1.68319:60:2:0.0081:0:2.3
    726. 

  726. 2	141202233	141202233	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon64:c.A10073G:p.Q3358R	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.012	0.151	B	0.022	0.184	B	0.000	0.843	D	0.999	0.458	D	-1.085	0.010	N	-3.69	0.953	D	0.31	0.040	N	0.211	0.259	-0.098	0.802	T	0.562	0.841	D	0.033	0.546	D	1.337	0.225	12.46	0.827	0.138	0.915	0.534	D	c	-0.320	-0.034	0.012	0.123	0.487	0.133	0	5.85	0.936	2.869	0.479	1.061	0.807	1.000	0.715	1.000	0.888	10.549	0.441	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	201	2	141202233	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=22;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.81202;SOR=0;LSEQ=CACACTGAAATCGGCCTGGC;RSEQ=GACATCTAAATTCAGCTAGG;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|64/91||NM_018557.3:c.10073A>G|NP_061027.2:p.Gln3358Arg|10360|10073|3358|Q/R|cAg/cGg|rs1558886859&COSV67261180||-1||EntrezGene||YES||||2:g.141202233T>C|3.99e-06|0|2.898e-05|0|0|0|0|0|0|2.898e-05|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:22:0:0,0:10,12:22,0:0:2,0:36.2:1:36.5:1:1:0:60:44:1:0:0	0/1:201:2:1,1:90,109:199,2:0.01:2,2:47.5:1:37:0:1:1.21:60:4:0.0101:0:1
    727. 

  727. 2	141202240	141202240	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon64:c.A10066G:p.R3356G	.	.	.	.	.	.	.	.	.	.	.	0.028	0.461	D	0.024	0.178	B	0.02	0.179	B	0.000	0.629	D	0.875	0.281	N	0.445	0.128	N	-3.7	0.954	D	-1.67	0.399	N	0.252	0.308	-0.154	0.788	T	0.683	0.890	D	0.035	0.562	D	4.661	0.625	24.5	0.985	0.423	0.983	0.816	D	c	-0.054	0.195	1.000	0.448	0.487	0.133	0	5.85	0.936	8.017	0.886	1.061	0.807	1.000	0.715	1.000	0.888	16.227	0.820	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	200	2	141202240	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=20;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.82607;SOR=0;LSEQ=AAATCGGCCTGGCTGACATC;RSEQ=AAATTCAGCTAGGGGAGAAA;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|64/91||NM_018557.3:c.10066A>G|NP_061027.2:p.Arg3356Gly|10353|10066|3356|R/G|Aga/Gga|||-1||EntrezGene||YES||||2:g.141202240T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:20:0:0,0:9,11:20,0:0:2,0:35.5:1:37:0:1:0:60:40:1:0:0	0/1:200:2:1,1:87,111:198,2:0.01:2,2:44.5:1:37:0:1:1.27:60:4:0.0101:0:1
    728. 

  728. 2	141208164	141208164	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon63:c.G10030A:p.D3344N	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	2.975	0.857	M	-4.36	0.973	D	-3.96	0.735	D	0.247	0.302	1.095	0.994	D	0.961	0.987	D	0.738	0.979	D	7.227	0.946	34	0.999	0.989	0.983	0.812	D	c	0.963	0.907	1.000	0.747	0.487	0.133	0	5.51	0.817	7.805	0.844	0.892	0.403	1.000	0.715	0.999	0.750	19.769	0.963	Low-density lipoprotein (LDL) receptor class A, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	80	2	141208164	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.56783;SOR=0;LSEQ=ATCAGGTTCATCAGATCCAT;RSEQ=ACCACAGTCATCCACGGTGT;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|63/91||NM_018557.3:c.10030G>A|NP_061027.2:p.Asp3344Asn|10317|10030|3344|D/N|Gat/Aat|||-1||EntrezGene||YES||||2:g.141208164C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:26:0:0,0:14,12:26,0:0:2,0:34.6:1:35.5:1:1:0:60:25:1:0:0.1	0/1:80:2:1,1:44,34:78,2:0.025:2,2:47.5:1:37:0:1:1.2899:60:4:0.025:0:1
    729. 

  729. 2	141208166	141208166	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon63:c.G10028T:p.G3343V	0.0002	.	.	.	.	.	.	.	.	rs372208989	rs372208989	0.004	0.654	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	1.96	0.533	M	-3.72	0.954	D	-4.44	0.776	D	0.859	0.846	0.973	0.968	D	0.928	0.976	D	0.481	0.949	D	7.418	0.951	34	0.997	0.823	0.987	0.853	D	c	0.863	0.833	1.000	0.747	0.487	0.133	0	5.51	0.817	7.805	0.844	0.892	0.403	1.000	0.715	0.998	0.697	19.769	0.963	Low-density lipoprotein (LDL) receptor class A, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	79	2	141208166	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.42184;SOR=0;LSEQ=CAGGTTCATCAGATCCATCA;RSEQ=CACAGTCATCCACGGTGTCA;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|63/91||NM_018557.3:c.10028G>T|NP_061027.2:p.Gly3343Val|10315|10028|3343|G/V|gGt/gTt|rs372208989&COSV101254178||-1||EntrezGene||YES||||2:g.141208166C>A|3.986e-06|6.155e-05|0|0|0|0|0|0|0|0.000227|AA||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:26:0:0,0:14,12:26,0:0:2,0:35.8:1:35.5:1:1:0:60:25:1:0:0.1	0/1:79:3:2,1:42,34:76,3:0.038:2,2:46.7:1:28.3:1:1:1.61:60:2:0.0267:0:1.3
    730. 

  730. 2	141214042	141214042	G	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon62:c.C9945A:p.S3315S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67259338;OCCURENCE=1(oesophagus)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU34849510	ESAD-UK|1|409|0.00244499	0.25	37	193	2	141214042	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=2;AF=0.0345;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.05269;SOR=inf;LSEQ=ACCTGGCTGGCTGTGCAGTT;RSEQ=GATAAGCAAGTCCTATTATC;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|62/91||NM_018557.3:c.9945C>A|NP_061027.2:p.Ser3315%3D|10232|9945|3315|S|tcC/tcA|COSV67259338||-1||EntrezGene||YES||||2:g.141214042G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:58:2:1,1:33,23:56,2:0.0345:2,2:41:0:37:0:1:1.42567:60:4:0.0351:0:1	0/0:193:0:0,0:121,72:193,0:0:2,0:38.9:1:36.2:1:1:0:60:63.333:1:0:0.1
    731. 

  731. 2	141214118	141214118	A	G	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon62:c.T9869C:p.L3290S	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	1.0	0.899	D	0.946	0.666	D	0.000	0.559	U	0.999	0.468	D	1.49	0.374	L	-3.95	0.962	D	-4.23	0.759	D	0.905	0.895	0.987	0.970	D	0.917	0.973	D	0.280	0.902	D	6.258	0.864	28.9	0.998	0.926	0.994	0.950	D	c	0.766	0.749	0.999	0.381	0.487	0.133	0	5.32	0.753	9.294	0.951	1.199	0.960	1.000	0.715	1.000	0.888	15.271	0.733	EGF-like domain|Growth factor receptor cysteine-rich domain	.	.	ID=COSV67257182;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	244	2	141214118	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=62;VD=2;AF=0.0323;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.04052;SOR=inf;LSEQ=TGTGGGTTTTTCCAGGGGCT;RSEQ=AAAGGCACAAATGACTGCAA;CSQ=G|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|62/91||NM_018557.3:c.9869T>C|NP_061027.2:p.Leu3290Ser|10156|9869|3290|L/S|tTa/tCa|COSV67257182||-1||EntrezGene||YES||||2:g.141214118A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:62:2:1,1:25,35:60,2:0.0323:2,2:45.5:1:37:0:1:1.39:60:4:0.0339:0:1	0/0:244:0:0,0:128,116:244,0:0:2,0:37.8:1:35.5:1:1:0:60:33.857:1:0:0.1
    732. 

  732. 2	141215072	141215072	G	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon61:c.C9774G:p.I3258M	.	.	.	.	.	.	.	.	.	.	.	0.231	0.182	T	0.998	0.715	D	0.96	0.686	D	0.000	0.843	U	0.911	0.364	D	2.02	0.555	M	-2.91	0.917	D	0.1	0.058	N	0.654	0.667	0.837	0.949	D	0.844	0.948	D	0.066	0.697	D	1.934	0.293	15.80	0.980	0.366	0.811	0.403	D	c	0.582	0.552	0.051	0.149	0.487	0.133	0	4.5	0.542	0.604	0.237	1.048	0.713	1.000	0.715	1.000	0.888	16.207	0.819	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	260	2	141215072	.	G	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=32;VD=2;AF=0.0625;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.01167;SOR=inf;LSEQ=TGATACACCTGGATATCTGT;RSEQ=ATGGCATGCCATGAGTAAAT;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|61/91||NM_018557.3:c.9774C>G|NP_061027.2:p.Ile3258Met|10061|9774|3258|I/M|atC/atG|||-1||EntrezGene||YES||||2:g.141215072G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:32:2:1,1:18,12:30,2:0.0625:2,2:12.5:1:37:0:1:1.48061:60:4:0.0625:0:1	0/0:260:0:0,0:155,104:259,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    733. 

  733. 2	141215081	141215081	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon61:c.G9765T:p.W3255C	.	.	.	.	.	.	.	.	.	.	.	0.192	0.210	T	1.0	0.899	D	0.956	0.680	D	0.000	0.629	U	1	0.810	D	1.495	0.376	L	-2.76	0.909	D	-1.45	0.356	N	0.861	0.848	0.744	0.937	D	0.827	0.942	D	0.157	0.839	D	5.661	0.772	26.7	0.988	0.462	0.959	0.662	D	c	0.813	0.802	1.000	0.747	0.487	0.133	0	5.46	0.799	7.879	0.856	0.935	0.490	1.000	0.715	1.000	0.888	19.315	0.942	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	278	2	141215081	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=2;AF=0.0541;SHIFT3=4;MSI=2;MSILEN=1;SSF=0.01347;SOR=inf;LSEQ=TGGATATCTGTGATGGCATG;RSEQ=CATGAGTAAATCAGTGAGAG;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|61/91||NM_018557.3:c.9765G>T|NP_061027.2:p.Trp3255Cys|10052|9765|3255|W/C|tgG/tgT|COSV67197436||-1||EntrezGene||YES||||2:g.141215081C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:2:1,1:21,14:35,2:0.0541:2,2:42:1:37:0:1:1.4832:60:4:0.0541:0:1	0/0:278:0:0,0:159,119:278,0:0:2,0:37.7:1:35.4:1:1:0:60:38.714:1:0:0.1
    734. 

  734. 2	141215191	141215191	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon61:c.G9655A:p.A3219T	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	0.993	0.637	D	0.782	0.555	P	0.000	0.523	U	1.000	0.537	D	2.22	0.631	M	-2.9	0.917	D	-3.22	0.649	D	0.662	0.674	0.817	0.946	D	0.831	0.943	D	0.129	0.812	D	6.451	0.890	29.9	0.999	0.957	0.951	0.630	D	c	0.783	0.783	1.000	0.747	0.487	0.133	0	5.46	0.799	7.879	0.856	0.935	0.490	1.000	0.715	1.000	0.888	19.315	0.942	Domain of unknown function DUF5050|Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	273	2	141215191	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=61;VD=2;AF=0.0328;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.03291;SOR=inf;LSEQ=GTCTTCAAACAATGTTAGTG;RSEQ=AATCACCCCTGGAATATCTT;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|61/91||NM_018557.3:c.9655G>A|NP_061027.2:p.Ala3219Thr|9942|9655|3219|A/T|Gca/Aca|||-1||EntrezGene||YES||||2:g.141215191C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:61:2:1,1:29,30:59,2:0.0328:2,2:62:1:37:0:1:1.03:60:4:0.0328:0:1.5	0/0:273:0:0,0:113,160:273,0:0:2,0:40.2:1:36:1:1:0:60:44.5:1:0:0.1
    735. 

  735. 2	141215201	141215201	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon61:c.A9645G:p.P3215P	0.0008	3.229e-05	0	0	0	0.0006	0	0	0	rs775991709	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	271	2	141215201	.	T	C	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=55;VD=2;AF=0.0364;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.13372;SOR=5.03815;LSEQ=AATGTTAGTGCAATCACCCC;RSEQ=GGAATATCTTGATTAGGGAC;CSQ=C|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|61/91||NM_018557.3:c.9645A>G|NP_061027.2:p.Pro3215%3D|9932|9645|3215|P|ccA/ccG|rs775991709||-1||EntrezGene||YES||||2:g.141215201T>C|5.183e-05|0|0|0|0.0007075|0|0|0|0|0.0007075|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:55:2:1,1:25,28:53,2:0.0364:2,2:39:1:37:0:1:1.12:60:4:0.037:0:1	0/0:271:2:1,1:105,164:269,2:0.0074:2,2:43.5:1:37:0:1:1.56:60:4:0.0075:0:1
    736. 

  736. 2	141215236	141215236	G	A	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	200	2	141215236	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=36;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.71763;SOR=0;LSEQ=AGGGACTGTAATAGGAGATG;RSEQ=TAAGATTAATGTTCAGTCTT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||60/90|NM_018557.3:c.9626-16C>T|||||||rs1274495953&COSV67257264||-1||EntrezGene||YES||||2:g.141215236G>A|4.006e-06|0|0|0|0|0|8.881e-06|0|0|8.881e-06|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:36:0:0,0:14,22:36,0:0:2,0:33.8:1:37:0:1:0:60:72:1:0:0.2	0/1:200:2:1,1:66,132:198,2:0.01:2,2:55.5:1:31:1:1:1.99:60:4:0.0104:0:1
    737. 

  737. 2	141232911	141232911	G	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	54	2	141232911	.	G	T	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.89662;SOR=0;LSEQ=AATCCAATACAAATATCTAG;RSEQ=AAAGAAAATCAATACTGATT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||59/90|NM_018557.3:c.9426-5C>A|||||||||-1||EntrezGene||YES||||2:g.141232911G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:47:1:33:1:1:0:60:6:1:0:0	0/1:54:2:1,1:15,37:52,2:0.037:2,2:67.5:1:37:0:0.50874:2.42:60:4:0.0392:0:1
    738. 

  738. 2	141242882	141242882	A	T	intronic	LRP1B	.	.	.	0.093	0.0679	0.0799	0.0298	0.0629	0.0006	0.0968	0.0632	0.0745	rs112109442	rs112109442	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV104431643;OCCURENCE=10(meninges)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	58	81	2	141242882	.	A	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=4;MSI=1;MSILEN=1;SSF=1e-05;SOR=inf;LSEQ=TGAATGTAATCCAGTCTTAA;RSEQ=CTTTAAGATTTTTAACAGTT;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||59/90|NM_018557.3:c.9425+30T>A|||||||rs112109442&COSV104431643||-1||EntrezGene||YES||||2:g.141242882A>T|0.04806|0.082|0.02529|0.06056|0.001138|0.09572|0.05107|0.05616|0.03072|0.09572|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:37:0:1:0:60:6:1:0:2	0/0:81:0:0,0:58,23:81,0:0:2,0:31.7:1:35.1:1:1:0:60:26:1:0:0.1
    739. 

  739. 2	141242918	141242918	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon59:c.A9419G:p.Q3140R	0.091	0.0658	0.0786	0.0274	0.0629	0.0006	0.0959	0.0602	0.0724	rs34488772	rs34488772	0.51	0.075	T	0.0	0.026	B	0.0	0.013	B	0.035	0.247	N	1.000	0.182	N	0.03	0.081	N	-2.74	0.907	D	-0.63	0.185	N	0.01	0.001	-0.901	0.479	T	0.035	0.150	T	.	.	.	-1.186	0.025	0.007	0.519	0.046	0.067	0.126	N	c	-1.924	-1.967	0.216	0.183	0.487	0.133	0	-9.9	0.004	-0.575	0.059	-1.072	0.019	0.149	0.234	0.963	0.446	12.399	0.546	Domain of unknown function DUF5050|Six-bladed beta-propeller, TolB-like	.	.	ID=COSV67182511;OCCURENCE=10(meninges),5(soft_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	.	.	0.25	74	144	2	141242918	.	T	C	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=4;AF=0.6667;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CAGTTTTTACAAACCCAGCT;RSEQ=GAGGATCTAAAGACAAGTCT;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|59/91||NM_018557.3:c.9419A>G|NP_061027.2:p.Gln3140Arg|9706|9419|3140|Q/R|cAa/cGa|rs34488772&COSV67182511||-1||EntrezGene||YES||||2:g.141242918T>C|0.04665|0.0813|0.02391|0.06111|0.001271|0.09512|0.04865|0.05574|0.03105|0.09512|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:6:4:3,1:1,1:2,4:0.6667:2,2:42.8:1:37:0:1:2.45:60:8:0.6667:0:1.8	0/0:144:0:0,0:92,52:144,0:0:2,0:33.7:1:35.3:1:1:0:60:27.8:1:0:0.1
    740. 

  740. 2	141259302	141259302	A	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon55:c.T8804A:p.V2935D	.	.	.	.	.	.	.	.	.	.	.	0.012	0.546	D	0.177	0.273	B	0.036	0.216	B	0.000	0.497	U	1.000	0.548	D	-0.1	0.047	N	-2.1	0.862	D	-3.4	0.670	D	0.534	0.573	-0.702	0.604	T	0.319	0.688	T	0.045	0.619	D	5.621	0.766	26.6	0.983	0.397	0.976	0.759	D	c	-0.320	-0.120	0.000	0.070	0.554	0.246	0	3.05	0.341	5.316	0.654	1.140	0.893	1.000	0.715	1.000	0.888	9.309	0.369	EGF-like calcium-binding domain|EGF-like domain|Growth factor receptor cysteine-rich domain;EGF-like calcium-binding domain|Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	155	2	141259302	.	A	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=2;AF=0.1111;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01028;SOR=inf;LSEQ=AGTCTTGAGAACATCCACTG;RSEQ=CTTTCTTACTCAAACATTCA;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|55/91||NM_018557.3:c.8804T>A|NP_061027.2:p.Val2935Asp|9091|8804|2935|V/D|gTc/gAc|||-1||EntrezGene||YES||||2:g.141259302A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:18:2:1,1:8,8:16,2:0.1111:2,2:10:0:37:0:1:1:60:4:0.1111:0:2	0/0:155:0:0,0:91,64:155,0:0:2,0:37.2:1:36.9:1:1:0:60:310:1:0:0.1
    741. 

  741. 2	141259346	141259346	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon55:c.A8760G:p.S2920S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	68	188	2	141259346	.	T	C	68	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=22;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.64015;SOR=0;LSEQ=ATATGGCAGTTTCTCTCATC;RSEQ=GAACCATCGCCACAGTCATC;CSQ=C|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|55/91||NM_018557.3:c.8760A>G|NP_061027.2:p.Ser2920%3D|9047|8760|2920|S|tcA/tcG|||-1||EntrezGene||YES||||2:g.141259346T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:22:0:0,0:11,11:22,0:0:2,0:48.5:1:35.9:1:1:0:60:44:1:0:1	0/1:188:4:2,2:97,87:184,4:0.0213:2,2:31:1:34:1:1:1.1143:60:8:0.0217:0:1
    742. 

  742. 2	141259376	141259376	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon55:c.C8730T:p.C2910C	0.3	0.2063	0.0852	0.1583	0.2252	0.0136	0.2952	0.2750	0.2740	rs35164907	rs35164907	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67182519;OCCURENCE=1(bone),12(soft_tissue),1(lung),1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU115441	LUSC-KR|1|170|0.00588235	0.25	132	201	2	141259376	.	G	A	132	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=22;VD=12;AF=0.5455;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CCACAGTCATCCTTATTGTC;RSEQ=CAAAGACCTCCACTGGGAAT;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|55/91||NM_018557.3:c.8730C>T|NP_061027.2:p.Cys2910%3D|9017|8730|2910|C|tgC/tgT|rs35164907&COSV67182519||-1||EntrezGene||YES||||2:g.141259376G>A|0.2114|0.08097|0.1244|0.2155|0.01674|0.3024|0.2679|0.2173|0.22|0.3024|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:22:12:6,6:5,5:10,12:0.5455:2,2:53.3:1:37:0:1:1:60:24:0.5714:0:1.8	0/0:201:0:0,0:97,104:201,0:0:2,0:37.7:1:35.9:1:1:0:60:32.5:1:0:0.1
    743. 

  743. 2	141259448	141259448	A	-	intronic	LRP1B	.	.	.	0.0035	.	.	.	.	.	.	.	.	rs750923821	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU91736305	ESAD-UK|2|409|0.00488998	0.25	37	140	2	141259447	.	GA	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=3;VD=0;AF=0;SHIFT3=7;MSI=8;MSILEN=1;SSF=0.95834;SOR=0;LSEQ=ACTGTTGCATGACTGTTCTG;RSEQ=AAAAAAATAAAACAAATGGA;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||54/90|NM_018557.3:c.8663-5del|||||||rs202023981||-1||EntrezGene||YES||||2:g.141259455del|3.786e-05|0|3.818e-05|0|6.313e-05|0|4.051e-05|0|8.26e-05|0.003516|AA|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:50.3:1:37:0:1:0:60:6:1:0:0	0/1:140:2:1,1:47,91:138,2:0.0143:2,2:59.5:1:37:0:1:1.93:60:4:0.0143:0:1
    744. 

  744. 2	141260507	141260507	T	C	intronic	LRP1B	.	.	.	0.33	0.2806	0.3252	0.1811	0.2433	0.0154	0.2963	0.2854	0.2910	rs4450541	rs4450541	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67279453;OCCURENCE=52(meninges),1(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	74	133	2	141260507	.	T	C	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGAAAACACTTTAGAGTAAA;RSEQ=GCGGTATTGTATATATTTCT;CSQ=C|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||54/90|NM_018557.3:c.8662+25A>G|||||||rs4450541&COSV67279453||-1||EntrezGene||YES||||2:g.141260507T>C|0.2394|0.3273|0.1444|0.2373|0.01747|0.3032|0.2814|0.2413|0.2338|0.3273|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:3,1:0,0:0,4:1:0,2:26.8:1:37:0:1:0:60:8:1:0:1	0/0:133:0:0,0:92,41:133,0:0:2,0:36.6:1:36.6:1:1:0:60:132:1:0:0.1
    745. 

  745. 2	141260533	141260533	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon54:c.A8661G:p.A2887A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	179	2	141260533	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.9063;SOR=0;LSEQ=ATTGTATATATTTCTGTACC;RSEQ=GCACTTTTACACTTTGGGTT;CSQ=C|splice_region_variant&synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|54/91||NM_018557.3:c.8661A>G|NP_061027.2:p.Ala2887%3D|8948|8661|2887|A|gcA/gcG|rs1465867790||-1||EntrezGene||YES||||2:g.141260533T>C|3.988e-06|0|0|0|0|0|8.822e-06|0|0|8.822e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:7,2:9,0:0:2,0:30.1:1:37:0:1:0:60:18:1:0:0.8	0/1:179:2:1,1:112,64:176,2:0.0112:2,2:11.5:1:37:0:1:1.74413:60:4:0.0112:0:1
    746. 

  746. 2	141260668	141260668	A	G	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon54:c.T8526C:p.Y2842Y	0.75	0.5463	0.4917	0.4580	0.4040	0.7593	0.5842	0.5528	0.5647	rs4444457	rs4444457	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67186049;OCCURENCE=1(lung),96(meninges),1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU115465	COCA-CN|5|321|0.0155763	0.75	223	153	2	141260668	.	A	G	223	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=13;AF=0.9286;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.00064;SOR=14.8348;LSEQ=TCTTCTGTACCACACTGTCG;RSEQ=TATCCTAGAGACGCAGAAAA;CSQ=G|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|54/91||NM_018557.3:c.8526T>C|NP_061027.2:p.Tyr2842%3D|8813|8526|2842|Y|taT/taC|rs4444457&COSV67186049||-1||EntrezGene||YES||||2:g.141260668A>G|0.548|0.4972|0.4603|0.4096|0.7559|0.5892|0.5524|0.5233|0.5539|0.7559|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:14:13:4,9:0,0:0,13:0.9286:0,2:18.4:1:37:0:1:0:60:26:0.9286:0:1	0/1:153:71:21,50:30,52:82,71:0.4641:2,2:36.8:1:36.3:1:0.39333:1.37077:60:70:0.4605:0:1.1
    747. 

  747. 2	141267628	141267628	G	A	intronic	LRP1B	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs772663069	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67220834;OCCURENCE=1(skin)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU37350948	SKCA-BR|1|100|0.01	0.25	37	165	2	141267628	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=197;VD=2;AF=0.0102;SHIFT3=4;MSI=3;MSILEN=1;SSF=0.29547;SOR=inf;LSEQ=CAGCACAGGTTATGGCACCT;RSEQ=AAACACAAAAACATAATGCC;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||51/90|NM_018557.3:c.8270-3C>T|||||||rs772663069&COSV67220834||-1||EntrezGene||YES||||2:g.141267628G>A|4.007e-06|0|0|0|5.482e-05|0|0|0|0|5.482e-05|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:197:2:1,1:60,135:195,2:0.0102:2,2:16.5:1:37:0:0.5245:2.24:60:4:0.0102:0:1	0/0:165:0:0,0:64,100:164,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    748. 

  748. 2	141267679	141267679	G	A	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	122	2	141267679	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=77;VD=2;AF=0.026;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14852;SOR=inf;LSEQ=CTCTGTGTCCACTGGAAAAT;RSEQ=TCTACCATTTACATTTTCTA;CSQ=A|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||51/90|NM_018557.3:c.8270-54C>T|||||||||-1||EntrezGene||YES||||2:g.141267679G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:77:2:1,1:22,52:74,2:0.026:2,2:25.5:1:37:0:0.51649:2.33:60:4:0.0263:0:1.5	0/0:122:0:0,0:35,87:122,0:0:2,0:37.2:1:36.6:1:1:0:60:121:1:0:0.5
    749. 

  749. 2	141272199	141272199	A	G	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	151	2	141272199	.	A	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.94889;SOR=0;LSEQ=TAATGCTTAAAAACTGATTG;RSEQ=GGACAGAAGATACACAACTT;CSQ=G|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||51/90|NM_018557.3:c.8269+23T>C|||||||||-1||EntrezGene||YES||||2:g.141272199A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:3,1:4,0:0:2,0:36.5:1:37:0:1:0:60:8:1:0:0	0/1:151:2:1,1:101,48:149,2:0.0132:2,2:33:0:37:0:0.54517:2.09292:60:4:0.0133:0:1
    750. 

  750. 2	141272360	141272360	-	A	intronic	LRP1B	.	.	.	0.14	0.0061	0.0023	0.0029	0.0041	0.0754	0.0028	0.0006	0.0030	rs201317136	rs201317136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112078028	BTCA-SG|1|71|0.0140845	0.25	62	132	2	141272360	.	G	GA	62	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=3;VD=0;AF=0;SHIFT3=11;MSI=12;MSILEN=1;SSF=0.93433;SOR=0;LSEQ=ATCTAGGAAACAAACAAAAG;RSEQ=AAAAAAAAAAATAGTTTGAG;CSQ=A|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||50/90|NM_018557.3:c.8150-20dup|||||||rs199711847||-1||EntrezGene||YES||||2:g.141272371dup|0.04122|0.01644|0.02438|0.05217|0.174|0.02027|0.02699|0.05042|0.06203|0.174|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:0,2:2,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:132:3:1,2:28,82:110,3:0.0227:2,2:24.2:1:39.5:0:1:1.46:64:6:0.0323:0:0
    751. 

  751. 2	141274537	141274537	A	G	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon50:c.T8070C:p.P2690P	0.0001	.	.	.	.	.	.	.	.	rs759884420	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	177	2	141274537	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.90532;SOR=0;LSEQ=TTCAAAATGCATCTTCCACT;RSEQ=GGACAACTAAAATAATTTTC;CSQ=G|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|50/91||NM_018557.3:c.8070T>C|NP_061027.2:p.Pro2690%3D|8357|8070|2690|P|ccT/ccC|rs759884420||-1||EntrezGene||YES||||2:g.141274537A>G|1.991e-05|0|0|0|0|0|0|0|0.0001634|0.0001634|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:4,5:9,0:0:2,0:41.7:1:37:0:1:0:60:18:1:0:0	0/1:177:2:1,1:74,101:175,2:0.0113:2,2:42:1:37:0:1:1.36:60:4:0.0113:0:2
    752. 

  752. 2	141274576	141274576	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon50:c.A8031G:p.Q2677Q	0.77	0.7137	0.6961	0.7542	0.8543	0.3999	0.6857	0.7578	0.7296	rs4954672	rs4954672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67186053;OCCURENCE=1(breast),3(haematopoietic_and_lymphoid_tissue),4(lung),1(upper_aerodigestive_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU800510	LAML-KR|4|205|0.0195122,LUSC-KR|3|170|0.0176471,COCA-CN|2|321|0.00623053,BRCA-KR|1|50|0.02	0.5	241	124	2	141274576	.	T	C	241	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTTCACATTTGTGTTTGTT;RSEQ=TGAACTGTGATAAAATATGG;CSQ=C|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|50/91||NM_018557.3:c.8031A>G|NP_061027.2:p.Gln2677%3D|8318|8031|2677|Q|caA/caG|rs4954672&COSV67186053||-1||EntrezGene||YES||||2:g.141274576T>C|0.7129|0.6888|0.7399|0.8386|0.4032|0.6849|0.7645|0.7507|0.6609|0.8386|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:2,4:6,0:0:2,0:39.7:1:37:0:1:0:60:12:1:0:0	1/1:124:123:45,78:0,0:0,123:0.9919:0,2:33.1:1:34.8:1:1:0:60:16.571:1:0:1.3
    753. 

  753. 2	141283603	141283603	T	G	intronic	LRP1B	.	.	.	1.	0.9851	0.9480	0.9964	1	1	1	0.9999	0.9969	rs1352047	rs1352047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81741430	COCA-CN|5|321|0.0155763	1	245	133	2	141283603	.	T	G	245	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAAAAAGTACCTCATTT;RSEQ=CAAAGATTATGAGCCTTCTA;CSQ=G|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||48/90|NM_018557.3:c.7877-41A>C|||||||rs1352047||-1||EntrezGene||YES||||2:g.141283603T>G|0.9962|0.9465|0.9982|0.9995|1|1|0.9999|0.998|0.9999|1|EAS&SAS&gnomAD_EAS&gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:3,2:0,0:0,5:1:0,2:19.2:1:37:0:1:0:60:10:1:0:1	1/1:133:133:44,89:0,0:0,133:1:0,2:35.5:1:34.8:1:1:0:60:15.625:1:0:1.1
    754. 

  754. 2	141283892	141283892	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon48:c.G7790A:p.R2597H	.	3.234e-05	0.0001	0	0	0	0	0	0	rs968042014	.	0.026	0.469	D	0.002	0.090	B	0.005	0.104	B	0.000	0.454	D	0.899	0.277	N	1.545	0.392	L	-3.92	0.961	D	-2.26	0.505	N	0.173	0.210	0.096	0.841	D	0.737	0.910	D	0.067	0.702	D	6.538	0.900	31	0.999	0.982	0.903	0.511	D	c	-0.252	-0.126	0.001	0.076	0.487	0.133	0	2.3	0.276	1.739	0.376	0.935	0.490	1.000	0.715	0.983	0.502	10.352	0.429	.	.	.	ID=COSV67204592;OCCURENCE=1(stomach)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU5590384	STAD-US|1|439|0.0022779	0.25	37	264	2	141283892	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=167;VD=2;AF=0.012;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.14958;SOR=inf;LSEQ=TACAAGTCCCATCTGCACAG;RSEQ=GGAACTCAACCGTGGCACAG;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|48/91||NM_018557.3:c.7790G>A|NP_061027.2:p.Arg2597His|8077|7790|2597|R/H|cGc/cAc|rs968042014&COSV67204592||-1||EntrezGene||YES||||2:g.141283892C>T|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:167:2:1,1:68,97:165,2:0.012:2,2:36:0:37:0:1:1.42:60:4:0.012:0:1	0/0:264:0:0,0:110,154:264,0:0:2,0:40.5:1:36.4:1:1:0:60:263:1:0:0.1
    755. 

  755. 2	141294286	141294286	A	-	intronic	LRP1B	.	.	.	0.42	0.0125	0.0134	0.0197	0.0227	0.0088	0.0658	0.0084	0.0120	rs755359693	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	777172	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112067517	BTCA-SG|6|71|0.084507	0.5	111	80	2	141294285	.	GA	G	111	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=46;VD=3;AF=0.0652;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.37716;SOR=0.63009;LSEQ=GGAGGAATTTTTAGCTGCAA;RSEQ=AAAAAAAAAAAAGTCAATAC;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||45/90|NM_018557.3:c.7514-8del|||||||rs748331070||-1||EntrezGene||YES||||2:g.141294298del|0.3611|0.3893|0.3628|0.3365|0.3733|0.3209|0.363|0.3486|0.3685|0.3893|gnomAD_AFR|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:46:3:1,2:16,27:43,3:0.0652:2,2:18:1:37:0:1:1.18087:60:6:0.0682:0:0	0/1:80:8:3,5:24,46:70,8:0.1:2,2:46.5:1:37:0:1:1.15:60:16:0.1:0:0.1
    756. 

  756. 2	141298674	141298674	T	C	intronic	LRP1B	.	.	.	0.48	0.3494	0.1858	0.3621	0.3742	0.3510	0.4485	0.4165	0.4083	rs13013854	rs13013854	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67182523;OCCURENCE=80(meninges),1(stomach),1(haematopoietic_and_lymphoid_tissue),16(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU585211	LICA-CN|2|402|0.00497512,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	141	298	2	141298674	.	T	C	141	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=29;VD=15;AF=0.5172;SHIFT3=1;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGGAGAAAGTTCACCTACAA;RSEQ=AAAGAGGGTGTATTGGTAAC;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||44/90|NM_018557.3:c.7388-7A>G|||||||rs13013854&COSV67182523||-1||EntrezGene||YES||||2:g.141298674T>C|0.3935|0.1757|0.3466|0.3748|0.3488|0.444|0.4274|0.3753|0.4374|0.4796|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:29:15:4,11:5,9:14,15:0.5172:2,2:27.2:1:36.2:1:0.69985:1.50543:60:30:0.5172:0:2	0/0:298:0:0,0:131,166:297,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    757. 

  757. 2	141298682	141298682	G	C	intronic	LRP1B	.	.	.	0.62	0.4973	0.4414	0.4233	0.4338	0.5985	0.5407	0.5137	0.5092	rs11694934	rs11694934	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67278757;OCCURENCE=98(meninges),1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13320946	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,COCA-CN|5|321|0.0155763	0.5	175	273	2	141298682	.	G	C	175	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=28;AF=1;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=GTTCACCTACAATAAAGAGG;RSEQ=TGTATTGGTAACATTTTATA;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||44/90|NM_018557.3:c.7388-15C>G|||||||rs11694934&COSV67278757||-1||EntrezGene||YES||||2:g.141298682G>C|0.5056|0.4364|0.3929|0.4397|0.5863|0.5393|0.5184|0.4614|0.5788|0.6176|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:28:28:8,20:0,0:0,28:1:0,2:22.8:1:36.6:1:1:0:60:56:1:0:1.6	0/0:273:0:0,0:111,162:273,0:0:2,0:37.7:1:36.6:1:1:0:60:272:1:0:0.1
    758. 

  758. 2	141299334	141299334	C	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	135	2	141299334	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=15;VD=2;AF=0.1333;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0094;SOR=inf;LSEQ=TGAAAAAACACATTTGCTTT;RSEQ=TATTATAACTTACAGCTATT;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||44/90|NM_018557.3:c.7387+14G>A|||||||||-1||EntrezGene||YES||||2:g.141299334C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:15:2:1,1:9,4:13,2:0.1333:2,2:39:1:37:0:1:2.12136:60:4:0.1333:0:2	0/0:135:0:0,0:86,49:135,0:0:2,0:38.1:1:34.7:1:1:0:60:21.5:1:0:0.1
    759. 

  759. 2	141299502	141299502	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon44:c.G7233T:p.L2411F	.	.	.	.	.	.	.	.	.	.	.	0.005	0.632	D	0.999	0.764	D	0.997	0.850	D	0.005	0.331	U	0.997	0.437	D	2.535	0.741	M	-3.05	0.924	D	-2.71	0.577	D	0.687	0.693	0.665	0.927	D	0.826	0.942	D	0.254	0.893	D	4.087	0.549	23.7	0.998	0.856	0.463	0.275	N	c	-0.022	-0.146	0.000	0.035	0.487	0.133	0	2.61	0.301	-0.286	0.084	0.013	0.140	0.384	0.258	0.993	0.574	8.586	0.326	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	130	2	141299502	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=2;AF=0.0714;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.03048;SOR=inf;LSEQ=ATATAATTGTCATAAACAGC;RSEQ=AAACTGAGGAAAGTCCCTGG;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|44/91||NM_018557.3:c.7233G>T|NP_061027.2:p.Leu2411Phe|7520|7233|2411|L/F|ttG/ttT|||-1||EntrezGene||YES||||2:g.141299502C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:28:2:1,1:10,16:26,2:0.0714:2,2:9:0:37:0:1:1.57:60:4:0.0714:0:1	0/0:130:0:0,0:50,80:130,0:0:2,0:37.8:1:36.1:1:1:0:60:64:1:0:0
    760. 

  760. 2	141359141	141359141	G	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon42:c.C6867A:p.T2289T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	25	313	2	141359141	.	G	T	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=115;VD=2;AF=0.0174;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.07173;SOR=inf;LSEQ=TGTCTGGTGATGGATGAGGT;RSEQ=GTAGAGCTTGTCCAGTACAG;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|42/91||NM_018557.3:c.6867C>A|NP_061027.2:p.Thr2289%3D|7154|6867|2289|T|acC/acA|||-1||EntrezGene||YES||||2:g.141359141G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:115:2:1,1:52,61:113,2:0.0174:2,2:49.5:1:25:0:1:1.17:60:4:0.0179:0:1	0/0:313:0:0,0:129,184:313,0:0:2,0:39.2:1:36.6:1:1:0:60:626:1:0:0.1
    761. 

  761. 2	141457956	141457956	A	G	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon41:c.T6662C:p.F2221S	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	0.442	0.341	B	0.193	0.348	B	0.000	0.843	U	1.000	0.511	D	1.085	0.274	L	-2.82	0.912	D	-2.04	0.468	N	0.769	0.762	0.190	0.857	D	0.624	0.868	D	0.078	0.729	D	4.570	0.612	24.4	0.996	0.730	0.989	0.876	D	c	0.241	0.333	0.975	0.296	0.487	0.133	0	4.47	0.536	9.268	0.948	1.140	0.893	1.000	0.715	1.000	0.888	14.042	0.640	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	131	2	141457956	.	A	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.9414;SOR=0;LSEQ=CCAAGGCTATGACATTCTTG;RSEQ=AATAACGTGGATTCTCATAT;CSQ=G|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|41/91||NM_018557.3:c.6662T>C|NP_061027.2:p.Phe2221Ser|6949|6662|2221|F/S|tTc/tCc|||-1||EntrezGene||YES||||2:g.141457956A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:28.5:1:37:0:1:0:60:8:1:0:0	0/1:131:2:1,1:83,46:129,2:0.0153:2,2:42:1:37:0:1:1.79567:60:4:0.0153:0:1
    762. 

  762. 2	141458173	141458173	T	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon41:c.A6445T:p.R2149W	0.0001	.	.	.	.	.	.	.	.	rs781779397	.	0.053	0.388	T	0.464	0.346	P	0.174	0.339	B	0.000	0.469	U	0.698	0.334	D	1.19	0.302	L	-3.77	0.956	D	-2.53	0.548	D	0.218	0.267	0.694	0.931	D	0.727	0.906	D	0.131	0.814	D	4.926	0.662	25.0	0.997	0.787	0.897	0.500	D	c	0.026	0.109	0.000	0.029	0.554	0.246	0	3.31	0.369	1.770	0.379	0.109	0.204	1.000	0.715	0.987	0.523	9.558	0.383	EGF-like domain|Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	61	266	2	141458173	.	T	A	61	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.45246;SOR=0;LSEQ=CTTACAGCCACCATTGTCCC;RSEQ=GGCACAAACATTGGTCCCTA;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|41/91||NM_018557.3:c.6445A>T|NP_061027.2:p.Arg2149Trp|6732|6445|2149|R/W|Agg/Tgg|rs781779397||-1||EntrezGene||YES||||2:g.141458173T>A|3.985e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:58:0:0,0:27,31:58,0:0:2,0:33.3:1:33.5:1:1:0:60:10.6:1:0:0	0/1:266:4:2,2:108,154:262,4:0.015:2,2:13:1:30.5:1:1:1.42:60:3:0.0118:0:2
    763. 

  763. 2	141458230	141458230	T	-	intronic	LRP1B	.	.	.	0.018	0.0009	0	0.0012	0	0.0155	0	6.687e-05	0	rs200561604	rs200561604	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	151	2	141458229	.	GT	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=15;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.82694;SOR=0;LSEQ=ACACACATGCACATGTTTAT;RSEQ=TTTTCTTTTGTTTTTGAAAC;CSQ=-|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||40/90|NM_018557.3:c.6428-40del|||||||rs200561604||-1||EntrezGene||YES||||2:g.141458234del|0.001137|0|0|0|0.01493|0|0|0.0001919|0.0001201|0.0179|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:4,11:15,0:0:2,0:32.1:1:36.2:1:1:0:60:30:1:0:0.1	0/1:151:2:1,1:43,105:148,2:0.0132:2,2:37.5:1:37:0:0.50201:2.43:60:4:0.0136:0:0.5
    764. 

  764. 2	141459291	141459291	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon40:c.A6426G:p.K2142K	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	197	2	141459291	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.70819;SOR=0;LSEQ=TTCTTTCAAGAGTGCTGACC;RSEQ=TTCTCTCTTACTCGGTTAAA;CSQ=C|splice_region_variant&synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|40/91||NM_018557.3:c.6426A>G|NP_061027.2:p.Lys2142%3D|6713|6426|2142|K|aaA/aaG|||-1||EntrezGene||YES||||2:g.141459291T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:37:0:0,0:25,12:37,0:0:2,0:23.6:1:34.7:1:1:0:60:36:1:0:0.1	0/1:197:2:1,1:130,65:195,2:0.0102:2,2:22.5:1:31:1:1:1.99247:60:4:0.0104:0:1
    765. 

  765. 2	141459354	141459354	G	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon40:c.C6363A:p.T2121T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	290	2	141459354	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=151;VD=2;AF=0.0132;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11673;SOR=inf;LSEQ=ACTCCAAGGCCGGTTCTCAT;RSEQ=GTTATCGTTTCTGTGGCATC;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|40/91||NM_018557.3:c.6363C>A|NP_061027.2:p.Thr2121%3D|6650|6363|2121|T|acC/acA|||-1||EntrezGene||YES||||2:g.141459354G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:151:2:1,1:95,54:149,2:0.0132:2,2:13:0:37:0:1:1.75225:60:4:0.0134:0:1	0/0:290:0:0,0:152,138:290,0:0:2,0:39:0:11:0:1:0:60:0:0:0:6
    766. 

  766. 2	141459451	141459451	C	T	intronic	LRP1B	.	.	.	0.0003	.	.	.	.	.	.	.	.	rs745352463	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU49187340	MELA-AU|1|183|0.00546448,PRAD-CN|1|65|0.0153846	0.25	31	190	2	141459451	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=2;AF=0.0135;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.191;SOR=inf;LSEQ=CATACATGATCAACAATCTT;RSEQ=GACTAATTAAAGTCAAGCCA;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||39/90|NM_018557.3:c.6303-37G>A|||||||rs745352463||-1||EntrezGene||YES||||2:g.141459451C>T|2.822e-05|0|0|0|0|0|1.785e-05|0|0.0001658|0.0001658|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:148:2:1,1:71,75:146,2:0.0135:2,2:51.5:1:31:1:1:1.06:60:4:0.0138:0:1	0/0:190:0:0,0:72,117:189,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    767. 

  767. 2	141459786	141459786	C	A	exonic	LRP1B	.	stopgain	LRP1B:NM_018557:exon39:c.G6226T:p.E2076X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.559	U	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.339	0.996	45	0.998	0.853	0.980	0.784	D	c	0.988	0.839	0.985	0.308	0.487	0.133	0	5.5	0.813	7.858	0.852	0.935	0.490	1.000	0.715	0.981	0.494	19.388	0.945	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV101261240;OCCURENCE=1(lung)	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU130704576	LUSC-US|1|485|0.00206186	0.25	37	331	2	141459786	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=2;AF=0.0144;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.08702;SOR=inf;LSEQ=GCTTCCTGACAGCACCATCT;RSEQ=GCGATTCCCTCCAGTCTCAA;CSQ=A|stop_gained|HIGH|LRP1B|53353|Transcript|NM_018557.3|protein_coding|39/91||NM_018557.3:c.6226G>T|NP_061027.2:p.Glu2076Ter|6513|6226|2076|E/*|Gag/Tag|COSV101261240&COSV67197518||-1||EntrezGene||YES||||2:g.141459786C>A|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:139:2:1,1:65,72:137,2:0.0144:2,2:64:0:37:0:1:1.11:60:4:0.0145:0:2.5	0/0:331:0:0,0:166,165:331,0:0:2,0:38.3:1:36.6:1:1:0:60:109.333:1:0:0.1
    768. 

  768. 2	141459810	141459810	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon39:c.G6202A:p.D2068N	.	.	.	.	.	.	.	.	.	.	.	0.355	0.121	T	0.05	0.209	B	0.011	0.145	B	0.001	0.422	U	0.986	0.403	D	0.395	0.123	N	-3.22	0.934	D	-1.06	0.277	N	0.02	0.004	-0.086	0.804	T	0.597	0.857	D	0.037	0.574	D	4.506	0.603	24.3	0.998	0.906	0.904	0.512	D	c	-0.107	0.139	0.463	0.206	0.487	0.133	0	5.6	0.849	5.619	0.672	0.935	0.490	1.000	0.715	0.996	0.625	19.627	0.957	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV67206516;OCCURENCE=1(breast),1(prostate),1(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU1912808	SKCA-BR|1|100|0.01,UCEC-US|2|531|0.00376648,BRCA-US|1|1020|0.000980392,PRAD-US|1|497|0.00201207	0.25	37	310	2	141459810	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=2;AF=0.0148;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09156;SOR=inf;LSEQ=ATTCCCTCCAGTCTCAAGGT;RSEQ=GATTCTCTCTATCTTGTCTG;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|39/91||NM_018557.3:c.6202G>A|NP_061027.2:p.Asp2068Asn|6489|6202|2068|D/N|Gac/Aac|COSV67206516||-1||EntrezGene||YES||||2:g.141459810C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:135:2:1,1:61,72:133,2:0.0148:2,2:52:0:37:0:1:1.18:60:4:0.0149:0:2.5	0/0:310:0:0,0:145,165:310,0:0:2,0:39.6:1:36.2:1:1:0:60:76.5:1:0:0.1
    769. 

  769. 2	141460066	141460066	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon38:c.A6080G:p.D2027G	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	1.0	0.899	D	0.999	0.916	D	0.000	0.447	U	1.000	0.588	D	3.72	0.949	H	-3.81	0.957	D	-6.71	0.925	D	0.943	0.938	1.101	0.997	D	0.955	0.985	D	0.731	0.978	D	5.777	0.790	27.0	0.999	0.955	0.979	0.781	D	c	0.973	0.865	0.998	0.366	0.487	0.133	0	5.16	0.704	7.970	0.875	1.061	0.807	1.000	0.715	1.000	0.888	15.292	0.735	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV67284061;OCCURENCE=1(liver)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU3648326	LIRI-JP|1|258|0.00387597	0.25	37	314	2	141460066	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=95;VD=2;AF=0.0211;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05351;SOR=inf;LSEQ=GGACAACCTTCTCTGAGCCA;RSEQ=CCAAGCGAGCCTTTCCAATA;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|38/91||NM_018557.3:c.6080A>G|NP_061027.2:p.Asp2027Gly|6367|6080|2027|D/G|gAt/gGt|COSV67284061||-1||EntrezGene||YES||||2:g.141460066T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:95:2:1,1:46,47:93,2:0.0211:2,2:26:0:37:0:1:1.02:60:4:0.0213:0:1	0/0:314:0:0,0:150,164:314,0:0:2,0:39.3:1:36.5:1:1:0:60:156:1:0:0.1
    770. 

  770. 2	141473502	141473502	C	A	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	184	2	141473502	.	C	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.95779;SOR=0;LSEQ=TCAATAGAACTTAGAAAACT;RSEQ=ACATAAAACTTGGAAGATAT;CSQ=A|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||37/90|NM_018557.3:c.6023+40G>T|||||||||-1||EntrezGene||YES||||2:g.141473502C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:51.5:1:37:0:1:0:60:8:1:0:0	0/1:184:2:1,1:124,58:182,2:0.0109:2,2:44:1:37:0:0.53968:2.12831:60:4:0.0111:0:1
    771. 

  771. 2	141528435	141528435	T	C	intronic	LRP1B	.	.	.	0.21	0.0672	0.1822	0.1247	0.0066	0.1702	0.0149	0.0026	0.0184	rs13382825	rs13382825	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67182633;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach),1(soft_tissue),9(meninges),1(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU585212	LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579	0.75	212	123	2	141528435	.	T	C	212	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.45161;SOR=inf;LSEQ=ATGAACCAGAGGTAAGGTTT;RSEQ=TCATGAACTCATACCTTGAC;CSQ=C|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||34/90|NM_018557.3:c.5626+15A>G|||||||rs13382825&COSV67182633||-1||EntrezGene||YES||||2:g.141528435T>C|0.03963|0.1894|0.1265|0.01372|0.1641|0.01651|0.001745|0.0212|0.00582|0.2148|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1:1:1,0:0,0:0,1:1:0,0:71:0:37:0:1:0:60:2:1:0:1	0/1:123:55:35,20:45,23:68,55:0.4472:2,2:41.6:1:36.8:1:0.84981:1.11699:60:110:0.4545:0:1
    772. 

  772. 2	141528592	141528592	T	C	intronic	LRP1B	.	.	.	1.	0.8586	0.7653	0.9111	0.8676	1	0.8989	0.8841	0.8755	rs7599219	rs7599219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81741507	COCA-CN|5|321|0.0155763	1	241	109	2	141528592	.	T	C	241	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGCATAGAATGAAAA;RSEQ=GAAACAAATTTCTTTAATGA;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||33/90|NM_018557.3:c.5501-17A>G|||||||rs7599219||-1||EntrezGene||YES||||2:g.141528592T>C|0.8766|0.7705|0.9263|0.8762|0.9994|0.9074|0.8751|0.8595|0.8035|0.9994|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:1,2:0,0:0,3:1:0,2:40.7:1:37:0:1:0:60:6:1:0:1	1/1:109:109:38,71:0,0:0,109:1:0,2:34.7:1:35.7:1:1:0:60:108:1:0:1
    773. 

  773. 2	141533662	141533662	T	C	intronic	LRP1B	.	.	.	1.	0.8591	0.7660	0.9117	0.8676	1	0.8985	0.8846	0.8758	rs996361	rs996361	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81741515	COCA-CN|5|321|0.0155763	1	250	113	2	141533662	.	T	C	250	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=25;VD=24;AF=0.96;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.18116;SOR=0;LSEQ=GCACAAATTCATTAGTGTGA;RSEQ=TTACCTTGCTGTGCTTCTTT;CSQ=C|splice_donor_5th_base_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||33/90|NM_018557.3:c.5500+5A>G|||||||rs996361||-1||EntrezGene||YES||||2:g.141533662T>C|0.8762|0.7684|0.9252|0.8739|0.9994|0.907|0.8755|0.8586|0.801|0.9994|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:25:24:15,9:0,0:0,24:0.96:0,2:37.2:1:36.5:1:1:0:60:48:1:0:1.1	1/1:113:113:73,40:0,0:0,113:1:0,2:43.6:1:36.8:1:1:0:60:112:1:0:1.1
    774. 

  774. 2	141533670	141533670	G	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon33:c.C5497A:p.Q1833K	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.000	0.463	D	0.551	0.321	D	-0.275	0.037	N	-2.48	0.891	D	-0.1	0.085	N	0.143	0.168	-0.589	0.653	T	0.332	0.700	T	0.013	0.324	T	1.043	0.194	10.90	0.535	0.049	0.916	0.536	D	c	-0.386	-0.115	0.003	0.098	0.487	0.133	0	4.49	0.540	7.199	0.772	0.912	0.422	1.000	0.715	1.000	0.888	15.610	0.763	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	127	2	141533670	.	G	T	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=2;AF=0.0667;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.03552;SOR=inf;LSEQ=TCATTAGTGTGATTTACCTT;RSEQ=CTGTGCTTCTTTATCATAGA;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|33/91||NM_018557.3:c.5497C>A|NP_061027.2:p.Gln1833Lys|5784|5497|1833|Q/K|Caa/Aaa|||-1||EntrezGene||YES||||2:g.141533670G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:30:2:1,1:18,10:28,2:0.0667:2,2:33:0:31:1:1:1.76317:60:4:0.0667:0:2	0/0:127:0:0,0:81,46:127,0:0:2,0:41.2:1:36.7:1:1:0:60:126:1:0:1
    775. 

  775. 2	141533671	141533671	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon33:c.G5496T:p.Q1832H	.	.	.	.	.	.	.	.	.	.	.	0.02	0.496	D	0.998	0.715	D	0.993	0.797	D	0.000	0.843	D	0.998	0.445	D	2.77	0.812	M	-2.99	0.921	D	-2.86	0.601	D	0.704	0.707	0.720	0.934	D	0.863	0.954	D	0.214	0.875	D	4.176	0.560	23.8	0.995	0.682	0.959	0.662	D	c	0.533	0.438	0.000	0.056	0.487	0.133	0	3.18	0.355	2.643	0.460	0.002	0.136	1.000	0.715	0.999	0.750	9.044	0.353	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV101258215;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU131043096	LAML-US|1|139|0.00719424	0.25	37	128	2	141533671	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.65533;SOR=0;LSEQ=CATTAGTGTGATTTACCTTG;RSEQ=TGTGCTTCTTTATCATAGAC;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|33/91||NM_018557.3:c.5496G>T|NP_061027.2:p.Gln1832His|5783|5496|1832|Q/H|caG/caT|COSV101258215||-1||EntrezGene||YES||||2:g.141533671C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:19,11:30,0:0:2,0:37.3:1:35.3:1:1:0:60:14:1:0:1	0/1:128:2:1,1:80,46:126,2:0.0156:2,2:34.5:1:37:0:1:1.73117:60:4:0.016:0:2
    776. 

  776. 2	141533673	141533673	G	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon33:c.C5494A:p.Q1832K	.	.	.	.	.	.	.	.	.	.	.	0.006	0.614	D	0.993	0.637	D	0.952	0.674	D	0.000	0.843	D	1.000	0.588	D	3.465	0.926	M	-2.95	0.919	D	-2.55	0.551	D	0.785	0.776	0.727	0.935	D	0.871	0.957	D	0.488	0.950	D	4.601	0.616	24.4	0.993	0.588	0.994	0.954	D	c	0.774	0.756	1.000	0.747	0.487	0.133	0	5.39	0.775	9.751	0.981	0.912	0.422	1.000	0.715	1.000	0.888	19.508	0.951	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV67279827;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU84232128	LICA-CN|1|402|0.00248756,LUAD-US|1|516|0.00193798	0.25	31	130	2	141533673	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.6592;SOR=0;LSEQ=TTAGTGTGATTTACCTTGCT;RSEQ=TGCTTCTTTATCATAGACTT;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|33/91||NM_018557.3:c.5494C>A|NP_061027.2:p.Gln1832Lys|5781|5494|1832|Q/K|Cag/Aag|COSV67279827||-1||EntrezGene||YES||||2:g.141533673G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:19,11:30,0:0:2,0:38.9:1:37:0:1:0:60:60:1:0:1	0/1:130:2:1,1:82,46:128,2:0.0154:2,2:61:1:31:1:1:1.77417:60:4:0.0155:0:2
    777. 

  777. 2	141571329	141571329	T	C	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon32:c.A5256G:p.S1752S	0.99	0.8491	0.7260	0.8098	0.8642	0.9932	0.8967	0.8937	0.8809	rs3749010	rs3749010	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67186059;OCCURENCE=1(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4547566	COCA-CN|5|321|0.0155763	1	231	91	2	141571329	.	T	C	231	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTTATGGTTCCATTCCC;RSEQ=GAACTGATCCAATAAAGCTT;CSQ=C|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|32/91||NM_018557.3:c.5256A>G|NP_061027.2:p.Ser1752%3D|5543|5256|1752|S|tcA/tcG|rs3749010&COSV67186059||-1||EntrezGene||YES||||2:g.141571329T>C|0.8705|0.7299|0.7804|0.8666|0.9891|0.8917|0.8855|0.8616|0.9076|0.9891|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:3,2:0,0:0,5:1:0,2:27.2:1:37:0:1:0:60:10:1:0:1.8	1/1:91:91:42,49:0,0:0,91:1:0,2:38.1:1:35.5:1:1:0:60:44.5:1:0:1.3
    778. 

  778. 2	141598473	141598473	-	T	intronic	LRP1B	.	.	.	1.	0.9811	0.9375	0.9880	1	1	1	0.9987	0.9888	rs35745624	rs35745624	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	261	162	2	141598473	.	A	AT	261	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=27;VD=27;AF=1;SHIFT3=0;MSI=10;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAAAAACTTTAAAAAAA;RSEQ=AATCATACTTTACCCCCTGA;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||30/90|NM_018557.3:c.5114+13_5114+14insA|||||||rs35745624||-1||EntrezGene||YES||||2:g.141598473_141598474insT|0.9931|0.9359|0.9957|0.9988|0.9988|0.9993|0.998|0.9955|0.9951|0.9995|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:27:27:19,8:0,0:0,27:1:0,2:24.7:1:36:1:1:0:60:26:1:0.2963:0.4	1/1:162:162:108,54:0,0:0,162:1:0,2:33.8:1:35.6:1:1:0:60:53:1:0.1975:0.3
    779. 

  779. 2	141598490	141598490	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon30:c.G5111A:p.R1704K	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.002	0.090	B	0.002	0.063	B	0.000	0.447	U	0.684	0.332	D	-0.12	0.045	N	-2.75	0.908	D	-1.02	0.268	N	0.15	0.178	-0.433	0.710	T	0.424	0.769	T	0.011	0.280	T	1.319	0.223	12.37	0.942	0.239	0.792	0.389	D	c	-0.341	-0.084	0.000	0.065	0.554	0.246	0	5.45	0.796	2.517	0.449	0.816	0.334	1.000	0.715	1.000	0.888	10.432	0.434	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	25	182	2	141598490	.	C	T	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=2;AF=0.04;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04572;SOR=inf;LSEQ=AAAAAATCATACTTTACCCC;RSEQ=TGACTGGGTGAGCTGCAAGA;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|30/91||NM_018557.3:c.5111G>A|NP_061027.2:p.Arg1704Lys|5398|5111|1704|R/K|aGg/aAg|rs1473207458||-1||EntrezGene||YES||||2:g.141598490C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:50:2:1,1:32,16:48,2:0.04:2,2:15:1:25:0:1:1.97043:60:4:0.04:0:2	0/0:182:0:0,0:121,61:182,0:0:2,0:36.2:1:35.7:1:1:0:60:29.333:1:0:0.3
    780. 

  780. 2	141607777	141607777	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon29:c.A4833G:p.I1611M	0.0011	9.684e-05	0	0	0	0	0.0006	6.663e-05	0	rs200412868	rs200412868	0.167	0.252	T	0.027	0.423	B	0.02	0.423	B	0.000	0.537	U	0.652	0.330	D	1.79	0.469	L	-2.94	0.919	D	-1.35	0.336	N	0.217	0.304	0.399	0.891	D	0.647	0.877	D	0.068	0.706	D	1.776	0.274	14.84	0.981	0.377	0.834	0.422	D	c	-0.066	0.032	0.000	0.042	0.487	0.133	0	4.36	0.515	0.867	0.274	1.011	0.635	1.000	0.715	1.000	0.888	7.225	0.250	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	133	2	141607777	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.88936;SOR=0;LSEQ=TCCTCAGATGCATCGAAGTC;RSEQ=ATCACAGTAACGTCATCAAT;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|29/91||NM_018557.3:c.4833A>G|NP_061027.2:p.Ile1611Met|5120|4833|1611|I/M|atA/atG|rs200412868||-1||EntrezGene||YES||||2:g.141607777T>C|3.979e-05|0|0|0|0|0.000462|0|0|0|0.000462|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:28.9:1:37:0:1:0:60:16:1:0:0.1	0/1:133:2:1,1:71,60:131,2:0.015:2,2:38.5:1:37:0:1:1.18183:60:4:0.0154:0:1
    781. 

  781. 2	141609267	141609267	C	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon28:c.G4665T:p.A1555A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	458	2	141609267	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=149;VD=2;AF=0.0134;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05995;SOR=inf;LSEQ=AGCTTCATCAAGTGGGGGCA;RSEQ=GCACAGGCAGCACTCCTATT;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|28/91||NM_018557.3:c.4665G>T|NP_061027.2:p.Ala1555%3D|4952|4665|1555|A|gcG/gcT|COSV67185720||-1||EntrezGene||YES||||2:g.141609267C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:149:2:1,1:80,67:147,2:0.0134:2,2:50.5:1:37:0:1:1.1926:60:4:0.0136:0:1	0/0:458:0:0,0:244,214:458,0:0:2,0:38.8:1:36.5:1:1:0:60:113.5:1:0:0.1
    782. 

  782. 2	141609364	141609364	C	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	333	2	141609364	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=101;VD=2;AF=0.0198;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.05375;SOR=inf;LSEQ=GATTGGGAGCTGTAATTACA;RSEQ=AGTGAAATATGAACAGTGAA;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||27/90|NM_018557.3:c.4580-12G>A|||||||COSV67290302||-1||EntrezGene||YES||||2:g.141609364C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:101:2:1,1:39,60:99,2:0.0198:2,2:11:0:37:0:1:1.53:60:4:0.0204:0:1	0/0:333:0:0,0:113,220:333,0:0:2,0:36.4:1:36.7:1:1:0:60:332:1:0:0.1
    783. 

  783. 2	141609383	141609383	A	G	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	275	2	141609383	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=74;VD=2;AF=0.027;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.04448;SOR=inf;LSEQ=ACAGTGAAATATGAACAGTG;RSEQ=AGAAGGAAGAATGTATTAGG;CSQ=G|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||27/90|NM_018557.3:c.4580-31T>C|||||||||-1||EntrezGene||YES||||2:g.141609383A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:74:2:1,1:24,48:72,2:0.027:2,2:21.5:1:37:0:1:1.98:60:4:0.0274:0:1	0/0:275:0:0,0:77,198:275,0:0:2,0:36.3:1:36.6:1:1:0:60:136.5:1:0:0.1
    784. 

  784. 2	141625122	141625122	T	C	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	196	2	141625122	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.67759;SOR=0;LSEQ=ATGATTAAGATGATAATACT;RSEQ=TCTGGGTGGTTAATCCATAA;CSQ=C|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||27/90|NM_018557.3:c.4579+37A>G|||||||||-1||EntrezGene||YES||||2:g.141625122T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:31,11:42,0:0:2,0:28.2:1:35.8:1:1:0:60:41:1:0:0	0/1:196:2:1,1:129,65:194,2:0.0102:2,2:45:1:31:1:1:1.9772:60:4:0.0105:0:1
    785. 

  785. 2	141625338	141625338	T	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon27:c.A4400T:p.E1467V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.291	0.764	B	0.157	0.832	B	0.000	0.843	D	1	0.810	D	2.09	0.581	M	-2.81	0.911	D	-3.57	0.877	D	0.548	0.886	0.811	0.946	D	0.829	0.943	D	0.128	0.811	D	4.840	0.650	24.8	0.990	0.503	0.980	0.783	D	c	0.551	0.597	0.999	0.381	0.487	0.133	0	5.42	0.786	7.963	0.874	1.061	0.807	1.000	0.715	0.990	0.544	15.453	0.749	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	336	2	141625338	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=62;VD=2;AF=0.0323;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.02394;SOR=inf;LSEQ=CAAAGGGATGGGAAAGGTAT;RSEQ=CATGACCTCGGATGATTTCT;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|27/91||NM_018557.3:c.4400A>T|NP_061027.2:p.Glu1467Val|4687|4400|1467|E/V|gAa/gTa|||-1||EntrezGene||YES||||2:g.141625338T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:62:2:1,1:20,40:60,2:0.0323:2,2:65.5:1:37:0:1:1.98:60:4:0.0323:0:1	0/0:336:0:0,0:140,196:336,0:0:2,0:36.7:1:36.3:1:1:0:60:47:1:0:0
    786. 

  786. 2	141625631	141625631	A	-	intronic	LRP1B	.	.	.	0.035	0.0031	0.0027	0.0190	0.0117	0.0031	0.0146	0.0008	0.0052	rs770477214	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112065151	COCA-CN|1|321|0.00311526,BTCA-SG|5|71|0.0704225	0.5	58	94	2	141625630	.	TA	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=29;VD=1;AF=0.0345;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.6641;SOR=1.08262;LSEQ=TGTTGTAAATATTATCTAAG;RSEQ=AAAAAAAAAATACAGAAAAG;CSQ=-|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||26/90|NM_018557.3:c.4334+37del|||||||rs565764708||-1||EntrezGene||YES||||2:g.141625641del|0.07364|0.0538|0.1088|0.1491|0.07803|0.02982|0.06371|0.1023|0.1307|0.1491|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:29:1:1,0:19,9:28,1:0.0345:2,0:71:0:37:0:1:0:60:2:0.0345:0:0	0/1:94:3:2,1:65,25:90,3:0.0319:2,2:50.3:1:37:0:1:1.29617:60:6:0.0323:0:0
    787. 

  787. 2	141625835	141625835	A	-	intronic	LRP1B	.	.	.	0.45	0.1958	0.1823	0.2286	0.1290	0.0578	0.3613	0.2143	0.2126	rs34488899	rs34488899	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	151	61	2	141625834	.	TA	T	151	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=22;VD=1;AF=0.0455;SHIFT3=18;MSI=19;MSILEN=1;SSF=0.01756;SOR=0.12544;LSEQ=GTCTGTCCAGAAAAGAATTC;RSEQ=AAAAAAAAAAAAAAAAAAGA;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding||25/90|NM_018557.3:c.4170-3del|||||||rs34488899||-1||EntrezGene||YES||||2:g.141625853del|0.302|0.2733|0.3332|0.3024|0.324|0.2609|0.3048|0.328|0.281|0.4539|AMR|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:22:1:0,1:6,15:21,1:0.0455:2,0:66:0:25:0:1:0:60:2:0.0455:0:1	0/1:61:17:2,15:13,27:40,17:0.2787:2,2:40.4:1:37:1:0.18712:3.54144:60:34:0.2833:0.0164:2
    788. 

  788. 2	141641411	141641411	C	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon25:c.G4144T:p.A1382S	.	.	.	.	.	.	.	.	.	.	.	0.008	0.586	D	0.948	0.899	P	0.926	0.875	D	0.000	0.843	D	1	0.810	D	1.42	0.358	L	-4.17	0.969	D	-2.11	0.550	N	0.332	0.658	0.986	0.970	D	0.917	0.972	D	0.141	0.824	D	4.994	0.672	25.1	0.997	0.813	0.990	0.891	D	c	0.753	0.769	1.000	0.747	0.487	0.133	0	5.55	0.832	7.836	0.849	0.892	0.403	1.000	0.715	0.998	0.697	19.848	0.967	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	64	2	141641411	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=115;VD=3;AF=0.0261;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.26268;SOR=inf;LSEQ=TCTTGGGTCCAAAGCAATGG;RSEQ=CCTGGGGTGTTCCATGGCTC;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|25/91||NM_018557.3:c.4144G>T|NP_061027.2:p.Ala1382Ser|4431|4144|1382|A/S|Gcc/Tcc|||-1||EntrezGene||YES||||2:g.141641411C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:115:3:2,1:80,32:112,3:0.0261:2,2:25.3:1:28.3:1:1:1.24751:60:2:0.0179:0:1	0/0:64:0:0,0:47,17:64,0:0:2,0:41.8:1:36.6:1:1:0:60:63:1:0:0.1
    789. 

  789. 2	141641471	141641471	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon25:c.G4084A:p.A1362T	.	.	.	.	.	.	.	.	.	.	.	0.003	0.721	D	0.779	0.423	P	0.794	0.561	P	0.000	0.629	D	1.000	0.520	D	2.795	0.818	M	-2.39	0.884	D	-2.8	0.663	D	0.324	0.723	0.674	0.929	D	0.797	0.931	D	0.042	0.605	D	4.481	0.600	24.2	0.998	0.846	0.967	0.702	D	c	0.482	0.472	0.953	0.280	0.487	0.133	0	4.74	0.596	6.118	0.711	0.020	0.144	1.000	0.715	0.995	0.604	15.964	0.796	Six-bladed beta-propeller, TolB-like	.	.	ID=COSV67250952;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	93	2	141641471	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=197;VD=2;AF=0.0102;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.46071;SOR=inf;LSEQ=TAGGGAGCCATCTAGTTTGG;RSEQ=CACTTCGATTTGGTCCAGAT;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|25/91||NM_018557.3:c.4084G>A|NP_061027.2:p.Ala1362Thr|4371|4084|1362|A/T|Gcc/Acc|COSV67250952||-1||EntrezGene||YES||||2:g.141641471C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:197:2:1,1:111,83:194,2:0.0102:2,2:49.5:1:31:1:1:1.33533:60:4:0.0105:0:1	0/0:93:0:0,0:54,39:93,0:0:2,0:33.2:1:36.2:1:1:0:60:45.5:1:0:0.1
    790. 

  790. 2	141641505	141641505	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon25:c.C4050T:p.Y1350Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	95	2	141641505	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=222;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08915;SOR=0;LSEQ=TCCAGATTGCTGTCTATCCA;RSEQ=TATATGTTTCCTGCTATCCA;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|25/91||NM_018557.3:c.4050C>T|NP_061027.2:p.Tyr1350%3D|4337|4050|1350|Y|taC/taT|||-1||EntrezGene||YES||||2:g.141641505G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:222:0:0,0:122,100:222,0:0:2,0:38.5:1:36.3:1:1:0:60:110:1:0:0.2	0/1:95:2:1,1:54,39:93,2:0.0211:2,2:34:1:37:0:1:1.37978:60:4:0.0211:0:1
    791. 

  791. 2	141660568	141660568	C	T	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon23:c.G3687A:p.E1229E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	262	2	141660568	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=114;VD=2;AF=0.0175;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.09136;SOR=inf;LSEQ=TTGACTGTGTGCTTGTGCTG;RSEQ=TCACATACTTGGCTGCACTT;CSQ=T|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|23/91||NM_018557.3:c.3687G>A|NP_061027.2:p.Glu1229%3D|3974|3687|1229|E|gaG/gaA|||-1||EntrezGene||YES||||2:g.141660568C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:114:2:1,1:67,45:112,2:0.0175:2,2:44:1:37:0:1:1.48353:60:4:0.0175:0:1	0/0:262:0:0,0:145,117:262,0:0:2,0:38.9:1:36.6:1:1:0:60:86.333:1:0:0.1
    792. 

  792. 2	141665499	141665499	A	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon22:c.T3467A:p.L1156H	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.996	0.715	D	0.967	0.699	D	0.000	0.523	D	1.000	0.484	D	2.03	0.557	M	-5.51	0.992	D	-5.42	0.852	D	0.561	0.635	1.114	0.999	D	0.963	0.988	D	0.511	0.953	D	6.097	0.840	28.2	0.984	0.409	0.989	0.879	D	c	0.760	0.767	1.000	0.414	0.487	0.133	0	5.58	0.843	9.268	0.948	1.136	0.884	1.000	0.715	1.000	0.888	15.745	0.776	Low-density lipoprotein (LDL) receptor class A, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	276	2	141665499	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=2;AF=0.0148;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.10735;SOR=inf;LSEQ=AATCCTTTTTCCCATTGCAG;RSEQ=GTTTCTCTGGCTGCAGGCAG;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|22/91||NM_018557.3:c.3467T>A|NP_061027.2:p.Leu1156His|3754|3467|1156|L/H|cTc/cAc|||-1||EntrezGene||YES||||2:g.141665499A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:135:2:1,1:77,56:133,2:0.0148:2,2:28.5:1:37:0:1:1.37169:60:4:0.0148:0:1	0/0:276:0:0,0:139,137:276,0:0:2,0:36.7:1:36.6:1:1:0:60:275:1:0:0
    793. 

  793. 2	141665539	141665539	A	G	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon22:c.T3427C:p.C1143R	.	.	.	.	.	.	.	.	.	.	.	0.002	0.784	D	1.0	0.899	D	0.995	0.832	D	0.000	0.629	D	1	0.810	D	4.71	0.995	H	-6.67	0.999	D	-6.88	0.982	D	0.512	0.950	0.898	0.956	D	0.998	0.999	D	0.779	0.983	D	5.748	0.785	27.0	0.998	0.883	0.989	0.878	D	c	1.069	0.965	1.000	0.414	0.554	0.246	0	5.58	0.843	9.268	0.948	1.136	0.884	1.000	0.715	1.000	0.888	15.745	0.776	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	260	2	141665539	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=144;VD=2;AF=0.0139;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.12648;SOR=inf;LSEQ=GACTGAGGTGTCATTAGCAC;RSEQ=AGGATGCTTGGGTGGTCCAC;CSQ=G|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|22/91||NM_018557.3:c.3427T>C|NP_061027.2:p.Cys1143Arg|3714|3427|1143|C/R|Tgt/Cgt|||-1||EntrezGene||YES||||2:g.141665539A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:144:2:1,1:69,73:142,2:0.0139:2,2:52:1:37:0:1:1.06:60:4:0.0144:0:1	0/0:260:0:0,0:109,151:260,0:0:2,0:38.3:1:35.9:1:1:0:60:42.333:1:0:0.1
    794. 

  794. 2	141665584	141665613	CATCTGACTGATCTTCGCAATCAATATCTC	-	exonic	LRP1B	.	nonframeshift deletion	LRP1B:NM_018557:exon22:c.3353_3382del:p.G1118_D1127del	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	35	198	2	141665583	.	TCATCTGACTGATCTTCGCAATCAATATCTC	T	35	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=106;VD=2;AF=0.0189;SHIFT3=4;MSI=2;MSILEN=1;SSF=0.12083;SOR=inf;LSEQ=AGAAACTGTCACAGTCATCT;RSEQ=CATCACACACCCATGCTTTG;CSQ=-|inframe_deletion|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|22/91||NM_018557.3:c.3353_3382del|NP_061027.2:p.Gly1118_Asp1127del|3640-3669|3353-3382|1118-1128|GDIDCEDQSDE/E|gGAGATATTGATTGCGAAGATCAGTCAGATGaa/gaa|||-1||EntrezGene||YES||||2:g.141665588_141665617del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:106:2:1,1:44,60:104,2:0.0189:2,2:50.5:1:35.5:1:1:1.36:60:4:0.019:0.0189:0	0/0:198:0:0,0:70,127:197,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    795. 

  795. 2	141680593	141680593	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon21:c.G3260A:p.G1087D	.	.	.	.	.	.	.	.	.	.	.	0.531	0.236	T	0.002	0.689	B	0.02	0.782	B	0.007	0.314	U	0.905	0.362	D	0.065	0.083	N	-3.54	0.948	D	-1.17	0.299	N	0.417	0.474	0.451	0.899	D	0.785	0.927	D	0.050	0.642	D	3.984	0.536	23.6	0.997	0.797	0.777	0.380	D	c	-0.095	0.011	0.000	0.035	0.554	0.246	0	4.3	0.504	1.106	0.305	0.040	0.155	0.820	0.297	0.915	0.391	11.349	0.486	Low-density lipoprotein (LDL) receptor class A, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	183	2	141680593	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.16236;SOR=inf;LSEQ=ATCGTATGGTACCATTGCAA;RSEQ=CTTTTTCATCACTACCATCT;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|21/91||NM_018557.3:c.3260G>A|NP_061027.2:p.Gly1087Asp|3547|3260|1087|G/D|gGt/gAt|COSV67227620||-1||EntrezGene||YES||||2:g.141680593C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:2:1,1:67,55:122,2:0.0161:2,2:37:1:37:0:1:1.21623:60:4:0.0168:0:1	0/0:183:0:0,0:108,75:183,0:0:2,0:34:1:36.1:1:1:0:60:44.75:1:0:0.1
    796. 

  796. 2	141709419	141709419	T	G	intronic	LRP1B	.	.	.	0.77	0.5993	0.3409	0.6400	0.6358	0.6889	0.7539	0.6946	0.6929	rs1429348	rs1429348	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67232115;OCCURENCE=2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU755724	LAML-KR|2|205|0.0097561,COCA-CN|6|321|0.0186916	1	245	86	2	141709419	.	T	G	245	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=112;VD=112;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTATACAGTGAGCATT;RSEQ=GGTACTTGCCAGAGTCGCAG;CSQ=G|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||19/90|NM_018557.3:c.2968+10A>C|||||||rs1429348&COSV67232115||-1||EntrezGene||YES||||2:g.141709419T>G|0.6532|0.3349|0.6452|0.6178|0.6756|0.7672|0.6837|0.6429|0.6382|0.7672|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:112:112:53,59:0,0:0,112:1:0,2:42.5:1:36.1:1:1:0:60:224:1:0:1.1	1/1:86:86:52,34:0,0:0,86:1:0,2:39.6:1:36:1:1:0:60:172:1:0:1
    797. 

  797. 2	141709457	141709457	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon19:c.C2940T:p.C980C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	108	2	141709457	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=119;VD=2;AF=0.0168;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.27371;SOR=inf;LSEQ=CAGTGCCATTTGCTGCTAAT;RSEQ=CATCTTCCACTTTTGCATAC;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|19/91||NM_018557.3:c.2940C>T|NP_061027.2:p.Cys980%3D|3227|2940|980|C|tgC/tgT|rs1171123264||-1||EntrezGene||YES||||2:g.141709457G>A|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:119:2:1,1:49,68:117,2:0.0168:2,2:12:0:37:0:1:1.38:60:4:0.0169:0:2	0/0:108:0:0,0:57,50:107,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    798. 

  798. 2	141747249	141747249	A	T	intronic	LRP1B	.	.	.	0.62	0.4156	0.5624	0.3708	0.4868	0.5962	0.3116	0.3405	0.3520	rs1429365	rs1429365	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63342039;OCCURENCE=79(meninges),1(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU26807724	LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.5	237	189	2	141747249	.	A	T	237	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=54;VD=1;AF=0.0185;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.01884;LSEQ=GGGAGGGAGGGGGAAGCAAG;RSEQ=TTAATTATTTAAAATTGGAT;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||16/90|NM_018557.3:c.2645-23T>A|||||||rs1429365&COSV63342039||-1||EntrezGene||YES||||2:g.141747249A>T|0.4102|0.566|0.3953|0.4914|0.5997|0.2973|0.3538|0.4054|0.4934|0.6181|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:54:1:0,1:16,37:53,1:0.0185:2,0:18:0:25:0:1:0:60:2:0.0185:0:1	1/0:189:95:34,61:35,58:93,95:0.5026:2,2:31.8:1:36.1:1:0.87989:1.0822:60:94:0.5:0:1.5
    799. 

  799. 2	141751592	141751592	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon16:c.C2616T:p.D872D	0.61	0.3874	0.5551	0.3553	0.4834	0.5853	0.2413	0.3080	0.3145	rs13007735	rs13007735	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63341570;OCCURENCE=1(urinary_tract),1(pancreas),3(lung),73(meninges),1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU26807821	PACA-CA|1|268|0.00373134,LUSC-KR|1|170|0.00588235,COCA-CN|5|321|0.0155763	0.25	234	196	2	141751592	.	G	A	234	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=125;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTGAATCCTCATCGCTTCC;RSEQ=TCTAGGCAGTCATCGTCGCC;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|16/91||NM_018557.3:c.2616C>T|NP_061027.2:p.Asp872%3D|2903|2616|872|D|gaC/gaT|rs13007735&COSV63341570&COSV63341855||-1||EntrezGene||YES||||2:g.141751592G>A|0.3832|0.5585|0.389|0.4837|0.5913|0.2372|0.3239|0.3818|0.4484|0.6141|EAS||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:125:0:0,0:63,62:125,0:0:2,0:32.7:1:36.9:1:1:0:60:250:1:0:0	0/1:196:93:49,44:55,48:103,93:0.4745:2,2:41.2:1:35.9:1:1:1.02877:60:92:0.4718:0:1.1
    800. 

  800. 2	141762971	141762971	G	A	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon15:c.C2436T:p.I812I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67273785;OCCURENCE=1(NS),2(skin)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	282	2	141762971	.	G	A	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.27125;SOR=2.93716;LSEQ=GCACACACCCGGCCTCCTGG;RSEQ=ATAGCCAAGCAAAGTGTACT;CSQ=A|synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|15/91||NM_018557.3:c.2436C>T|NP_061027.2:p.Ile812%3D|2723|2436|812|I|atC/atT|COSV67205600&COSV67263105&COSV67273785||-1||EntrezGene||YES||||2:g.141762971G>A|||||||||||||1&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:47,48:95,2:0.0206:2,2:52:1:37:0:1:1.02:60:4:0.0208:0:1	0/0:282:2:1,1:151,129:280,2:0.0071:2,2:46:1:37:0:1:1.16988:60:4:0.0072:0:1
    801. 

  801. 2	141763051	141763051	G	T	intronic	LRP1B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	249	2	141763051	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=2;AF=0.0541;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.01634;SOR=inf;LSEQ=AAGAGGAAGAAAGCAAATGT;RSEQ=TCAGAGAACTCTGATTCACG;CSQ=T|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||14/90|NM_018557.3:c.2381-25C>A|||||||||-1||EntrezGene||YES||||2:g.141763051G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:2:1,1:11,24:35,2:0.0541:2,2:19:0:37:0:1:2.13:60:4:0.0556:0:1	0/0:249:0:0,0:95,154:249,0:0:2,0:37.5:1:36.5:1:1:0:60:123.5:1:0:0.1
    802. 

  802. 2	141773367	141773367	C	T	exonic	LRP1B	.	stopgain	LRP1B:NM_018557:exon13:c.G2088A:p.W696X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.537	U	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.285	0.982	39	0.997	0.778	0.975	0.752	D	c	0.888	0.767	1.000	0.747	0.487	0.133	0	4.87	0.627	7.807	0.845	0.935	0.490	1.000	0.715	1.000	0.888	17.187	0.867	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	268	2	141773367	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=198;VD=2;AF=0.0101;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.18001;SOR=inf;LSEQ=TCCAGAGTTAAACCGTTTGG;RSEQ=CACAGCATCTTTGAAGTCAC;CSQ=T|stop_gained|HIGH|LRP1B|53353|Transcript|NM_018557.3|protein_coding|13/91||NM_018557.3:c.2088G>A|NP_061027.2:p.Trp696Ter|2375|2088|696|W/*|tgG/tgA|||-1||EntrezGene||YES||||2:g.141773367C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:198:2:1,1:93,103:196,2:0.0101:2,2:45:1:37:0:1:1.11:60:4:0.0103:0:1	0/0:268:0:0,0:145,123:268,0:0:2,0:39.9:1:36.1:1:1:0:60:88.333:1:0:0.1
    803. 

  803. 2	141773378	141773378	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon13:c.A2077G:p.K693E	.	.	.	.	.	.	.	.	.	.	.	0.163	0.234	T	0.801	0.431	P	0.334	0.404	B	0.000	0.629	U	0.981	0.397	D	1.27	0.322	L	-3.76	0.956	D	-1.22	0.309	N	0.314	0.375	0.525	0.909	D	0.761	0.918	D	0.044	0.612	D	4.010	0.539	23.6	0.998	0.927	0.978	0.771	D	c	0.368	0.483	1.000	0.747	0.487	0.133	0	5.75	0.904	7.918	0.868	1.061	0.807	1.000	0.715	1.000	0.888	16.353	0.830	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU114528809	COCA-CN|1|321|0.00311526	0.25	37	269	2	141773378	.	T	C	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.18133;SOR=inf;LSEQ=ACCGTTTGGCCACAGCATCT;RSEQ=TGAAGTCACAAAAATCTGCC;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|13/91||NM_018557.3:c.2077A>G|NP_061027.2:p.Lys693Glu|2364|2077|693|K/E|Aag/Gag|COSV67261161||-1||EntrezGene||YES||||2:g.141773378T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:91,107:198,2:0.01:2,2:7:0:37:0:1:1.17:60:4:0.0102:0:1	0/0:269:0:0,0:137,132:269,0:0:2,0:41.2:1:36.2:1:1:0:60:52.8:1:0:0.1
    804. 

  804. 2	141806782	141806782	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon11:c.A1562G:p.N521S	.	.	.	.	.	.	.	.	.	.	.	0.319	0.136	T	0.013	0.154	B	0.006	0.112	B	0.000	0.491	U	0.745	0.338	D	1.41	0.357	L	-2.53	0.894	D	-1.45	0.356	N	0.005	0.000	-0.140	0.792	T	0.484	0.803	T	0.026	0.487	D	0.092	0.102	3.521	0.981	0.376	0.986	0.840	D	c	-0.250	-0.072	0.764	0.235	0.487	0.133	0	5.49	0.809	5.835	0.689	0.924	0.433	1.000	0.715	1.000	0.888	15.592	0.762	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	25	190	2	141806782	.	T	C	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.53326;SOR=0;LSEQ=CATAAAAGAGGAACAACTCA;RSEQ=TCTTTGGTCCTGCAGAGGAA;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|11/91||NM_018557.3:c.1562A>G|NP_061027.2:p.Asn521Ser|1849|1562|521|N/S|aAt/aGt|||-1||EntrezGene||YES||||2:g.141806782T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:70:0:0,0:20,50:70,0:0:2,0:40.1:1:32.1:1:1:0:60:6:1:0:0.2	0/1:190:2:1,1:64,124:188,2:0.0105:2,2:34:1:25:0:1:1.93:60:4:0.0106:0:1
    805. 

  805. 2	141816621	141816621	A	G	exonic	LRP1B	.	synonymous SNV	LRP1B:NM_018557:exon9:c.T1239C:p.V413V	1.	0.9499	0.8252	0.9916	1	1	1	0.9996	0.9918	rs1525579	rs1525579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67186066;OCCURENCE=1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU81741570	COCA-CN|5|321|0.0155763	0.5	169	25	2	141816621	.	A	G	169	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATACCATAAAGATGTCT;RSEQ=ACCTATAAAGAGGGCAAAAC;CSQ=G|splice_region_variant&synonymous_variant|LOW|LRP1B|53353|Transcript|NM_018557.3|protein_coding|9/91||NM_018557.3:c.1239T>C|NP_061027.2:p.Val413%3D|1526|1239|413|V|gtT/gtC|rs1525579&COSV67186066||-1||EntrezGene||YES||||2:g.141816621A>G|0.9872|0.8207|0.9942|1|1|1|0.9997|0.9949|0.9996|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:25:25:8,17:0,0:0,25:1:0,2:46.6:1:36.5:1:1:0:60:50:1:0:1.1
    806. 

  806. 2	141819678	141819678	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon8:c.A1178G:p.Y393C	.	.	.	.	.	.	.	.	.	.	.	0.028	0.461	D	0.0	0.026	B	0.0	0.013	B	0.015	0.285	N	0.984	0.401	D	2.525	0.740	M	-3.37	0.941	D	-5.49	0.857	D	0.699	0.703	-0.276	0.757	T	0.675	0.887	D	0.027	0.496	D	0.990	0.189	10.60	0.975	0.338	0.843	0.431	D	c	-0.361	-0.311	0.000	0.038	0.487	0.133	0	-1.51	0.082	0.794	0.264	0.153	0.239	0.986	0.359	0.996	0.625	4.016	0.091	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	124	2	141819678	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.67338;SOR=0;LSEQ=GATAGTCCACTACTCCCACA;RSEQ=AGTCCAAGTAAAGATCTACC;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|8/91||NM_018557.3:c.1178A>G|NP_061027.2:p.Tyr393Cys|1465|1178|393|Y/C|tAt/tGt|||-1||EntrezGene||YES||||2:g.141819678T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:27:0:0,0:18,9:27,0:0:2,0:29.8:1:36.1:1:1:0:60:54:1:0:0.1	0/1:124:2:1,1:73,49:122,2:0.0161:2,2:27.5:1:37:0:1:1.48485:60:4:0.0164:0:1
    807. 

  807. 2	141819828	141819828	G	A	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon8:c.C1028T:p.T343I	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.996	0.832	D	0.000	0.843	D	1	0.810	D	3.45	0.924	M	-3.58	0.949	D	-4.3	0.765	D	0.881	0.869	1.025	0.976	D	0.933	0.978	D	0.202	0.869	D	5.461	0.741	26.1	0.999	0.932	0.992	0.925	D	c	1.034	0.985	1.000	0.747	0.487	0.133	0	5.63	0.861	9.941	0.989	1.048	0.713	1.000	0.715	1.000	0.888	20.040	0.976	Six-bladed beta-propeller, TolB-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	93	2	141819828	.	G	A	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.58926;SOR=0;LSEQ=TGGCGACATTCCCGTAGTCA;RSEQ=TAAAGAAAAGTTTTCTGTTG;CSQ=A|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|8/91||NM_018557.3:c.1028C>T|NP_061027.2:p.Thr343Ile|1315|1028|343|T/I|aCt/aTt|||-1||EntrezGene||YES||||2:g.141819828G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:28:0:0,0:10,17:27,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:93:2:1,1:34,55:89,2:0.0215:2,2:12.5:1:31:1:1:1.61:60:4:0.025:0:1
    808. 

  808. 2	141946153	141946153	C	T	splicing	LRP1B	NM_018557:exon7:c.851-1G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.626	0.766	26.6	0.995	0.662	0.991	0.904	D	c	1.168	1.014	1.000	0.747	0.061	0.009	0	5.2	0.716	7.640	0.824	0.935	0.490	1.000	0.715	1.000	0.888	18.728	0.916	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU119895583	SKCA-BR|1|100|0.01	0.25	37	199	2	141946153	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=34;VD=2;AF=0.0588;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02076;SOR=inf;LSEQ=AATCGCCATTTGTTGCACAT;RSEQ=TGAAAAACACATACACAAAA;CSQ=T|splice_acceptor_variant|HIGH|LRP1B|53353|Transcript|NM_018557.3|protein_coding||6/90|NM_018557.3:c.851-1G>A|||||||||-1||EntrezGene||YES||||2:g.141946153C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:2:0,2:12,20:32,2:0.0588:2,0:12.5:1:37:0:0.52941:0:60:4:0.0588:0:1	0/0:199:0:0,0:78,121:199,0:0:2,0:38.1:1:36:1:1:0:60:38.8:1:0:0
    809. 

  809. 2	142012036	142012036	T	G	intronic	LRP1B	.	.	.	0.57	0.3064	0.1170	0.4797	0.2815	0.5394	0.4311	0.3495	0.3691	rs9973397	rs9973397	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67223616;OCCURENCE=1(breast),2(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18154191	LICA-CN|1|402|0.00248756,LUSC-KR|2|170|0.0117647,BRCA-KR|1|50|0.02	0.5	164	22	2	142012036	.	T	G	164	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGATGTCTGCTTACATT;RSEQ=CTGTTAACTAAGCCTCTATA;CSQ=G|intron_variant|MODIFIER|LRP1B|53353|Transcript|NM_018557.3|protein_coding||4/90|NM_018557.3:c.463+55A>C|||||||rs9973397&COSV67223616||-1||EntrezGene||YES||||2:g.142012036T>G||||||||||0.5655|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:22:22:19,3:0,0:0,22:1:0,2:41.6:1:37:0:1:0:60:44:1:0:1.1
    810. 

  810. 2	142238000	142238000	C	T	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon3:c.G308A:p.C103Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	4.445	0.988	H	-4.02	0.964	D	-8.68	0.976	D	0.987	0.991	1.069	0.986	D	0.971	0.991	D	0.585	0.963	D	6.533	0.900	31	0.997	0.829	0.977	0.764	D	c	1.104	0.990	1.000	0.747	0.487	0.133	0	5.51	0.817	7.311	0.781	0.935	0.490	1.000	0.715	0.920	0.395	19.784	0.964	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	435	2	142238000	.	C	T	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=135;VD=2;AF=0.0148;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05578;SOR=inf;LSEQ=CTTCGTCATACCCATCTGGG;RSEQ=AGTCCAAGACACCATTGCAC;CSQ=T|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|3/91||NM_018557.3:c.308G>A|NP_061027.2:p.Cys103Tyr|595|308|103|C/Y|tGc/tAc|||-1||EntrezGene||YES||||2:g.142238000C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:135:2:1,1:72,61:133,2:0.0148:2,2:31:0:31:1:1:1.17887:60:4:0.0148:0:1	0/0:435:0:0,0:249,186:435,0:0:2,0:38.9:1:36.8:1:1:0:60:434:1:0:0.1
    811. 

  811. 2	142567910	142567910	T	C	exonic	LRP1B	.	nonsynonymous SNV	LRP1B:NM_018557:exon2:c.A143G:p.Q48R	0.4	0.1856	0.0954	0.1986	0.3477	0.4038	0.1832	0.2105	0.2010	rs12990449	rs12990449	0.329	0.132	T	0.001	0.067	B	0.003	0.104	B	0.002	0.377	N	0.797	0.291	P	-0.31	0.036	N	-3.68	0.953	D	-1.2	0.305	N	0.269	0.327	-1.072	0.091	T	0.000	0.000	T	.	.	.	1.379	0.229	12.68	0.990	0.498	0.816	0.407	D	c	-0.340	-0.121	0.001	0.075	0.560	0.301	0	4.45	0.532	3.604	0.536	0.964	0.580	1.000	0.715	1.000	0.888	7.876	0.286	EGF-like domain;Low-density lipoprotein (LDL) receptor class A, conserved site	.	.	ID=COSV67182532;OCCURENCE=69(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),7(soft_tissue),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU760781	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763	0.75	303	316	2	142567910	.	T	C	303	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=34;AF=0.4857;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCATCACACAGCCAGCTC;RSEQ=GGGAGACACAAGTCACGTGA;CSQ=C|missense_variant|MODERATE|LRP1B|53353|Transcript|NM_018557.3|protein_coding|2/91||NM_018557.3:c.143A>G|NP_061027.2:p.Gln48Arg|430|143|48|Q/R|cAg/cGg|rs12990449&COSV67182532||-1||EntrezGene||YES||||2:g.142567910T>C|0.2369|0.09151|0.2016|0.3387|0.4003|0.1672|0.2174|0.2442|0.3425|0.4003|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:70:34:18,16:18,18:36,34:0.4857:2,2:38.6:1:36.2:1:0.81605:1.12:60:33:0.4783:0:1	1/1:316:316:136,180:0,0:0,316:1:0,2:41.1:1:36.6:1:1:0:60:157:1:0:1.1
    812. 

  812. 2	173420877	173420877	G	A	UTR5	PDK1	NM_002610:c.-2G>A;NM_001278549:c.-2G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	17	2	173420877	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=149;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00993;SOR=0;LSEQ=GGCTTCTCTAGCGGGACTCG;RSEQ=CATGAGGCTGGCGCGGCTGC;CSQ=A|5_prime_UTR_variant|MODIFIER|PDK1|5163|Transcript|NM_001278549.2|protein_coding|1/12||NM_001278549.2:c.-2G>A||60|||||rs1452242829||1||EntrezGene||YES||||2:g.173420877G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|5_prime_UTR_variant|MODIFIER|PDK1|5163|Transcript|NM_002610.5|protein_coding|1/11||NM_002610.5:c.-2G>A||60|||||rs1452242829||1||EntrezGene||||||2:g.173420877G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|1/12||NR_103729.2:n.60G>A||60|||||rs1452242829||1||EntrezGene||||||2:g.173420877G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||1/13|NR_103731.1:n.347+430G>A|||||||rs1452242829||1||EntrezGene||||||2:g.173420877G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:149:0:0,0:97,52:149,0:0:2,0:39.6:1:36.7:1:1:0:60:298:1:0:0.2	0/1:17:2:1,1:10,5:15,2:0.1176:2,2:64.5:1:37:0:1:1.91491:60:4:0.1176:0:1
    813. 

  813. 2	173420920	173420920	C	-	exonic	PDK1	.	frameshift deletion	PDK1:NM_001278549:exon1:c.42delC:p.P15Rfs*45,PDK1:NM_002610:exon1:c.42delC:p.P15Rfs*45	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	16	2	173420919	.	GC	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=151;VD=2;AF=0.0132;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.81704;SOR=inf;LSEQ=TCGCGGAGCCGCCTTGGCCG;RSEQ=CCGGGCCCGGGGCTGCGCGC;CSQ=-|frameshift_variant|HIGH|PDK1|5163|Transcript|NM_001278549.2|protein_coding|1/12||NM_001278549.2:c.44del|NP_001265478.1:p.Pro15ArgfsTer45|103|42|14|G/X|ggC/gg|||1||EntrezGene||YES|||2|2:g.173420922del||||||||||||||,-|frameshift_variant|HIGH|PDK1|5163|Transcript|NM_002610.5|protein_coding|1/11||NM_002610.5:c.44del|NP_002601.1:p.Pro15ArgfsTer45|103|42|14|G/X|ggC/gg|||1||EntrezGene|||||2|2:g.173420922del||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|1/12||NR_103729.2:n.105del||103|||||||1||EntrezGene||||||2:g.173420922del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||1/13|NR_103731.1:n.347+475del|||||||||1||EntrezGene||||||2:g.173420922del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:151:2:1,1:89,60:149,2:0.0132:2,2:31:0:37:0:1:1.47933:60:4:0.0133:0:0	0/0:16:0:0,0:10,6:16,0:0:2,0:41.8:1:37:0:1:0:60:32:1:0:0.1
    814. 

  814. 2	173420938	173420938	C	T	exonic	PDK1	.	synonymous SNV	PDK1:NM_001278549:exon1:c.C60T:p.R20R,PDK1:NM_002610:exon1:c.C60T:p.R20R	0.	.	.	.	.	.	.	.	.	rs775353017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	18	2	173420938	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=2;AF=0.0135;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.7943;SOR=inf;LSEQ=GGCCCGGGCCCGGGGCTGCG;RSEQ=GCCGCCGGCTTCAGCCGCAG;CSQ=T|synonymous_variant|LOW|PDK1|5163|Transcript|NM_001278549.2|protein_coding|1/12||NM_001278549.2:c.60C>T|NP_001265478.1:p.Arg20%3D|121|60|20|R|cgC/cgT|rs775353017||1||EntrezGene||YES||||2:g.173420938C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|synonymous_variant|LOW|PDK1|5163|Transcript|NM_002610.5|protein_coding|1/11||NM_002610.5:c.60C>T|NP_002601.1:p.Arg20%3D|121|60|20|R|cgC/cgT|rs775353017||1||EntrezGene||||||2:g.173420938C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|1/12||NR_103729.2:n.121C>T||121|||||rs775353017||1||EntrezGene||||||2:g.173420938C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||1/13|NR_103731.1:n.347+491C>T|||||||rs775353017||1||EntrezGene||||||2:g.173420938C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:148:2:1,1:82,64:146,2:0.0135:2,2:23.5:1:37:0:1:1.27908:60:4:0.0136:0:1	0/0:18:0:0,0:13,5:18,0:0:2,0:34.6:1:37:0:1:0:60:36:1:0:0.4
    815. 

  815. 2	173420990	173420990	T	C	exonic	PDK1	.	nonsynonymous SNV	PDK1:NM_001278549:exon1:c.T112C:p.S38P,PDK1:NM_002610:exon1:c.T112C:p.S38P	.	.	.	.	.	.	.	.	.	.	.	0.087	0.329	T	0.0	0.026	B	0.0	0.013	B	0.610	0.109	N	1	0.209	N	0	0.065	N	1.2	0.376	T	-0.98	0.260	N	0.095	0.114	-1.017	0.245	T	0.028	0.122	T	0.089	0.753	D	2.446	0.355	19.12	0.894	0.182	0.006	0.025	N	c	-1.392	-1.423	1.000	0.747	0.442	0.072	0	-6.71	0.016	-1.280	0.029	-0.710	0.037	0.003	0.159	0.010	0.111	6.463	0.210	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	22	2	173420990	.	T	C	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=167;VD=2;AF=0.012;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.7802;SOR=inf;LSEQ=ACTCGGGCTCCAGCCCGGCG;RSEQ=CCGAGCGCGGCGTTCCGGGC;CSQ=C|missense_variant|MODERATE|PDK1|5163|Transcript|NM_001278549.2|protein_coding|1/12||NM_001278549.2:c.112T>C|NP_001265478.1:p.Ser38Pro|173|112|38|S/P|Tcc/Ccc|||1||EntrezGene||YES||||2:g.173420990T>C||||||||||||||,C|missense_variant|MODERATE|PDK1|5163|Transcript|NM_002610.5|protein_coding|1/11||NM_002610.5:c.112T>C|NP_002601.1:p.Ser38Pro|173|112|38|S/P|Tcc/Ccc|||1||EntrezGene||||||2:g.173420990T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|1/12||NR_103729.2:n.173T>C||173|||||||1||EntrezGene||||||2:g.173420990T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||1/13|NR_103731.1:n.347+543T>C|||||||||1||EntrezGene||||||2:g.173420990T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:167:2:1,1:80,83:163,2:0.012:2,2:38:0:31:1:1:1.04:60:4:0.0128:0:1	0/0:22:0:0,0:13,9:22,0:0:2,0:27.5:1:34.2:1:1:0:60:21:1:0:0.3
    816. 

  816. 2	173423597	173423597	T	C	intronic	PDK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	177	2	173423597	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=521;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.06403;SOR=0;LSEQ=GGTAAGATTCTCATCTTGTG;RSEQ=TTGCAATTTGATGGAGTTGT;CSQ=C|intron_variant|MODIFIER|PDK1|5163|Transcript|NM_001278549.2|protein_coding||2/11|NM_001278549.2:c.338+20T>C|||||||||1||EntrezGene||YES||||2:g.173423597T>C||||||||||||||,C|intron_variant|MODIFIER|PDK1|5163|Transcript|NM_002610.5|protein_coding||2/10|NM_002610.5:c.338+20T>C|||||||||1||EntrezGene||||||2:g.173423597T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA||2/11|NR_103729.2:n.399+20T>C|||||||||1||EntrezGene||||||2:g.173423597T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||2/13|NR_103731.1:n.489+20T>C|||||||||1||EntrezGene||||||2:g.173423597T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:521:0:0,0:233,288:521,0:0:2,0:39.8:1:35.7:1:1:0:60:56.889:1:0:0.1	0/1:177:2:1,1:67,108:175,2:0.0113:2,2:39.5:1:31:1:1:1.61:60:4:0.0114:0:1
    817. 

  817. 2	173427569	173427569	T	C	intronic	PDK1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	152	2	173427569	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.93712;SOR=0;LSEQ=AATAACCCATATACCAGAAT;RSEQ=GGTAAACCAAAGTATTTGCC;CSQ=C|intron_variant|MODIFIER|PDK1|5163|Transcript|NM_001278549.2|protein_coding||4/11|NM_001278549.2:c.470+41T>C|||||||||1||EntrezGene||YES||||2:g.173427569T>C||||||||||||||,C|intron_variant|MODIFIER|PDK1|5163|Transcript|NM_002610.5|protein_coding||3/10|NM_002610.5:c.410+550T>C|||||||||1||EntrezGene||||||2:g.173427569T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA||3/11|NR_103729.2:n.471+550T>C|||||||||1||EntrezGene||||||2:g.173427569T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA||3/13|NR_103731.1:n.561+550T>C|||||||||1||EntrezGene||||||2:g.173427569T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:3,2:5,0:0:2,0:30.2:1:37:0:1:0:60:10:1:0:0	0/1:152:2:1,1:68,82:150,2:0.0132:2,2:48:1:37:0:1:1.2:60:4:0.0134:0:1
    818. 

  818. 2	173429313	173429313	G	A	exonic	PDK1	.	nonsynonymous SNV	PDK1:NM_002610:exon4:c.G493A:p.E165K,PDK1:NM_001278549:exon5:c.G553A:p.E185K	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.765	0.418	P	0.525	0.486	P	0.000	0.629	D	1	0.810	D	1.545	0.392	L	1.56	0.299	T	-3.59	0.692	D	0.571	0.709	-1.100	0.041	T	0.104	0.382	T	0.017	0.386	T	5.370	0.727	25.9	0.999	0.987	0.992	0.923	D	c	0.428	0.526	1.000	0.747	0.737	0.974	0	5.3	0.746	10.003	0.997	0.998	0.613	1.000	0.715	1.000	0.888	18.956	0.926	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	.	.	ID=COSV104388149;OCCURENCE=1(central_nervous_system)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	415	2	173429313	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=2;AF=0.0127;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.07499;SOR=inf;LSEQ=AGGGTGTGATTGAATACAAG;RSEQ=AGAGCTTTGGGGTGGATCCT;CSQ=A|missense_variant|MODERATE|PDK1|5163|Transcript|NM_001278549.2|protein_coding|5/12||NM_001278549.2:c.553G>A|NP_001265478.1:p.Glu185Lys|614|553|185|E/K|Gag/Aag|||1||EntrezGene||YES||||2:g.173429313G>A||||||||||||||,A|missense_variant|MODERATE|PDK1|5163|Transcript|NM_002610.5|protein_coding|4/11||NM_002610.5:c.493G>A|NP_002601.1:p.Glu165Lys|554|493|165|E/K|Gag/Aag|||1||EntrezGene||||||2:g.173429313G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|4/12||NR_103729.2:n.554G>A||554|||||||1||EntrezGene||||||2:g.173429313G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA|4/14||NR_103731.1:n.644G>A||644|||||||1||EntrezGene||||||2:g.173429313G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:157:2:1,1:77,78:155,2:0.0127:2,2:44:1:37:0:1:1.01:60:4:0.0129:0:1	0/0:415:0:0,0:203,211:414,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    819. 

  819. 2	173429336	173429336	C	A	exonic	PDK1	.	synonymous SNV	PDK1:NM_002610:exon4:c.C516A:p.V172V,PDK1:NM_001278549:exon5:c.C576A:p.V192V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	407	2	173429336	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=152;VD=2;AF=0.0132;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07358;SOR=inf;LSEQ=AGCTTTGGGGTGGATCCTGT;RSEQ=ACCAGCCAGAATGTTCAGTA;CSQ=A|synonymous_variant|LOW|PDK1|5163|Transcript|NM_001278549.2|protein_coding|5/12||NM_001278549.2:c.576C>A|NP_001265478.1:p.Val192%3D|637|576|192|V|gtC/gtA|COSV99961473||1||EntrezGene||YES||||2:g.173429336C>A|||||||||||||1|1,A|synonymous_variant|LOW|PDK1|5163|Transcript|NM_002610.5|protein_coding|4/11||NM_002610.5:c.516C>A|NP_002601.1:p.Val172%3D|577|516|172|V|gtC/gtA|COSV99961473||1||EntrezGene||||||2:g.173429336C>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|4/12||NR_103729.2:n.577C>A||577|||||COSV99961473||1||EntrezGene||||||2:g.173429336C>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA|4/14||NR_103731.1:n.667C>A||667|||||COSV99961473||1||EntrezGene||||||2:g.173429336C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:152:2:1,1:69,81:150,2:0.0132:2,2:16:0:37:0:1:1.17:60:4:0.0134:0:1	0/0:407:0:0,0:183,224:407,0:0:2,0:39.2:1:36.8:1:1:0:60:406:1:0:0.1
    820. 

  820. 2	173460621	173460621	A	G	exonic	PDK1	.	nonsynonymous SNV	PDK1:NM_002610:exon11:c.A1235G:p.N412S,PDK1:NM_001278549:exon12:c.A1295G:p.N432S	.	.	.	.	.	.	.	.	.	.	.	0.083	0.330	T	0.0	0.026	B	0.0	0.080	B	0.000	0.486	N	0.983	0.281	N	-0.345	0.033	N	1.33	0.350	T	-0.58	0.174	N	0.1	0.103	-0.998	0.306	T	0.109	0.393	T	0.010	0.272	T	2.028	0.305	16.39	0.991	0.531	0.953	0.641	D	c	-0.250	-0.026	1.000	0.402	0.707	0.730	0	4.76	0.600	4.301	0.586	1.199	0.960	1.000	0.715	0.995	0.604	8.723	0.334	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	226	2	173460621	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=2;AF=0.0101;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.21866;SOR=inf;LSEQ=AGCTGCCTGGAAGCATTACA;RSEQ=CACCAACCACGAGGCTGATG;CSQ=G|missense_variant|MODERATE|PDK1|5163|Transcript|NM_001278549.2|protein_coding|12/12||NM_001278549.2:c.1295A>G|NP_001265478.1:p.Asn432Ser|1356|1295|432|N/S|aAc/aGc|||1||EntrezGene||YES||||2:g.173460621A>G||||||||||||||,G|missense_variant|MODERATE|PDK1|5163|Transcript|NM_002610.5|protein_coding|11/11||NM_002610.5:c.1235A>G|NP_002601.1:p.Asn412Ser|1296|1235|412|N/S|aAc/aGc|||1||EntrezGene||||||2:g.173460621A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|11/12||NR_103729.2:n.1296A>G||1296|||||||1||EntrezGene||||||2:g.173460621A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA|11/14||NR_103731.1:n.1386A>G||1386|||||||1||EntrezGene||||||2:g.173460621A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:199:2:1,1:113,84:197,2:0.0101:2,2:51.5:1:37:0:1:1.34319:60:4:0.0102:0:1	0/0:226:0:0,0:120,106:226,0:0:2,0:38.8:1:36:1:1:0:60:55.5:1:0:0
    821. 

  821. 2	173460659	173460659	A	C	exonic	PDK1	.	synonymous SNV	PDK1:NM_002610:exon11:c.A1273C:p.R425R,PDK1:NM_001278549:exon12:c.A1333C:p.R445R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	52	240	2	173460659	.	A	C	52	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=249;VD=3;AF=0.012;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.13125;SOR=inf;LSEQ=ATGACTGGTGCGTCCCCAGC;RSEQ=GAGAACCCAAAGACATGACG;CSQ=C|synonymous_variant|LOW|PDK1|5163|Transcript|NM_001278549.2|protein_coding|12/12||NM_001278549.2:c.1333A>C|NP_001265478.1:p.Arg445%3D|1394|1333|445|R|Aga/Cga|||1||EntrezGene||YES||||2:g.173460659A>C||||||||||||||,C|synonymous_variant|LOW|PDK1|5163|Transcript|NM_002610.5|protein_coding|11/11||NM_002610.5:c.1273A>C|NP_002601.1:p.Arg425%3D|1334|1273|425|R|Aga/Cga|||1||EntrezGene||||||2:g.173460659A>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103729.2|misc_RNA|11/12||NR_103729.2:n.1334A>C||1334|||||||1||EntrezGene||||||2:g.173460659A>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|PDK1|5163|Transcript|NR_103731.1|misc_RNA|11/14||NR_103731.1:n.1424A>C||1424|||||||1||EntrezGene||||||2:g.173460659A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:249:3:2,1:122,124:246,3:0.012:2,2:51.7:1:33:1:0.62197:2.03:60:6:0.0128:0:1	0/0:240:0:0,0:121,119:240,0:0:2,0:39.9:1:36.6:1:1:0:60:119:1:0:0.1
    822. 

  822. 2	178095520	178095520	T	C	exonic	NFE2L2	.	nonsynonymous SNV	NFE2L2:NM_001313902:exon4:c.A1721G:p.K574R,NFE2L2:NM_001145412:exon5:c.A1763G:p.K588R,NFE2L2:NM_001145413:exon5:c.A1742G:p.K581R,NFE2L2:NM_001313900:exon5:c.A1763G:p.K588R,NFE2L2:NM_001313901:exon5:c.A1763G:p.K588R,NFE2L2:NM_001313903:exon5:c.A1592G:p.K531R,NFE2L2:NM_001313904:exon5:c.A1511G:p.K504R,NFE2L2:NM_006164:exon5:c.A1811G:p.K604R	.	3.229e-05	0.0001	0	0	0	0	0	0	rs1015105997	.	0.076	0.346	T	0.053	0.211	B	0.012	0.149	B	0.097	0.200	N	0.648	0.305	N	0	0.065	N	2.2	0.186	T	0.08	0.064	N	0.094	0.132	-1.100	0.041	T	0.040	0.171	T	0.005	0.120	T	0.748	0.165	9.135	0.997	0.799	0.918	0.540	D	c	-0.227	-0.050	1.000	0.517	0.732	0.924	0	4.16	0.480	1.101	0.304	1.057	0.759	1.000	0.715	1.000	0.888	12.016	0.524	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	174	2	178095520	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=29;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.73409;SOR=0;LSEQ=AATCCTCCTAAATCTAGTTT;RSEQ=TCTTAACATCTGGCTTCTTA;CSQ=C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|5/5||NM_001145412.3:c.1763A>G|NP_001138884.1:p.Lys588Arg|2495|1763|588|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|5/5||NM_001145413.3:c.1742A>G|NP_001138885.1:p.Lys581Arg|2474|1742|581|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|5/5||NM_001313900.1:c.1763A>G|NP_001300829.1:p.Lys588Arg|2369|1763|588|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|5/5||NM_001313901.1:c.1763A>G|NP_001300830.1:p.Lys588Arg|2461|1763|588|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|4/4||NM_001313902.1:c.1721A>G|NP_001300831.1:p.Lys574Arg|2276|1721|574|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|5/5||NM_001313903.1:c.1592A>G|NP_001300832.1:p.Lys531Arg|2147|1592|531|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|5/5||NM_001313904.1:c.1511A>G|NP_001300833.1:p.Lys504Arg|2424|1511|504|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||||||2:g.178095520T>C|||||||||||||0&1|0&1,C|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|5/5||NM_006164.5:c.1811A>G|NP_006155.2:p.Lys604Arg|1962|1811|604|K/R|aAa/aGa|rs1015105997&COSV67963032||-1||EntrezGene||YES||||2:g.178095520T>C|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:29:0:0,0:22,7:29,0:0:2,0:31:1:35.7:1:1:0:60:28:1:0:0.1	0/1:174:2:1,1:110,62:172,2:0.0115:2,2:34:1:37:0:1:1.76795:60:4:0.0116:0:1
    823. 

  823. 2	178095623	178095623	C	T	exonic	NFE2L2	.	nonsynonymous SNV	NFE2L2:NM_001313902:exon4:c.G1618A:p.D540N,NFE2L2:NM_001145412:exon5:c.G1660A:p.D554N,NFE2L2:NM_001145413:exon5:c.G1639A:p.D547N,NFE2L2:NM_001313900:exon5:c.G1660A:p.D554N,NFE2L2:NM_001313901:exon5:c.G1660A:p.D554N,NFE2L2:NM_001313903:exon5:c.G1489A:p.D497N,NFE2L2:NM_001313904:exon5:c.G1408A:p.D470N,NFE2L2:NM_006164:exon5:c.G1708A:p.D570N	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	3.175	0.890	M	1.26	0.367	T	-4.43	0.789	D	0.224	0.359	-0.531	0.675	T	0.284	0.656	T	0.033	0.546	D	6.256	0.864	28.9	0.999	0.969	0.978	0.771	D	c	0.959	0.939	1.0	0.983	0.707	0.730	0	6.03	0.978	7.902	0.860	0.931	0.441	1.000	0.715	0.998	0.697	20.640	0.995	Basic leucine zipper domain, Maf-type|Basic-leucine zipper domain	.	.	ID=COSV67961697;OCCURENCE=1(skin),1(upper_aerodigestive_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU131161735	HNSC-US|1|508|0.0019685	0.25	37	264	2	178095623	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=2;AF=0.0206;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.07165;SOR=inf;LSEQ=ATAAGGTTTTCCATCTTCAT;RSEQ=ACGTAGCATGCTGAAAACTT;CSQ=T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|5/5||NM_001145412.3:c.1660G>A|NP_001138884.1:p.Asp554Asn|2392|1660|554|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|5/5||NM_001145413.3:c.1639G>A|NP_001138885.1:p.Asp547Asn|2371|1639|547|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|5/5||NM_001313900.1:c.1660G>A|NP_001300829.1:p.Asp554Asn|2266|1660|554|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|5/5||NM_001313901.1:c.1660G>A|NP_001300830.1:p.Asp554Asn|2358|1660|554|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|4/4||NM_001313902.1:c.1618G>A|NP_001300831.1:p.Asp540Asn|2173|1618|540|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|5/5||NM_001313903.1:c.1489G>A|NP_001300832.1:p.Asp497Asn|2044|1489|497|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|5/5||NM_001313904.1:c.1408G>A|NP_001300833.1:p.Asp470Asn|2321|1408|470|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||||||2:g.178095623C>T|||||||||||||1|1,T|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|5/5||NM_006164.5:c.1708G>A|NP_006155.2:p.Asp570Asn|1859|1708|570|D/N|Gat/Aat|COSV67961697||-1||EntrezGene||YES||||2:g.178095623C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:97:2:1,1:48,47:95,2:0.0206:2,2:52.5:1:37:0:1:1.02106:60:4:0.0208:0:1	0/0:264:0:0,0:122,142:264,0:0:2,0:39:1:36.3:1:1:0:60:43:1:0:0.1
    824. 

  824. 2	178098035	178098035	G	A	exonic	NFE2L2	.	synonymous SNV	NFE2L2:NM_001145412:exon3:c.C297T:p.Y99Y,NFE2L2:NM_001145413:exon3:c.C297T:p.Y99Y,NFE2L2:NM_001313900:exon3:c.C297T:p.Y99Y,NFE2L2:NM_001313901:exon3:c.C297T:p.Y99Y,NFE2L2:NM_001313903:exon3:c.C126T:p.Y42Y,NFE2L2:NM_001313904:exon3:c.C45T:p.Y15Y,NFE2L2:NM_006164:exon3:c.C345T:p.Y115Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	374	2	178098035	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=89;VD=2;AF=0.0225;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03661;SOR=inf;LSEQ=AGCTGCATGCAGTCATCAAA;RSEQ=TACAAAGCATCTGATTTGGG;CSQ=A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|3/5||NM_001145412.3:c.297C>T|NP_001138884.1:p.Tyr99%3D|1029|297|99|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|3/5||NM_001145413.3:c.297C>T|NP_001138885.1:p.Tyr99%3D|1029|297|99|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|3/5||NM_001313900.1:c.297C>T|NP_001300829.1:p.Tyr99%3D|903|297|99|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|3/5||NM_001313901.1:c.297C>T|NP_001300830.1:p.Tyr99%3D|995|297|99|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|intron_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding||2/3|NM_001313902.1:c.312+698C>T|||||||||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|3/5||NM_001313903.1:c.126C>T|NP_001300832.1:p.Tyr42%3D|681|126|42|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|3/5||NM_001313904.1:c.45C>T|NP_001300833.1:p.Tyr15%3D|958|45|15|Y|taC/taT|||-1||EntrezGene||||||2:g.178098035G>A||||||||||||||,A|synonymous_variant|LOW|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|3/5||NM_006164.5:c.345C>T|NP_006155.2:p.Tyr115%3D|496|345|115|Y|taC/taT|||-1||EntrezGene||YES||||2:g.178098035G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:89:2:1,1:43,44:87,2:0.0225:2,2:17:0:37:0:1:1.02:60:4:0.0225:0:1	0/0:374:0:0,0:168,206:374,0:0:2,0:37.6:1:35.7:1:1:0:60:36.4:1:0:0.1
    825. 

  825. 2	178098951	178098951	C	A	exonic;splicing	NFE2L2;NFE2L2	NM_001313903:exon2:c.93+1G>T	nonsynonymous SNV	NFE2L2:NM_001145412:exon2:c.G46T:p.V16L,NFE2L2:NM_001145413:exon2:c.G46T:p.V16L,NFE2L2:NM_001313900:exon2:c.G46T:p.V16L,NFE2L2:NM_001313901:exon2:c.G46T:p.V16L,NFE2L2:NM_001313902:exon2:c.G94T:p.V32L,NFE2L2:NM_006164:exon2:c.G94T:p.V32L	.	.	.	.	.	.	.	.	.	.	.	0.019	0.721	D	0.199	0.299	B	0.079	0.310	B	0.000	0.629	D	0.999	0.454	D	2.045	0.562	M	1.54	0.301	T	-0.99	0.404	N	0.173	0.256	-0.979	0.352	T	0.116	0.410	T	0.013	0.329	T	4.882	0.656	24.9	0.996	0.729	0.991	0.906	D	c	0.353	0.493	1.000	0.747	0.732	0.924	0	5.78	0.914	7.568	0.814	0.935	0.490	1.000	0.715	0.998	0.697	19.998	0.974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	123	2	178098951	.	C	A	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.32015;SOR=0;LSEQ=GTCAAATACTTCTCGACTTA;RSEQ=TCCAAGATCTATATCTTGCC;CSQ=A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|2/5||NM_001145412.3:c.46G>T|NP_001138884.1:p.Val16Leu|778|46|16|V/L|Gta/Tta|||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|2/5||NM_001145413.3:c.46G>T|NP_001138885.1:p.Val16Leu|778|46|16|V/L|Gta/Tta|||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|2/5||NM_001313900.1:c.46G>T|NP_001300829.1:p.Val16Leu|652|46|16|V/L|Gta/Tta|||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|2/5||NM_001313901.1:c.46G>T|NP_001300830.1:p.Val16Leu|744|46|16|V/L|Gta/Tta|||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|2/4||NM_001313902.1:c.94G>T|NP_001300831.1:p.Val32Leu|649|94|32|V/L|Gta/Tta|||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|splice_donor_variant|HIGH|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding||2/4|NM_001313903.1:c.93+1G>T|||||||||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|2/5||NM_001313904.1:c.-136G>T||778|||||||-1||EntrezGene||||||2:g.178098951C>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|2/5||NM_006164.5:c.94G>T|NP_006155.2:p.Val32Leu|245|94|32|V/L|Gta/Tta|||-1||EntrezGene||YES||||2:g.178098951C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:94:0:0,0:24,70:94,0:0:2,0:34.7:1:34.4:1:1:0:60:14.667:1:0:0.2	0/1:123:2:2,0:36,85:121,2:0.0163:2,0:24.5:1:25:0:0.0937:0:60:4:0.0174:0:3.5
    826. 

  826. 2	178129279	178129279	G	A	exonic	NFE2L2	.	nonsynonymous SNV	NFE2L2:NM_001313902:exon1:c.C26T:p.P9L,NFE2L2:NM_001313903:exon1:c.C26T:p.P9L,NFE2L2:NM_006164:exon1:c.C26T:p.P9L	.	.	.	.	.	.	.	.	.	.	.	0.19	0.912	T	0.569	0.366	P	0.05	0.239	B	0.131	0.186	U	0.999	0.810	D	1.39	0.351	L	1.46	0.629	T	-0.13	0.229	N	0.259	0.315	-0.819	0.540	T	0.154	0.484	T	0.921	0.994	D	2.431	0.353	19.02	0.957	0.270	0.768	0.374	D	c	-0.037	-0.004	1.000	0.747	0.442	0.072	0	3.85	0.434	2.898	0.481	0.819	0.335	0.998	0.411	0.991	0.552	11.993	0.523	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	25	2	178129279	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=2;AF=0.0163;SHIFT3=2;MSI=3;MSILEN=3;SSF=0.68974;SOR=inf;LSEQ=CCTGCTGGGACGGGAGTCCC;RSEQ=GCGGCGGCAGCTCCAAGTCC;CSQ=A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|||||||||||420|-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|||||||||||420|-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|||||||||||420|-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|||||||||||420|-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|1/4||NM_001313902.1:c.26C>T|NP_001300831.1:p.Pro9Leu|581|26|9|P/L|cCg/cTg|||-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|1/5||NM_001313903.1:c.26C>T|NP_001300832.1:p.Pro9Leu|581|26|9|P/L|cCg/cTg|||-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|||||||||||420|-1||EntrezGene||||||2:g.178129279G>A||||||||||||||,A|missense_variant|MODERATE|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|1/5||NM_006164.5:c.26C>T|NP_006155.2:p.Pro9Leu|177|26|9|P/L|cCg/cTg|||-1||EntrezGene||YES||||2:g.178129279G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:60,61:121,2:0.0163:2,2:15.5:1:37:0:1:1.02:60:4:0.0163:0:1	0/0:25:0:0,0:12,13:25,0:0:2,0:33.6:1:37:0:1:0:60:50:1:0:0.1
    827. 

  827. 2	178129320	178129320	G	A	UTR5	NFE2L2	NM_006164:c.-16C>T;NM_001313903:c.-16C>T;NM_001313902:c.-16C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	16	2	178129320	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=113;VD=2;AF=0.0177;SHIFT3=0;MSI=3;MSILEN=2;SSF=0.76647;SOR=inf;LSEQ=ATCATGATGAGCTGTGGACC;RSEQ=TGTGTTGGGGCTCCCCGACG;CSQ=A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|||||||||||461|-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|||||||||||461|-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|||||||||||461|-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|||||||||||461|-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|1/4||NM_001313902.1:c.-16C>T||540|||||||-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|1/5||NM_001313903.1:c.-16C>T||540|||||||-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|||||||||||461|-1||EntrezGene||||||2:g.178129320G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|1/5||NM_006164.5:c.-16C>T||136|||||||-1||EntrezGene||YES||||2:g.178129320G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:113:2:1,1:50,61:111,2:0.0177:2,2:23:0:37:0:1:1.22:60:4:0.0179:0:1	0/0:16:0:0,0:4,12:16,0:0:2,0:42.5:1:37:0:1:0:60:32:1:0:0.1
    828. 

  828. 2	178129326	178129326	T	C	UTR5	NFE2L2	NM_006164:c.-22A>G;NM_001313903:c.-22A>G;NM_001313902:c.-22A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	16	2	178129326	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=110;VD=2;AF=0.0182;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.76127;SOR=inf;LSEQ=ATGAGCTGTGGACCGTGTGT;RSEQ=GGGGCTCCCCGACGGCGGCC;CSQ=C|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|||||||||||467|-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|||||||||||467|-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|||||||||||467|-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|||||||||||467|-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|1/4||NM_001313902.1:c.-22A>G||534|||||||-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|1/5||NM_001313903.1:c.-22A>G||534|||||||-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|||||||||||467|-1||EntrezGene||||||2:g.178129326T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|1/5||NM_006164.5:c.-22A>G||130|||||||-1||EntrezGene||YES||||2:g.178129326T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:110:2:1,1:50,58:108,2:0.0182:2,2:12:0:37:0:1:1.16:60:4:0.0185:0:1	0/0:16:0:0,0:4,12:16,0:0:2,0:39.5:1:35.4:1:1:0:60:15:1:0:0.1
    829. 

  829. 2	178129340	178129340	G	T	UTR5	NFE2L2	NM_006164:c.-36C>A;NM_001313903:c.-36C>A;NM_001313902:c.-36C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	14	2	178129340	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=91;VD=2;AF=0.022;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.75;SOR=inf;LSEQ=GTGTGTTGGGGCTCCCCGAC;RSEQ=GCGGCCCTGTTCCGGCTGCC;CSQ=T|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145412.3|protein_coding|||||||||||481|-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001145413.3|protein_coding|||||||||||481|-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313900.1|protein_coding|||||||||||481|-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313901.1|protein_coding|||||||||||481|-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313902.1|protein_coding|1/4||NM_001313902.1:c.-36C>A||520|||||||-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313903.1|protein_coding|1/5||NM_001313903.1:c.-36C>A||520|||||||-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|NFE2L2|4780|Transcript|NM_001313904.1|protein_coding|||||||||||481|-1||EntrezGene||||||2:g.178129340G>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|NFE2L2|4780|Transcript|NM_006164.5|protein_coding|1/5||NM_006164.5:c.-36C>A||116|||||||-1||EntrezGene||YES||||2:g.178129340G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:91:2:1,1:40,49:89,2:0.022:2,2:49:1:37:0:1:1.22:60:4:0.022:0:1.5	0/0:14:0:0,0:4,10:14,0:0:2,0:36.6:1:37:0:1:0:60:28:1:0:0.1
    830. 

  830. 2	190660568	190660568	T	A	exonic	PMS1	.	nonsynonymous SNV	PMS1:NM_000534:exon3:c.T206A:p.M69K,PMS1:NM_001128143:exon3:c.T206A:p.M69K,PMS1:NM_001128144:exon3:c.T206A:p.M69K,PMS1:NM_001321044:exon3:c.T206A:p.M69K,PMS1:NM_001321047:exon3:c.T206A:p.M69K,PMS1:NM_001321049:exon3:c.T206A:p.M69K,PMS1:NM_001321051:exon3:c.T206A:p.M69K,PMS1:NM_001321045:exon4:c.T206A:p.M69K,PMS1:NM_001321048:exon4:c.T206A:p.M69K	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.995	0.832	D	0.000	0.843	D	1	0.810	D	2.905	0.843	M	-0.81	0.900	T	-5.16	0.851	D	0.978	0.980	0.900	0.957	D	0.856	0.952	D	0.256	0.894	D	6.418	0.886	29.7	0.987	0.448	0.986	0.846	D	c	0.815	0.785	1.000	0.747	0.732	0.924	0	5.78	0.914	6.232	0.721	1.051	0.754	1.000	0.715	1.000	0.888	16.112	0.810	Histidine kinase-like ATPase, C-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	358	2	190660568	.	T	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=2;AF=0.0339;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01973;SOR=inf;LSEQ=GGCTGTTGATGCACCTGTAA;RSEQ=GGCAATGAAGTACTACACCT;CSQ=A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_000534.5|protein_coding|3/13||NM_000534.5:c.206T>A|NP_000525.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001128143.2|protein_coding|3/12||NM_001128143.2:c.206T>A|NP_001121615.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001128144.2|protein_coding|3/12||NM_001128144.2:c.206T>A|NP_001121616.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|PMS1|5378|Transcript|NM_001289408.2|protein_coding|3/12||NM_001289408.2:c.-220T>A||370|||||||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001289409.2|protein_coding||2/10|NM_001289409.2:c.-111+3901T>A|||||||||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321044.2|protein_coding|3/11||NM_001321044.2:c.206T>A|NP_001307973.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321045.2|protein_coding|4/14||NM_001321045.2:c.206T>A|NP_001307974.1:p.Met69Lys|496|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321046.2|protein_coding||2/11|NM_001321046.2:c.132+3901T>A|||||||||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321047.2|protein_coding|3/13||NM_001321047.2:c.206T>A|NP_001307976.1:p.Met69Lys|547|206|69|M/K|aTg/aAg|||1||EntrezGene||YES||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321048.2|protein_coding|4/14||NM_001321048.2:c.206T>A|NP_001307977.1:p.Met69Lys|467|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321049.2|protein_coding|3/4||NM_001321049.2:c.206T>A|NP_001307978.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321051.2|protein_coding|3/5||NM_001321051.2:c.206T>A|NP_001307980.1:p.Met69Lys|370|206|69|M/K|aTg/aAg|||1||EntrezGene||||||2:g.190660568T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|PMS1|5378|Transcript|NR_110332.2|misc_RNA|4/13||NR_110332.2:n.467T>A||467|||||||1||EntrezGene||||||2:g.190660568T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:59:2:1,1:30,27:57,2:0.0339:2,2:42:0:37:0:1:1.10912:60:4:0.0345:0:1	0/0:358:0:0,0:170,188:358,0:0:2,0:36.3:1:36.4:1:1:0:60:88.5:1:0:0.1
    831. 

  831. 2	190660570	190660570	G	A	exonic	PMS1	.	nonsynonymous SNV	PMS1:NM_000534:exon3:c.G208A:p.A70T,PMS1:NM_001128143:exon3:c.G208A:p.A70T,PMS1:NM_001128144:exon3:c.G208A:p.A70T,PMS1:NM_001321044:exon3:c.G208A:p.A70T,PMS1:NM_001321047:exon3:c.G208A:p.A70T,PMS1:NM_001321049:exon3:c.G208A:p.A70T,PMS1:NM_001321051:exon3:c.G208A:p.A70T,PMS1:NM_001321045:exon4:c.G208A:p.A70T,PMS1:NM_001321048:exon4:c.G208A:p.A70T	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	1.0	0.899	D	0.998	0.916	D	0.000	0.629	D	1	0.810	D	1.61	0.413	L	-0.67	0.919	T	-3.24	0.670	D	0.674	0.720	0.642	0.925	D	0.834	0.944	D	0.103	0.777	D	6.805	0.925	32	0.996	0.758	0.994	0.951	D	c	0.813	0.839	1.000	0.747	0.732	0.924	0	5.78	0.914	9.947	0.989	1.038	0.658	1.000	0.715	1.000	0.888	20.016	0.975	Histidine kinase-like ATPase, C-terminal domain	.	.	ID=COSV59716357;OCCURENCE=1(stomach)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU5626649	STAD-US|1|439|0.0022779	0.25	37	354	2	190660570	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=2;AF=0.0339;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02011;SOR=inf;LSEQ=CTGTTGATGCACCTGTAATG;RSEQ=CAATGAAGTACTACACCTCA;CSQ=A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_000534.5|protein_coding|3/13||NM_000534.5:c.208G>A|NP_000525.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001128143.2|protein_coding|3/12||NM_001128143.2:c.208G>A|NP_001121615.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001128144.2|protein_coding|3/12||NM_001128144.2:c.208G>A|NP_001121616.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|5_prime_UTR_variant|MODIFIER|PMS1|5378|Transcript|NM_001289408.2|protein_coding|3/12||NM_001289408.2:c.-218G>A||372|||||COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001289409.2|protein_coding||2/10|NM_001289409.2:c.-111+3903G>A|||||||COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321044.2|protein_coding|3/11||NM_001321044.2:c.208G>A|NP_001307973.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321045.2|protein_coding|4/14||NM_001321045.2:c.208G>A|NP_001307974.1:p.Ala70Thr|498|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321046.2|protein_coding||2/11|NM_001321046.2:c.132+3903G>A|||||||COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321047.2|protein_coding|3/13||NM_001321047.2:c.208G>A|NP_001307976.1:p.Ala70Thr|549|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||YES||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321048.2|protein_coding|4/14||NM_001321048.2:c.208G>A|NP_001307977.1:p.Ala70Thr|469|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321049.2|protein_coding|3/4||NM_001321049.2:c.208G>A|NP_001307978.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|missense_variant|MODERATE|PMS1|5378|Transcript|NM_001321051.2|protein_coding|3/5||NM_001321051.2:c.208G>A|NP_001307980.1:p.Ala70Thr|372|208|70|A/T|Gca/Aca|COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|PMS1|5378|Transcript|NR_110332.2|misc_RNA|4/13||NR_110332.2:n.469G>A||469|||||COSV59716357||1||EntrezGene||||||2:g.190660570G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:59:2:1,1:30,27:57,2:0.0339:2,2:8.5:1:37:0:1:1.10912:60:4:0.0339:0:1	0/0:354:0:0,0:167,187:354,0:0:2,0:36.5:1:35.8:1:1:0:60:38.333:1:0:0.1
    832. 

  832. 2	190717517	190717517	-	A	intronic	PMS1	.	.	.	0.0036	0.0001	0	0.0014	0	0	0	0.0001	0	rs768049373	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU115345260	PRAD-CA|2|306|0.00653595	0.25	39	64	2	190717517	.	G	GA	39	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=4;VD=0;AF=0;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.88499;SOR=0;LSEQ=CTTAAAGGTAGTATGCTTTA;RSEQ=AAAAAAAAAATTATTTGAAT;CSQ=A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_000534.5|protein_coding||7/12|NM_000534.5:c.822+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001128143.2|protein_coding||6/11|NM_001128143.2:c.705+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001128144.2|protein_coding||7/11|NM_001128144.2:c.822+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001289408.2|protein_coding||6/11|NM_001289408.2:c.294+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001289409.2|protein_coding||5/10|NM_001289409.2:c.294+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321044.2|protein_coding||6/10|NM_001321044.2:c.705+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321045.2|protein_coding||8/13|NM_001321045.2:c.822+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321046.2|protein_coding||6/11|NM_001321046.2:c.639+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321047.2|protein_coding||7/12|NM_001321047.2:c.822+24dup|||||||rs759972095||1||EntrezGene||YES||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant|MODIFIER|PMS1|5378|Transcript|NM_001321048.2|protein_coding||8/13|NM_001321048.2:c.822+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|PMS1|5378|Transcript|NR_110332.2|misc_RNA||7/12|NR_110332.2:n.966+24dup|||||||rs759972095||1||EntrezGene||||||2:g.190717527dup|0.001415|0.0006213|0.00189|0.001158|0.001345|0.0003192|0.001582|0.001575|0.001699|0.00189|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:35:1:37:0:1:0:60:8:1:0:0	0/1:64:2:0,2:21,38:59,2:0.0312:2,0:23.3:1:39.2:0:0.54098:0:63.6:4:0.0333:0:0
    833. 

  833. 2	191896247	191896247	A	G	ncRNA_intronic	LOC105373805	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	80	2	191896247	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTTGGTCTTGAAACTGG;RSEQ=AAACAAAAAGGCACAATGTT;CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||21/23|NM_001243835.2:c.2045-5T>C|||||||||-1||EntrezGene||YES||||2:g.191896247A>G||||||||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||21/23|NM_003151.4:c.2045-5T>C|||||||||-1||EntrezGene||||||2:g.191896247A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|LOC105373805|105373805|Transcript|NR_136318.1|lncRNA||2/2|NR_136318.1:n.243+424A>G|||||||||1||EntrezGene||YES||||2:g.191896247A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:80:2:1,1:39,39:78,2:0.025:2,2:48:1:37:0:1:1:60:4:0.025:0:1
    834. 

  834. 2	191898370	191898370	A	G	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	139	2	191898370	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.86985;SOR=0;LSEQ=TACCTAAAAATAGAACATGC;RSEQ=TTATTTCATCTGATCATTAT;CSQ=G|intron_variant|MODIFIER|STAT4|6775|Transcript|NM_001243835.2|protein_coding||19/23|NM_001243835.2:c.1716-18T>C|||||||||-1||EntrezGene||YES||||2:g.191898370A>G||||||||||||||,G|intron_variant|MODIFIER|STAT4|6775|Transcript|NM_003151.4|protein_coding||19/23|NM_003151.4:c.1716-18T>C|||||||||-1||EntrezGene||||||2:g.191898370A>G||||||||||||||,G|downstream_gene_variant|MODIFIER|LOC105373805|105373805|Transcript|NR_136318.1|lncRNA|||||||||||1330|1||EntrezGene||YES||||2:g.191898370A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:2,8:10,0:0:2,0:24.6:1:33.2:1:1:0:60:9:1:0:0	0/1:139:2:1,1:43,94:137,2:0.0144:2,2:44:1:37:0:0.53446:2.17:60:4:0.0147:0:1
    835. 

  835. 2	191901037	191901037	T	A	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61831066;OCCURENCE=1(prostate)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	208	2	191901037	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=162;VD=2;AF=0.0123;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.19103;SOR=inf;LSEQ=AACCAAGTTCTGAAATAGAG;RSEQ=CAAGATGATAATTTGTTAAT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||16/23|NM_001243835.2:c.1435-12A>T|||||||COSV61831066||-1||EntrezGene||YES||||2:g.191901037T>A|||||||||||||1|1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||16/23|NM_003151.4:c.1435-12A>T|||||||COSV61831066||-1||EntrezGene||||||2:g.191901037T>A|||||||||||||1|1,A|downstream_gene_variant|MODIFIER|LOC105373805|105373805|Transcript|NR_136318.1|lncRNA||||||||||COSV61831066|3997|1||EntrezGene||YES||||2:g.191901037T>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:162:2:0,2:50,110:160,2:0.0123:2,0:11:1:37:0:1:0:60:4:0.0127:0:1.5	0/0:208:0:0,0:71,137:208,0:0:2,0:34.3:1:36.8:1:1:0:60:416:1:0:0.1
    836. 

  836. 2	191905888	191905888	A	T	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	199	2	191905888	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=2;AF=0.1176;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00586;SOR=inf;LSEQ=GACAGCCCTAAGGAAGAGAG;RSEQ=AATAAATTGTTACCTCACAA;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||14/23|NM_001243835.2:c.1252-14T>A|||||||||-1||EntrezGene||YES||||2:g.191905888A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||14/23|NM_003151.4:c.1252-14T>A|||||||||-1||EntrezGene||||||2:g.191905888A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:17:2:1,1:6,9:15,2:0.1176:2,2:19.5:1:37:0:1:1.46:60:4:0.1176:0:1	0/0:199:0:0,0:85,114:199,0:0:2,0:39.7:1:36.7:1:1:0:60:98.5:1:0:0.1
    837. 

  837. 2	191922841	191922841	G	A	intronic	STAT4	.	.	.	0.74	0.5778	0.2175	0.5168	0.7185	0.5229	0.7042	0.7574	0.6857	rs3024866	rs3024866	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61831638;OCCURENCE=2(haematopoietic_and_lymphoid_tissue)	389452	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13402894	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.75	266	158	2	191922841	.	G	A	266	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=4;AF=0.3077;SHIFT3=1;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=GTACAAATCTTCGGTTGCTG;RSEQ=AGAGGAAATCTTAGCTATTT;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||12/23|NM_001243835.2:c.1113-4C>T|||||||rs3024866&COSV61831638||-1||EntrezGene||YES||||2:g.191922841G>A|0.6416|0.2103|0.512|0.6654|0.5171|0.6922|0.7442|0.6669|0.6624|0.7442|EA&gnomAD_NFE|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||12/23|NM_003151.4:c.1113-4C>T|||||||rs3024866&COSV61831638||-1||EntrezGene||||||2:g.191922841G>A|0.6416|0.2103|0.512|0.6654|0.5171|0.6922|0.7442|0.6669|0.6624|0.7442|EA&gnomAD_NFE|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:13:4:1,3:1,8:9,4:0.3077:2,2:28:1:34:1:1:2.45:60:8:0.3333:0:1.2	1/1:158:158:76,82:0,0:0,158:1:0,2:38.4:1:36.5:1:1:0:60:157:1:0:1.1
    838. 

  838. 2	191937928	191937928	A	G	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	175	2	191937928	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=65;VD=2;AF=0.0308;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07252;SOR=inf;LSEQ=TAGAGGCCCCTGGAAAAAGA;RSEQ=TGTCTTGAAATCTCTCTGGT;CSQ=G|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||4/23|NM_001243835.2:c.373-12T>C|||||||||-1||EntrezGene||YES||||2:g.191937928A>G||||||||||||||,G|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||4/23|NM_003151.4:c.373-12T>C|||||||||-1||EntrezGene||||||2:g.191937928A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:65:2:1,1:28,35:63,2:0.0308:2,2:44:1:37:0:1:1.25:60:4:0.0308:0:1	0/0:175:0:0,0:72,103:175,0:0:2,0:36.9:1:36.3:1:1:0:60:86.5:1:0:0
    839. 

  839. 2	191941054	191941054	-	A	intronic	STAT4	.	.	.	0.097	0.0050	0.0038	0.0084	0.0075	0	0.0132	0.0050	0.0085	rs760220932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU2185838	COCA-CN|1|321|0.00311526,BTCA-SG|1|71|0.0140845	0.25	62	115	2	191941054	.	G	GA	62	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=12;VD=0;AF=0;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.74062;SOR=0;LSEQ=ATTTCCATGAAATTTTCCCT;RSEQ=AAAAAAAAAACAATGAGCAA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||3/23|NM_001243835.2:c.274-4dup|||||||rs760220932||-1||EntrezGene||YES||||2:g.191941064dup|0.03102|0.0218|0.05006|0.0502|0.03082|0.01304|0.02794|0.04679|0.04266|0.0502|gnomAD_ASJ|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||3/23|NM_003151.4:c.274-4dup|||||||rs760220932||-1||EntrezGene||||||2:g.191941064dup|0.03102|0.0218|0.05006|0.0502|0.03082|0.01304|0.02794|0.04679|0.04266|0.0502|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:4,8:12,0:0:2,0:36:1:30.7:1:1:0:60:5:1:0:0.7	0/1:115:3:1,2:34,70:104,3:0.0261:2,2:43.5:1:39.2:0:1:1.03:63.6:6:0.0319:0:0.4
    840. 

  840. 2	192011485	192011485	-	A	splicing	STAT4	NM_003151:exon3:c.129-2->T;NM_001243835:exon3:c.129-2->T	.	.	0.25	0.0018	0.0009	0.0129	0	0	0.0201	0.0009	0	rs778032891	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU9586697	BTCA-SG|2|71|0.028169	0.25	37	82	2	192011485	.	T	TA	37	d5;v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=Insertion;DP=0;VD=0;AF=0;SHIFT3=11;MSI=12;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTTAGAAGCTGCCTCCC;RSEQ=AAAAAAAAAAAGGATTATTA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||2/23|NM_001243835.2:c.129-3dup|||||||rs754067021||-1||EntrezGene||YES||||2:g.192011496dup|0.1193|0.09836|0.1357|0.1651|0.1503|0.1095|0.1037|0.1355|0.1627|0.1651|gnomAD_ASJ|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||2/23|NM_003151.4:c.129-3dup|||||||rs754067021||-1||EntrezGene||||||2:g.192011496dup|0.1193|0.09836|0.1357|0.1651|0.1503|0.1095|0.1037|0.1355|0.1627|0.1651|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:82:2:1,1:31,42:73,2:0.0244:2,2:22.4:1:37.2:1:1:1.35:64:4:0.0312:0.0122:0.5
    841. 

  841. 2	192012940	192012940	A	-	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	196	2	192012939	.	GA	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=5;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.95075;SOR=0;LSEQ=CACTGAGACATGCTATAAAA;RSEQ=AGGTGTAGAATTAGAGTTTT;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||1/23|NM_001243835.2:c.-1-10del|||||||||-1||EntrezGene||YES||||2:g.192012941del||||||||||||||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||1/23|NM_003151.4:c.-1-10del|||||||||-1||EntrezGene||||||2:g.192012941del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:2,3:5,0:0:2,0:17.2:1:37:0:1:0:60:10:1:0:0	0/1:196:2:1,1:73,120:193,2:0.0102:2,2:45:1:37:0:1:1.64:60:4:0.0105:0:0
    842. 

  842. 2	192012941	192012941	A	T	intronic	STAT4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	195	2	192012941	.	A	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.9505;SOR=0;LSEQ=CTGAGACATGCTATAAAAGA;RSEQ=GGTGTAGAATTAGAGTTTTA;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_001243835.2|protein_coding||1/23|NM_001243835.2:c.-1-11T>A|||||||||-1||EntrezGene||YES||||2:g.192012941A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|STAT4|6775|Transcript|NM_003151.4|protein_coding||1/23|NM_003151.4:c.-1-11T>A|||||||||-1||EntrezGene||||||2:g.192012941A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:2,3:5,0:0:2,0:16.2:1:37:0:1:0:60:10:1:0:0	0/1:195:2:1,1:72,121:193,2:0.0103:2,2:51:1:31:1:1:1.68:60:4:0.0104:0:1
    843. 

  843. 2	198257795	198257795	T	C	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon24:c.A3657G:p.V1219V	0.88	0.6804	0.8292	0.5299	0.7517	0.5310	0.5539	0.6499	0.6245	rs4685	rs4685	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59206298;OCCURENCE=1(breast),1(large_intestine),2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU137937	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579	0.75	324	244	2	198257795	.	T	C	324	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=475;VD=473;AF=0.9958;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=194.977;LSEQ=ACATGAGGAGATGTCTCAAA;RSEQ=ACATTGGGCCATACATAGTT;CSQ=C|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|24/25||NM_012433.4:c.3657A>G|NP_036565.2:p.Val1219%3D|3686|3657|1219|V|gtA/gtG|rs4685&COSV59206298||-1||EntrezGene||YES||||2:g.198257795T>C|0.6584|0.8405|0.4958|0.7534|0.5326|0.5766|0.681|0.6982|0.7555|0.8835|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:475:473:260,213:0,0:0,473:0.9958:0,2:39.7:1:36.5:1:1:0:60:77.833:0.9957:0:1.1	1/0:244:133:69,64:59,52:111,133:0.5451:2,2:35.4:1:36.6:1:0.8978:1.05214:60:266:0.5473:0:1
    844. 

  844. 2	198263146	198263146	T	C	intronic	SF3B1	.	.	.	0.27	0.1794	0.0810	0.1981	0.2417	0.2860	0.2013	0.2167	0.1955	rs16865262	rs16865262	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59207562;OCCURENCE=1(breast),2(haematopoietic_and_lymphoid_tissue),7(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13407932	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.75	239	157	2	198263146	.	T	C	239	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.20661;SOR=inf;LSEQ=AAAGTGGCCAAATTTGAAAA;RSEQ=TGATACTGCTTATAAAAATG;CSQ=C|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||21/24|NM_012433.4:c.3134+39A>G|||||||rs16865262&COSV59207562||-1||EntrezGene||YES||||2:g.198263146T>C|0.2025|0.0779|0.2048|0.2411|0.2658|0.2063|0.2222|0.2292|0.1328|0.2658|gnomAD_EAS||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:37:0:1:0:60:6:1:0:1	1/0:157:92:68,24:47,18:65,92:0.586:2,2:40.2:1:36.7:1:0.8561:1.08:60:91:0.5871:0:1
    845. 

  845. 2	198263768	198263768	A	G	intronic	SF3B1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	158	2	198263768	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=117;VD=2;AF=0.0171;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.18012;SOR=inf;LSEQ=GGATGGTATTTACACCTACG;RSEQ=AGAGAGAAAAAAGGAGGCAG;CSQ=G|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||20/24|NM_012433.4:c.3014-463T>C|||||||||-1||EntrezGene||YES||||2:g.198263768A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:117:2:1,1:66,49:115,2:0.0171:2,2:42:0:37:0:1:1.34345:60:4:0.0171:0:1	0/0:158:0:0,0:69,89:158,0:0:2,0:35.8:1:36.4:1:1:0:60:51.667:1:0:0.1
    846. 

  846. 2	198265132	198265132	G	T	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon19:c.C2745A:p.G915G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	213	2	198265132	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=2;AF=0.0187;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11111;SOR=inf;LSEQ=CCAAGAGCATTAACCACTGT;RSEQ=CCAAAGCCGTTCAACATTAC;CSQ=T|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|19/25||NM_012433.4:c.2745C>A|NP_036565.2:p.Gly915%3D|2774|2745|915|G|ggC/ggA|||-1||EntrezGene||YES||||2:g.198265132G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:41,64:105,2:0.0187:2,2:69.5:1:37:0:1:1.55:60:4:0.019:0:2	0/0:213:0:0,0:73,139:212,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    847. 

  847. 2	198265171	198265171	T	-	intronic	SF3B1	.	.	.	0.0012	.	.	.	.	.	.	.	.	rs111354698	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114598806	COCA-CN|1|321|0.00311526	0.25	37	133	2	198265170	.	AT	A	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=60;VD=2;AF=0.0333;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.22857;SOR=4.51182;LSEQ=TACTGAGTCCTAAAAAATAA;RSEQ=TTAAAAAAAAGACATATTCA;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding||18/24|NM_012433.4:c.2719-13del|||||||rs111354698||-1||EntrezGene||YES||||2:g.198265173del|9.383e-05|6.926e-05|0.0001115|0|0|5.214e-05|8.044e-05|0|0.0002873|0.0002873|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:60:2:1,1:18,40:58,2:0.0333:2,2:29.5:1:37:0:0.53672:2.19:60:4:0.0351:0:0	0/0:133:1:0,1:33,99:132,1:0.0075:2,0:29:0:37:0:1:0:60:2:0.0078:0:0
    848. 

  848. 2	198265173	198265173	T	A	intronic	SF3B1	.	.	.	0.88	0.6813	0.8299	0.5255	0.7433	0.5281	0.5566	0.6509	0.6255	rs788017	rs788017	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59214857;OCCURENCE=2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13407940	LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579	0.75	215	133	2	198265173	.	T	A	215	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=56;AF=0.9492;SHIFT3=0;MSI=8;MSILEN=1;SSF=0;SOR=21.736;LSEQ=TGAGTCCTAAAAAATAAATT;RSEQ=AAAAAAAAGACATATTCATT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding||18/24|NM_012433.4:c.2719-15A>T|||||||rs788017&COSV59207593&COSV59214857||-1||EntrezGene||YES||||2:g.198265173T>A|0.6538|0.8364|0.4982|0.7394|0.5263|0.5734|0.6738|0.6839|0.7493|0.8828|AFR||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:59:56:18,38:1,2:3,56:0.9492:2,2:28.1:1:36.8:1:1:1.05458:60:112:0.9492:0:1.2	0/1:133:61:15,46:18,50:68,61:0.4586:2,2:33.9:1:36.4:1:0.84219:1.10315:60:60:0.4688:0:1
    849. 

  849. 2	198265526	198265526	A	G	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon18:c.T2631C:p.G877G	0.88	0.6806	0.8284	0.5310	0.7450	0.5255	0.5545	0.6510	0.6301	rs788018	rs788018	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59206309;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU137951	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579	0.75	177	75	2	198265526	.	A	G	177	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=6;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.006;SOR=inf;LSEQ=ATATCTGCTGCTCCCAAATT;RSEQ=CCCATAATTTTCTCAATTGT;CSQ=G|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|18/25||NM_012433.4:c.2631T>C|NP_036565.2:p.Gly877%3D|2660|2631|877|G|ggT/ggC|rs788018&COSV59206309||-1||EntrezGene||YES||||2:g.198265526A>G|0.6578|0.8383|0.4951|0.7497|0.5262|0.577|0.6812|0.6976|0.7567|0.8812|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:6:6:4,2:0,0:0,6:1:0,2:39:1:37:0:1:0:60:12:1:0:1	0/1:75:30:20,10:27,18:45,30:0.4:2,2:33.5:1:36.2:1:0.63072:1.33:60:60:0.4:0:1
    850. 

  850. 2	198265669	198265669	A	G	intronic	SF3B1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	98	2	198265669	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.85409;SOR=0;LSEQ=AGTATCAACTAACTAAAAAG;RSEQ=ACAGAAAAACAAAAAACCTT;CSQ=G|splice_polypyrimidine_tract_variant&intron_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding||17/24|NM_012433.4:c.2497-9T>C|||||||||-1||EntrezGene||YES||||2:g.198265669A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:3,5:8,0:0:2,0:29.9:1:37:0:1:0:60:16:1:0:0	0/1:98:2:1,1:40,56:96,2:0.0204:2,2:47:0:31:1:1:1.4:60:4:0.0211:0:1
    851. 

  851. 2	198266732	198266732	C	A	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_012433:exon15:c.G2200T:p.G734C	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	3.905	0.962	H	-0.16	0.654	T	-8.49	0.973	D	0.9	0.889	0.434	0.896	D	0.602	0.858	D	0.121	0.802	D	7.546	0.953	34	0.997	0.802	0.997	0.986	D	c	1.045	0.970	1.000	0.747	0.707	0.730	0	5.75	0.904	7.443	0.795	0.935	0.490	1.000	0.715	1.000	0.888	19.956	0.972	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	210	2	198266732	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=2;AF=0.0282;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.06317;SOR=inf;LSEQ=TCCTCTGTGTTGGCGGATAC;RSEQ=CTTCCATAAAGGCTTTAACA;CSQ=A|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|15/25||NM_012433.4:c.2200G>T|NP_036565.2:p.Gly734Cys|2229|2200|734|G/C|Ggt/Tgt|||-1||EntrezGene||YES||||2:g.198266732C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:71:2:1,1:43,26:69,2:0.0282:2,2:18.5:1:37:0:1:1.64163:60:4:0.0294:0:1	0/0:210:0:0,0:125,85:210,0:0:2,0:13:0:11:0:1:0:60:0:0:0:2
    852. 

  852. 2	198266809	198266809	G	A	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_012433:exon15:c.C2123T:p.A708V	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.837	0.444	P	0.616	0.494	P	0.000	0.843	D	1	0.810	D	3.32	0.909	M	-0.48	0.703	T	-2.96	0.617	D	0.843	0.830	0.159	0.852	D	0.537	0.829	D	0.095	0.765	D	6.811	0.926	32	0.999	0.991	0.994	0.952	D	c	0.880	0.894	1.000	0.747	0.672	0.522	0	6.02	0.975	9.416	0.967	1.048	0.713	1.000	0.715	1.000	0.888	20.537	0.992	Armadillo-like helical|Armadillo-type fold	.	.	ID=COSV59207213;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU130389905	COAD-US|1|402|0.00248756	0.25	37	249	2	198266809	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=152;VD=2;AF=0.0132;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.14309;SOR=inf;LSEQ=CTTCAGCCAAGGCAGCAATG;RSEQ=CCAAAGCACTGATGGTCCGA;CSQ=A|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|15/25||NM_012433.4:c.2123C>T|NP_036565.2:p.Ala708Val|2152|2123|708|A/V|gCc/gTc|COSV59207213||-1||EntrezGene||YES||||2:g.198266809G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:152:2:1,1:74,76:150,2:0.0132:2,2:43.5:1:37:0:1:1.03:60:4:0.0134:0:1	0/0:249:0:0,0:122,126:248,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    853. 

  853. 2	198266891	198266891	C	A	intronic	SF3B1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	184	2	198266891	.	C	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=2;AF=0.0282;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07673;SOR=inf;LSEQ=AGGTTTTAACTATGCCCCAA;RSEQ=ATTACCTAAGTTACACAATA;CSQ=A|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||14/24|NM_012433.4:c.2078-37G>T|||||||||-1||EntrezGene||YES||||2:g.198266891C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:71:2:1,1:26,43:69,2:0.0282:2,2:14.5:1:31:1:1:1.64:60:4:0.0286:0:1	0/0:184:0:0,0:63,121:184,0:0:2,0:40.9:1:36.9:1:1:0:60:368:1:0:0.6
    854. 

  854. 2	198267244	198267244	A	-	intronic	SF3B1	.	.	.	0.25	0.0027	0.0009	0.0126	0	0	0.0264	0.0015	0.0021	rs752109835	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	66	2	198267243	.	GA	G	37	d5;v3;pSTD;MSI12;MSI12	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=4;VD=1;AF=0.25;SHIFT3=12;MSI=13;MSILEN=1;SSF=0.16405;SOR=9.81984;LSEQ=GTAAGACCCTGTCTCCTAAA;RSEQ=AAAAAAAAAAAAGACAAAGT;CSQ=-|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||14/24|NM_012433.4:c.2077+36del|||||||rs752109835||-1||EntrezGene||YES||||2:g.198267256del|0.149|0.1169|0.1254|0.1473|0.113|0.1758|0.1619|0.1202|0.1587|0.1758|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:4:1:0,1:3,0:3,1:0.25:0,0:25:0:37:0:0.25:0:60:2:0.25:0:1	0/1:66:2:2,0:55,7:62,2:0.0303:2,0:32.5:1:37:0:1:0:60:4:0.0303:0:0
    855. 

  855. 2	198267447	198267447	G	A	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_012433:exon14:c.C1910T:p.S637F	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.986	0.754	D	0.000	0.843	D	1	0.810	D	3.18	0.890	M	-0.28	0.676	T	-5.52	0.860	D	0.904	0.894	0.443	0.897	D	0.622	0.867	D	0.124	0.806	D	6.490	0.895	30	0.999	0.940	0.996	0.977	D	c	1.056	0.994	1.0	0.983	0.719	0.830	0	5.68	0.880	9.805	0.982	1.047	0.674	1.000	0.715	1.000	0.888	19.799	0.965	Armadillo-type fold	.	.	ID=COSV105246696;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	324	2	198267447	.	G	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=145;VD=2;AF=0.0138;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09513;SOR=inf;LSEQ=AAGAAGGAATGCCCAGGGCA;RSEQ=AGGCTACAACAGCAAAAGCT;CSQ=A|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|14/25||NM_012433.4:c.1910C>T|NP_036565.2:p.Ser637Phe|1939|1910|637|S/F|tCt/tTt|COSV59220246||-1||EntrezGene||YES||||2:g.198267447G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:145:2:1,1:60,83:143,2:0.0138:2,2:29:1:31:1:1:1.38:60:4:0.0138:0:1	0/0:324:0:0,0:138,186:324,0:0:2,0:36.7:1:36.6:1:1:0:60:107:1:0:0.1
    856. 

  856. 2	198267770	198267770	-	AA	intronic	SF3B1	.	.	.	0.88	0.6793	0.8259	0.5323	0.7450	0.5323	0.5537	0.6492	0.6268	rs3217350	rs3217350	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	207	81	2	198267770	.	G	GAA	207	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2;VD=2;AF=1;SHIFT3=4;MSI=6;MSILEN=1;SSF=0.37467;SOR=inf;LSEQ=CCACGAGGATCTGAAAAAGA;RSEQ=AAAAGAGAAGAAGCTACACT;CSQ=AA|splice_polypyrimidine_tract_variant&intron_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding||12/24|NM_012433.4:c.1720-13_1720-12dup|||||||rs3217350||-1||EntrezGene||YES||||2:g.198267773_198267774dup|0.6575|0.8373|0.4944|0.7493|0.5292|0.576|0.6806|0.6966|0.7572|0.879|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:15.8:1:37.7:0:1:0:61.2:4:1:0:0	1/0:81:49:25,24:10,22:32,49:0.6049:2,2:45.9:1:37:1:0.10875:2.27:61.2:98:0.6125:0.037:0
    857. 

  857. 2	198268484	198268484	G	A	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_012433:exon12:c.C1544T:p.A515V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.996	0.670	D	0.963	0.692	D	0.000	0.843	D	1	0.810	D	3.3	0.907	M	-1.0	0.760	T	-3.73	0.709	D	0.92	0.911	0.634	0.923	D	0.706	0.899	D	0.215	0.875	D	6.726	0.919	32	0.999	0.992	0.998	0.995	D	c	1.037	0.967	1.000	0.747	0.707	0.730	0	5.63	0.861	9.827	0.983	0.998	0.613	1.000	0.715	0.981	0.494	19.689	0.960	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	197	2	198268484	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=40;VD=2;AF=0.05;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02789;SOR=inf;LSEQ=TATCAGTAATCTGACGCAAT;RSEQ=CAGCCTGGGAAAAAGAGCAG;CSQ=A|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|12/25||NM_012433.4:c.1544C>T|NP_036565.2:p.Ala515Val|1573|1544|515|A/V|gCa/gTa|||-1||EntrezGene||YES||||2:g.198268484G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:40:2:1,1:14,24:38,2:0.05:2,2:18:0:37:0:1:1.69:60:4:0.05:0:1	0/0:197:0:0,0:79,118:197,0:0:2,0:38.4:1:36.1:1:1:0:60:97.5:1:0:0.1
    858. 

  858. 2	198270146	198270146	C	T	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon10:c.G1290A:p.K430K	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	278	2	198270146	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=73;VD=2;AF=0.0274;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.04278;SOR=inf;LSEQ=GGTGTTGGAGTAGCTGTCAG;RSEQ=TTTCGAGCTGGAGTTCGAAT;CSQ=T|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|10/25||NM_012433.4:c.1290G>A|NP_036565.2:p.Lys430%3D|1319|1290|430|K|aaG/aaA|||-1||EntrezGene||YES||||2:g.198270146C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:73:2:1,1:34,36:70,2:0.0274:2,2:42.5:1:31:1:1:1.06:60:4:0.0282:0:2	0/0:278:0:0,0:133,145:278,0:0:2,0:39.2:1:35.9:1:1:0:60:45.333:1:0:0.1
    859. 

  859. 2	198272695	198272695	C	T	intronic	SF3B1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	79	2	198272695	.	C	T	37	v3;pSTD	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=2;AF=0.2;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.03236;SOR=18.1486;LSEQ=ATAAATGTATATCCTAAATA;RSEQ=CACCTCATTCAAATTTGATG;CSQ=T|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||9/24|NM_012433.4:c.1239+27G>A|||||||||-1||EntrezGene||YES||||2:g.198272695C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:10:2:1,1:5,3:8,2:0.2:2,2:46:0:37:0:1:1.58108:60:4:0.2:0:1	0/1:79:1:1,0:57,21:78,1:0.0127:2,0:16:0:37:0:1:0:60:2:0.0127:0:1
    860. 

  860. 2	198273187	198273187	T	C	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon8:c.A1023G:p.T341T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	156	2	198273187	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=360;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.09099;SOR=0;LSEQ=CCACCCATCTGACTAGCTGG;RSEQ=GTTTCATCCCACCGTGATTT;CSQ=C|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|8/25||NM_012433.4:c.1023A>G|NP_036565.2:p.Thr341%3D|1052|1023|341|T|acA/acG|||-1||EntrezGene||YES||||2:g.198273187T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:360:0:0,0:196,164:360,0:0:2,0:39.6:1:36.1:1:1:0:60:89:1:0:0.1	0/1:156:2:1,1:78,76:154,2:0.0128:2,2:37:1:37:0:1:1.02615:60:4:0.0131:0:1
    861. 

  861. 2	198273190	198273190	T	C	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon8:c.A1020G:p.E340E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	151	2	198273190	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=364;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.08557;SOR=0;LSEQ=CCCATCTGACTAGCTGGTGT;RSEQ=TCATCCCACCGTGATTTTCT;CSQ=C|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|8/25||NM_012433.4:c.1020A>G|NP_036565.2:p.Glu340%3D|1049|1020|340|E|gaA/gaG|||-1||EntrezGene||YES||||2:g.198273190T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:364:0:0,0:192,172:364,0:0:2,0:39.1:1:36.1:1:1:0:60:59.667:1:0:0.1	0/1:151:2:1,1:77,72:149,2:0.0132:2,2:29:1:31:1:1:1.06894:60:4:0.0135:0:1.5
    862. 

  862. 2	198274621	198274621	G	T	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_012433:exon7:c.C777A:p.S259R	.	.	.	.	.	.	.	.	.	.	.	0.115	0.285	T	0.421	0.336	B	0.095	0.287	B	0.000	0.843	D	1.000	0.588	D	1.355	0.339	L	.	.	.	-0.81	0.223	N	0.735	0.733	-1.109	0.032	T	0.076	0.306	T	0.017	0.391	T	1.746	0.271	14.67	0.989	0.483	0.884	0.480	D	c	-0.463	-0.402	0.000	0.062	0.707	0.730	0	-3.02	0.051	0.445	0.212	-0.010	0.132	0.995	0.385	0.992	0.562	13.152	0.587	.	.	.	ID=COSV59219473;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	192	2	198274621	.	G	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=753;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.04111;SOR=0;LSEQ=GCAGCTCCCGCTGGTGTGTG;RSEQ=CTAGGTGTAGGATCCCATAT;CSQ=T|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|7/25||NM_012433.4:c.777C>A|NP_036565.2:p.Ser259Arg|806|777|259|S/R|agC/agA|COSV59219473||-1||EntrezGene||YES||||2:g.198274621G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:753:0:0,0:319,433:752,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:192:2:1,1:92,98:190,2:0.0104:2,2:28.5:1:37:0:1:1.06:60:4:0.0105:0:3.5
    863. 

  863. 2	198283305	198283305	T	C	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_012433:exon5:c.A423G:p.K141K	0.89	0.6838	0.8395	0.5311	0.7450	0.5273	0.5554	0.6508	0.6281	rs788023	rs788023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59205521;OCCURENCE=1(breast),3(haematopoietic_and_lymphoid_tissue),20(soft_tissue),1(prostate),1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU137962	LICA-CN|1|402|0.00248756,LAML-KR|3|205|0.0146341,COCA-CN|3|321|0.00934579	0.75	166	53	2	198283305	.	T	C	166	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00617;SOR=inf;LSEQ=TTCATTTTAGGATCAGGGGT;RSEQ=TTCCCTCCTGCAGAAAAGAA;CSQ=C|downstream_gene_variant|MODIFIER|SF3B1|23451|Transcript|NM_001005526.2|protein_coding||||||||||rs788023&COSV59205521|215|-1||EntrezGene||||||2:g.198283305T>C|0.6584|0.8507|0.4946|0.7497|0.5286|0.5768|0.681|0.6975|0.7557|0.8903|AFR||0&1|0&1,C|downstream_gene_variant|MODIFIER|SF3B1|23451|Transcript|NM_001308824.1|protein_coding||||||||||rs788023&COSV59205521|215|-1||EntrezGene||||||2:g.198283305T>C|0.6584|0.8507|0.4946|0.7497|0.5286|0.5768|0.681|0.6975|0.7557|0.8903|AFR||0&1|0&1,C|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|5/25||NM_012433.4:c.423A>G|NP_036565.2:p.Lys141%3D|452|423|141|K|aaA/aaG|rs788023&COSV59205521||-1||EntrezGene||YES||||2:g.198283305T>C|0.6584|0.8507|0.4946|0.7497|0.5286|0.5768|0.681|0.6975|0.7557|0.8903|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:8:8:4,4:0,0:0,8:1:0,2:41.5:1:37:0:1:0:60:16:1:0:1.1	0/1:53:26:13,13:10,17:27,26:0.4906:2,2:39.3:1:35.5:1:0.41166:1.68:60:25:0.4808:0:1.2
    864. 

  864. 2	198283679	198283679	G	T	UTR3	SF3B1	NM_001308824:c.*1423C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	74	2	198283679	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=2;AF=0.1111;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.03655;SOR=inf;LSEQ=AGCAGCAGAATAGAAGCCTA;RSEQ=AAAATTATCTCTTTACCATT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SF3B1|23451|Transcript|NM_001005526.2|protein_coding||4/4|NM_001005526.2:c.416-4C>A|||||||||-1||EntrezGene||||||2:g.198283679G>T||||||||||||||,T|3_prime_UTR_variant|MODIFIER|SF3B1|23451|Transcript|NM_001308824.1|protein_coding|4/4||NM_001308824.1:c.*1423C>A||1982|||||||-1||EntrezGene||||||2:g.198283679G>T||||||||||||||,T|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||4/24|NM_012433.4:c.416-367C>A|||||||||-1||EntrezGene||YES||||2:g.198283679G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:18:2:1,1:7,9:16,2:0.1111:2,2:17.5:1:37:0:1:1.27:60:4:0.1176:0:1	0/0:74:0:0,0:31,43:74,0:0:2,0:36.9:1:36.2:1:1:0:60:73:1:0:0.1
    865. 

  865. 2	198285179	198285179	G	T	exonic	SF3B1	.	nonsynonymous SNV	SF3B1:NM_001005526:exon4:c.C388A:p.P130T,SF3B1:NM_001308824:exon4:c.C388A:p.P130T,SF3B1:NM_012433:exon4:c.C388A:p.P130T	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	1.0	0.899	D	0.996	0.832	D	0.000	0.843	D	1	0.810	D	3.31	0.908	M	.	.	.	-6.59	0.943	D	0.835	0.822	0.215	0.862	D	0.582	0.850	D	0.100	0.772	D	4.508	0.604	24.3	0.996	0.769	0.996	0.981	D	c	1.045	1.018	1.000	0.747	0.707	0.730	0	6.06	0.983	9.891	0.986	1.038	0.658	1.000	0.715	1.000	0.888	20.623	0.995	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	348	2	198285179	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=43;VD=2;AF=0.0465;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01184;SOR=inf;LSEQ=AAAAGGATCAAGACGCTCTG;RSEQ=GGAAATTATCATGGTCCGCC;CSQ=T|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_001005526.2|protein_coding|4/5||NM_001005526.2:c.388C>A|NP_001005526.1:p.Pro130Thr|482|388|130|P/T|Cca/Aca|||-1||EntrezGene||||||2:g.198285179G>T||||||||||||||,T|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_001308824.1|protein_coding|4/4||NM_001308824.1:c.388C>A|NP_001295753.1:p.Pro130Thr|482|388|130|P/T|Cca/Aca|||-1||EntrezGene||||||2:g.198285179G>T||||||||||||||,T|missense_variant|MODERATE|SF3B1|23451|Transcript|NM_012433.4|protein_coding|4/25||NM_012433.4:c.388C>A|NP_036565.2:p.Pro130Thr|417|388|130|P/T|Cca/Aca|||-1||EntrezGene||YES||||2:g.198285179G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:43:2:1,1:19,22:41,2:0.0465:2,2:17:0:37:0:1:1.15:60:4:0.0465:0:1	0/0:348:0:0,0:186,162:348,0:0:2,0:39.9:1:35.9:1:1:0:60:48.714:1:0:0.1
    866. 

  866. 2	198285240	198285240	A	G	exonic	SF3B1	.	synonymous SNV	SF3B1:NM_001005526:exon4:c.T327C:p.P109P,SF3B1:NM_001308824:exon4:c.T327C:p.P109P,SF3B1:NM_012433:exon4:c.T327C:p.P109P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	350	2	198285240	.	A	G	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=48;VD=2;AF=0.0417;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.01428;SOR=inf;LSEQ=TCCCGGTCTGCAATCTTTGG;RSEQ=GGTCTGTGCTCAGCAAATGG;CSQ=G|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_001005526.2|protein_coding|4/5||NM_001005526.2:c.327T>C|NP_001005526.1:p.Pro109%3D|421|327|109|P|ccT/ccC|||-1||EntrezGene||||||2:g.198285240A>G||||||||||||||,G|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_001308824.1|protein_coding|4/4||NM_001308824.1:c.327T>C|NP_001295753.1:p.Pro109%3D|421|327|109|P|ccT/ccC|||-1||EntrezGene||||||2:g.198285240A>G||||||||||||||,G|synonymous_variant|LOW|SF3B1|23451|Transcript|NM_012433.4|protein_coding|4/25||NM_012433.4:c.327T>C|NP_036565.2:p.Pro109%3D|356|327|109|P|ccT/ccC|||-1||EntrezGene||YES||||2:g.198285240A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:48:2:1,1:21,25:46,2:0.0417:2,2:26:1:31:1:1:1.19:60:4:0.0417:0:1.5	0/0:350:0:0,0:151,199:350,0:0:2,0:38:1:36.4:1:1:0:60:115.667:1:0:0.1
    867. 

  867. 2	198285818	198285818	G	A	exonic	SF3B1	.	stopgain	SF3B1:NM_001005526:exon3:c.C235T:p.Q79X,SF3B1:NM_001308824:exon3:c.C235T:p.Q79X,SF3B1:NM_012433:exon3:c.C235T:p.Q79X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.127	0.972	37	0.997	0.799	0.994	0.951	D	c	1.161	1.045	1.000	0.747	0.707	0.730	0	5.8	0.921	9.263	0.947	1.038	0.658	1.000	0.715	1.000	0.888	20.037	0.976	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	136	2	198285818	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=24;VD=0;AF=0;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.7217;SOR=0;LSEQ=ATGATATCCTGGCTTCTTCT;RSEQ=ACCAAGCAAACTCGTAGATG;CSQ=A|stop_gained|HIGH|SF3B1|23451|Transcript|NM_001005526.2|protein_coding|3/5||NM_001005526.2:c.235C>T|NP_001005526.1:p.Gln79Ter|329|235|79|Q/*|Cag/Tag|||-1||EntrezGene||||||2:g.198285818G>A||||||||||||||,A|stop_gained|HIGH|SF3B1|23451|Transcript|NM_001308824.1|protein_coding|3/4||NM_001308824.1:c.235C>T|NP_001295753.1:p.Gln79Ter|329|235|79|Q/*|Cag/Tag|||-1||EntrezGene||||||2:g.198285818G>A||||||||||||||,A|stop_gained|HIGH|SF3B1|23451|Transcript|NM_012433.4|protein_coding|3/25||NM_012433.4:c.235C>T|NP_036565.2:p.Gln79Ter|264|235|79|Q/*|Cag/Tag|||-1||EntrezGene||YES||||2:g.198285818G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:24:0:0,0:11,13:24,0:0:2,0:43.7:1:34.3:1:1:0:60:11:1:0:0.1	0/1:136:2:1,1:66,68:134,2:0.0147:2,2:50:0:37:0:1:1.03:60:4:0.0147:0:1
    868. 

  868. 2	198288506	198288506	C	G	intronic	SF3B1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	170	2	198288506	.	C	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=123;VD=2;AF=0.0163;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.17539;SOR=inf;LSEQ=CTCTCTCAAAAAAATAACTG;RSEQ=CTCTTGTACATAATTTGTAA;CSQ=G|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_001005526.2|protein_coding||2/4|NM_001005526.2:c.195+26G>C|||||||||-1||EntrezGene||||||2:g.198288506C>G||||||||||||||,G|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_001308824.1|protein_coding||2/3|NM_001308824.1:c.195+26G>C|||||||||-1||EntrezGene||||||2:g.198288506C>G||||||||||||||,G|intron_variant|MODIFIER|SF3B1|23451|Transcript|NM_012433.4|protein_coding||2/24|NM_012433.4:c.195+26G>C|||||||||-1||EntrezGene||YES||||2:g.198288506C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:89,32:121,2:0.0163:2,2:35.5:1:37:0:0.46621:2.75413:60:4:0.0168:0:1	0/0:170:0:0,0:134,36:170,0:0:2,0:36.7:1:36.3:1:1:0:60:169:1:0:0.1
    869. 

  869. 2	202122995	202122995	A	G	exonic	CASP8	.	nonsynonymous SNV	CASP8:NM_001080125:exon1:c.A41G:p.K14R	0.71	0.6618	0.5774	0.5658	0.6167	0.7326	0.6444	0.7127	0.6714	rs3769823	rs3769823	1.0	0.010	T	0.008	0.135	B	0.015	0.162	B	0.000	0.003	U	1	0.202	P	.	.	.	4.26	0.026	T	0.1	0.058	N	0.066	0.058	-0.995	0.313	T	0.000	0.000	T	.	.	.	-0.732	0.043	0.061	0.974	0.332	0.181	0.199	N	c	-0.907	-0.875	1.000	0.747	0.267	0.040	1	2.78	0.316	1.727	0.375	0.107	0.202	0.989	0.365	0.001	0.043	6.134	0.193	Death effector domain|Death-like domain	ENSG00000155749.8|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000155749.8|ENSG00000155749.8|ENSG00000155749.8|ENSG00000064012.17|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000155749.8|ENSG00000155749.8|ENSG00000155749.8|ENSG00000064012.17|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000155749.8|ENSG00000155749.8|ENSG00000064012.17|ENSG00000003400.10|ENSG00000155749.8|ENSG00000155749.8|ENSG00000155749.8|ENSG00000064012.17|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000064012.17|ENSG00000155749.8|ENSG00000064012.17|ENSG00000064012.17|ENSG00000155749.8|ENSG00000155749.8|ENSG00000064012.17	Adipose_Subcutaneous|Adipose_Subcutaneous|Adipose_Visceral_Omentum|Adipose_Visceral_Omentum|Artery_Aorta|Artery_Tibial|Brain_Caudate_basal_ganglia|Brain_Cerebellar_Hemisphere|Brain_Cerebellum|Brain_Cortex|Brain_Cortex|Brain_Frontal_Cortex_BA9|Brain_Frontal_Cortex_BA9|Brain_Nucleus_accumbens_basal_ganglia|Brain_Putamen_basal_ganglia|Breast_Mammary_Tissue|Breast_Mammary_Tissue|Cells_Transformed_fibroblasts|Colon_Transverse|Colon_Transverse|Esophagus_Gastroesophageal_Junction|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Mucosa|Esophagus_Muscularis|Heart_Atrial_Appendage|Lung|Lung|Muscle_Skeletal|Nerve_Tibial|Pancreas|Skin_Not_Sun_Exposed_Suprapubic|Skin_Sun_Exposed_Lower_leg|Skin_Sun_Exposed_Lower_leg|Stomach|Testis|Thyroid|Whole_Blood	ID=COSV51848843;OCCURENCE=1(large_intestine),1(thyroid)	389468	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU4567656	LAML-KR|1|205|0.00487805,COCA-CN|6|321|0.0186916	0.75	413	291	2	202122995	.	A	G	413	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3171;VD=3167;AF=0.9987;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=914.374;LSEQ=CAGGGTGGTTATTGAAAGTA;RSEQ=AAGAAACTTCTTCCTGGGAG;CSQ=G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001080124.2|protein_coding||2/8|NM_001080124.2:c.-26-8189A>G|||||||rs3769823&COSV51848843||1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|missense_variant|MODERATE|CASP8|841|Transcript|NM_001080125.2|protein_coding|1/9||NM_001080125.2:c.41A>G|NP_001073594.1:p.Lys14Arg|238|41|14|K/R|aAa/aGa|rs3769823&COSV51848843||1||EntrezGene||YES||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001228.4|protein_coding||2/9|NM_001228.4:c.-26-8189A>G|||||||rs3769823&COSV51848843||1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|upstream_gene_variant|MODIFIER|CASP8|841|Transcript|NM_001372051.1|protein_coding||||||||||rs3769823&COSV51848843|2264|1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033355.3|protein_coding||2/9|NM_033355.3:c.1-8215A>G|||||||rs3769823&COSV51848843||1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|upstream_gene_variant|MODIFIER|CASP8|841|Transcript|NM_033356.4|protein_coding||||||||||rs3769823&COSV51848843|2264|1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033358.4|protein_coding||2/7|NM_033358.4:c.-26-8189A>G|||||||rs3769823&COSV51848843||1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|CASP8|841|Transcript|NR_111983.2|misc_RNA|1/9||NR_111983.2:n.238A>G||238|||||rs3769823&COSV51848843||1||EntrezGene||||||2:g.202122995A>G|0.66|0.5761|0.5385|0.5769|0.7099|0.648|0.7056|0.6469|0.6801|0.7099|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3171:3167:1665,1502:0,1:1,3167:0.9987:0,2:37.2:1:35.6:1:0.47443:0:60:34.189:0.999:0:1.2	0/1:291:135:78,57:87,68:155,135:0.4639:2,2:38.9:1:36.1:1:0.81267:1.07:60:66.5:0.4667:0:1.2
    870. 

  870. 2	202131178	202131178	A	T	intronic	CASP8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	203	2	202131178	.	A	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=164;VD=3;AF=0.0183;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08833;SOR=inf;LSEQ=TGAACATACCATTTATTTTG;RSEQ=CTTAGATTATATTCTCCTGC;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_001080124.2|protein_coding||2/8|NM_001080124.2:c.-26-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_001080125.2|protein_coding||1/8|NM_001080125.2:c.152-6A>T|||||||||1||EntrezGene||YES||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_001228.4|protein_coding||2/9|NM_001228.4:c.-26-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_001372051.1|protein_coding||1/8|NM_001372051.1:c.-26-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033355.3|protein_coding||2/9|NM_033355.3:c.1-32A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_033356.4|protein_coding||1/7|NM_033356.4:c.-26-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CASP8|841|Transcript|NM_033358.4|protein_coding||2/7|NM_033358.4:c.-26-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|CASP8|841|Transcript|NR_111983.2|misc_RNA||1/8|NR_111983.2:n.349-6A>T|||||||||1||EntrezGene||||||2:g.202131178A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:164:3:2,1:120,41:161,3:0.0183:2,2:33.7:1:37:0:1:1.45973:60:6:0.0183:0:1	0/0:203:0:0,0:153,50:203,0:0:2,0:32.4:1:36.2:1:1:0:60:49.75:1:0:0.1
    871. 

  871. 2	202134223	202134223	T	C	intronic	CASP8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	169	2	202134223	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1142;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01653;SOR=0;LSEQ=TCTTGTGCCCACCATCTTGG;RSEQ=CCTTTGAAGGTTCCACTTCT;CSQ=C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001080124.2|protein_coding||3/8|NM_001080124.2:c.306-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001080125.2|protein_coding||2/8|NM_001080125.2:c.483-2016T>C|||||||||1||EntrezGene||YES||||2:g.202134223T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|CASP8|841|Transcript|NM_001228.4|protein_coding||3/9|NM_001228.4:c.306-10T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001372051.1|protein_coding||2/8|NM_001372051.1:c.306-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033355.3|protein_coding||3/9|NM_033355.3:c.306-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033356.4|protein_coding||2/7|NM_033356.4:c.306-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033358.4|protein_coding||3/7|NM_033358.4:c.306-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|CASP8|841|Transcript|NR_111983.2|misc_RNA||2/8|NR_111983.2:n.680-2016T>C|||||||||1||EntrezGene||||||2:g.202134223T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1142:0:0,0:583,559:1142,0:0:2,0:43.3:1:36.5:1:1:0:60:284.5:1:0:0.1	0/1:169:2:1,1:95,72:167,2:0.0118:2,2:56:1:37:0:1:1.31724:60:4:0.012:0:1
    872. 

  872. 2	202139672	202139672	C	A	exonic	CASP8	.	stopgain	CASP8:NM_033356:exon5:c.C611A:p.S204X,CASP8:NM_001080124:exon6:c.C611A:p.S204X,CASP8:NM_001080125:exon6:c.C833A:p.S278X,CASP8:NM_001228:exon7:c.C707A:p.S236X,CASP8:NM_033355:exon7:c.C656A:p.S219X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.006	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.414	0.951	34	0.984	0.401	0.035	0.085	N	c	-0.074	-0.410	0.002	0.088	0.732	0.924	0	0.818	0.178	0.012	0.131	0.875	0.382	0.000	0.063	0.457	0.264	3.101	0.059	Caspase-like domain|Peptidase C14,  p20 domain|Peptidase C14A, homology domain;Death-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	2	202139672	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=173;VD=2;AF=0.0116;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.27574;SOR=inf;LSEQ=AAGAGAACAGGATAGTGAAT;RSEQ=ACAGGTAGACGGAAACCTCC;CSQ=A|stop_gained|HIGH|CASP8|841|Transcript|NM_001080124.2|protein_coding|6/9||NM_001080124.2:c.611C>A|NP_001073593.1:p.Ser204Ter|826|611|204|S/*|tCa/tAa|||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|stop_gained|HIGH|CASP8|841|Transcript|NM_001080125.2|protein_coding|6/9||NM_001080125.2:c.833C>A|NP_001073594.1:p.Ser278Ter|1030|833|278|S/*|tCa/tAa|||1||EntrezGene||YES||||2:g.202139672C>A||||||||||||||,A|stop_gained|HIGH|CASP8|841|Transcript|NM_001228.4|protein_coding|7/10||NM_001228.4:c.707C>A|NP_001219.2:p.Ser236Ter|1010|707|236|S/*|tCa/tAa|||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|stop_gained|HIGH|CASP8|841|Transcript|NM_001372051.1|protein_coding|6/9||NM_001372051.1:c.656C>A|NP_001358980.1:p.Ser219Ter|760|656|219|S/*|tCa/tAa|||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|stop_gained|HIGH|CASP8|841|Transcript|NM_033355.3|protein_coding|7/10||NM_033355.3:c.656C>A|NP_203519.1:p.Ser219Ter|865|656|219|S/*|tCa/tAa|||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|stop_gained|HIGH|CASP8|841|Transcript|NM_033356.4|protein_coding|5/8||NM_033356.4:c.611C>A|NP_203520.1:p.Ser204Ter|715|611|204|S/*|tCa/tAa|||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033358.4|protein_coding||6/7|NM_033358.4:c.596-1878C>A|||||||||1||EntrezGene||||||2:g.202139672C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|CASP8|841|Transcript|NR_111983.2|misc_RNA|6/9||NR_111983.2:n.1030C>A||1030|||||||1||EntrezGene||||||2:g.202139672C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:173:2:1,1:69,102:171,2:0.0116:2,2:26.5:1:37:0:1:1.47:60:4:0.0119:0:1	0/0:156:0:0,0:68,88:156,0:0:2,0:43:0:11:0:1:0:60:0:0:0:8
    873. 

  873. 2	202151163	202151163	A	G	intronic	CASP8	.	.	.	0.86	0.7305	0.7850	0.5670	0.6424	0.7249	0.6720	0.7251	0.7137	rs3769818	rs3769818	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51844734;OCCURENCE=1(liver),1(lung),2(upper_aerodigestive_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18189875	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|6|321|0.0186916	0.75	332	227	2	202151163	.	A	G	332	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=573;VD=572;AF=0.9983;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=705.117;LSEQ=CCCCCACAGACAGTCACAAT;RSEQ=TTATGTGATGTATTTCAGAG;CSQ=G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001080124.2|protein_coding||8/8|NM_001080124.2:c.1260-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001080125.2|protein_coding||8/8|NM_001080125.2:c.1482-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||YES||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|downstream_gene_variant|MODIFIER|ALS2CR12|130540|Transcript|NM_001127391.3|protein_coding||||||||||rs3769818&COSV51844734|1831|-1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001228.4|protein_coding||9/9|NM_001228.4:c.1356-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|downstream_gene_variant|MODIFIER|ALS2CR12|130540|Transcript|NM_001289993.2|protein_coding||||||||||rs3769818&COSV51844734|1831|-1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_001372051.1|protein_coding||8/8|NM_001372051.1:c.1305-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033355.3|protein_coding||9/9|NM_033355.3:c.1305-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant|MODIFIER|CASP8|841|Transcript|NM_033356.4|protein_coding||7/7|NM_033356.4:c.1260-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|downstream_gene_variant|MODIFIER|CASP8|841|Transcript|NM_033358.4|protein_coding||||||||||rs3769818&COSV51844734|4523|1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|downstream_gene_variant|MODIFIER|ALS2CR12|130540|Transcript|NM_139163.4|protein_coding||||||||||rs3769818&COSV51844734|1831|-1||EntrezGene||YES||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|downstream_gene_variant|MODIFIER|ALS2CR12|130540|Transcript|NR_110620.2|misc_RNA||||||||||rs3769818&COSV51844734|1831|-1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1,G|intron_variant&non_coding_transcript_variant|MODIFIER|CASP8|841|Transcript|NR_111983.2|misc_RNA||8/8|NR_111983.2:n.1815-19A>G|||||||rs3769818&COSV51844734||1||EntrezGene||||||2:g.202151163A>G|0.7014|0.7876|0.5309|0.6119|0.7048|0.6729|0.7213|0.6845|0.8246|0.862|SAS||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:573:572:314,258:0,0:0,572:0.9983:0,2:39.1:1:36.3:1:1:0:60:80.714:1:0:1.1	0/1:227:101:52,49:68,57:125,101:0.4449:2,2:41.2:1:36.1:1:0.68911:1.12357:60:32.667:0.4516:0:1
    874. 

  874. 2	204732714	204732714	A	G	exonic	CTLA4	.	nonsynonymous SNV	CTLA4:NM_001037631:exon1:c.A49G:p.T17A,CTLA4:NM_005214:exon1:c.A49G:p.T17A	0.67	0.4250	0.3731	0.4282	0.3013	0.6571	0.5209	0.4100	0.4265	rs231775	rs231775	0.181	0.219	T	0.015	0.158	B	0.006	0.112	B	0.072	0.023	N	1	0.090	P	1.1	0.281	L	1.73	0.264	T	0.28	0.305	N	0.071	0.081	-0.908	0.471	T	0.000	0.000	T	.	.	.	-1.474	0.017	0.003	0.458	0.036	0.042	0.095	N	c	-1.274	-1.363	0.996	0.341	0.487	0.133	0	-2.84	0.054	-0.309	0.081	0.131	0.216	0.000	0.063	0.060	0.171	4.360	0.106	.	ENSG00000163599.10	Testis	ID=COSV55592023;OCCURENCE=1(large_intestine),2(pancreas),1(skin)	31960	Hashimoto_thyroiditis,_susceptibility_to|TYPE_1_DIABETES_MELLITUS_12,_SUSCEPTIBILITY_TO|Thyroid-associated_orbitopathy,_susceptibility_to|Celiac_disease_3|Systemic_lupus_erythematosus,_susceptibility_to|not_specified	.|.|.|MONDO:MONDO:0012341,MedGen:C1857845,OMIM:609755|MedGen:C3862275|MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU157238	COCA-CN|5|321|0.0155763	0.75	368	238	2	204732714	.	A	G	368	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1055;VD=1048;AF=0.9934;SHIFT3=3;MSI=2;MSILEN=1;SSF=0;SOR=175.833;LSEQ=AGGCTCAGCTGAACCTGGCT;RSEQ=CCAGGACCTGGCCCTGCACT;CSQ=G|missense_variant|MODERATE|CTLA4|1493|Transcript|NM_001037631.3|protein_coding|1/3||NM_001037631.3:c.49A>G|NP_001032720.1:p.Thr17Ala|221|49|17|T/A|Acc/Gcc|rs231775&CM970403&COSV55592023||1||EntrezGene||||||2:g.204732714A>G|0.4151|0.3738|0.4619|0.3016|0.6664|0.5279|0.3819|0.3898|0.3193|0.6664|gnomAD_EAS|risk_factor&benign|0&0&1|1&1&1,G|missense_variant|MODERATE|CTLA4|1493|Transcript|NM_005214.5|protein_coding|1/4||NM_005214.5:c.49A>G|NP_005205.2:p.Thr17Ala|221|49|17|T/A|Acc/Gcc|rs231775&CM970403&COSV55592023||1||EntrezGene||YES||||2:g.204732714A>G|0.4151|0.3738|0.4619|0.3016|0.6664|0.5279|0.3819|0.3898|0.3193|0.6664|gnomAD_EAS|risk_factor&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1055:1048:573,475:0,0:0,1048:0.9934:0,2:38.4:1:36.7:1:1:0:60:173.667:0.9981:0:1.1	0/1:238:109:60,49:76,53:129,109:0.458:2,2:39:1:36.5:1:0.59969:1.17029:60:108:0.4596:0:1.1
    875. 

  875. 2	204737524	204737524	C	-	exonic	CTLA4	.	frameshift deletion	CTLA4:NM_005214:exon4:c.661delC:p.I222Sfs*7	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	159	2	204737523	.	TC	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=47;VD=2;AF=0.0426;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.0512;SOR=inf;LSEQ=CAATTTCAGCCTTATTTTAT;RSEQ=CCATCAATTGAGAAACCATT;CSQ=-|3_prime_UTR_variant|MODIFIER|CTLA4|1493|Transcript|NM_001037631.3|protein_coding|3/3||NM_001037631.3:c.*28del||723|||||||1||EntrezGene||||||2:g.204737526del||||||||||||||,-|frameshift_variant|HIGH|CTLA4|1493|Transcript|NM_005214.5|protein_coding|4/4||NM_005214.5:c.663del|NP_005205.2:p.Ile222SerfsTer7|833|661|221|P/X|Ccc/cc|||1||EntrezGene||YES|||2|2:g.204737526del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:47:2:1,1:20,25:45,2:0.0426:2,2:65:1:37:0:1:1.24:60:4:0.0435:0:0	0/0:159:0:0,0:71,88:159,0:0:2,0:35.9:1:35.4:1:1:0:60:25.5:1:0:0.2
    876. 

  876. 2	209101906	209101906	A	-	intronic	IDH1	.	.	.	1.	0.9861	0.9526	0.9964	1	1	1	0.9994	0.9938	rs57383668	rs57383668	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	208	55	2	209101905	.	GA	G	208	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=4;VD=4;AF=1;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.74936;SOR=inf;LSEQ=CGTTGCACACTAACGGGAAG;RSEQ=AAAAAAAAAGAAAATTTAGT;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding||9/9|NM_001282386.1:c.1155-13del|||||||rs57383668||-1||EntrezGene||||||2:g.209101915del|0.9935|0.9508|0.9953|0.9985|0.9975|0.9954|0.9962|0.9964|0.9977|0.999|EAS&EUR&SAS|||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding||9/9|NM_001282387.1:c.1155-13del|||||||rs57383668||-1||EntrezGene||YES||||2:g.209101915del|0.9935|0.9508|0.9953|0.9985|0.9975|0.9954|0.9962|0.9964|0.9977|0.999|EAS&EUR&SAS|||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding||9/9|NM_005896.4:c.1155-13del|||||||rs57383668||-1||EntrezGene||||||2:g.209101915del|0.9935|0.9508|0.9953|0.9985|0.9975|0.9954|0.9962|0.9964|0.9977|0.999|EAS&EUR&SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:3,1:0,0:0,4:1:0,2:34.5:1:37:0:1:0:60:8:1:0:0.2	1/1:55:51:25,26:2,2:4,51:0.9273:2,2:40.8:1:36.8:1:1:1.03927:60:102:0.9273:0:0.3
    877. 

  877. 2	209103876	209103876	G	T	exonic	IDH1	.	nonsynonymous SNV	IDH1:NM_001282386:exon9:c.C1073A:p.A358D,IDH1:NM_001282387:exon9:c.C1073A:p.A358D,IDH1:NM_005896:exon9:c.C1073A:p.A358D	.	.	.	.	.	.	.	.	.	.	.	0.126	0.272	T	0.429	0.337	B	0.136	0.317	B	0.000	0.477	D	1.000	0.588	D	1.515	0.384	L	-0.4	0.693	T	-2.26	0.505	N	0.653	0.735	-0.630	0.636	T	0.228	0.593	T	0.042	0.605	D	3.572	0.487	23.1	0.990	0.505	0.965	0.695	D	c	0.152	0.249	0.959	0.283	0.707	0.730	0	3.71	0.416	4.723	0.614	0.998	0.613	0.994	0.380	1.000	0.888	13.173	0.589	Isopropylmalate dehydrogenase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	38	277	2	209103876	.	G	T	38	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=364;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0802;SOR=0;LSEQ=CAATAGAGACTTCTTCCAAA;RSEQ=CATTTGCAAAGAAGGCAAGC;CSQ=T|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282386.1|protein_coding|9/10||NM_001282386.1:c.1073C>A|NP_001269315.1:p.Ala358Asp|1279|1073|358|A/D|gCt/gAt|||-1||EntrezGene||||||2:g.209103876G>T||||||||||||||,T|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282387.1|protein_coding|9/10||NM_001282387.1:c.1073C>A|NP_001269316.1:p.Ala358Asp|1436|1073|358|A/D|gCt/gAt|||-1||EntrezGene||YES||||2:g.209103876G>T||||||||||||||,T|missense_variant|MODERATE|IDH1|3417|Transcript|NM_005896.4|protein_coding|9/10||NM_005896.4:c.1073C>A|NP_005887.2:p.Ala358Asp|1296|1073|358|A/D|gCt/gAt|||-1||EntrezGene||||||2:g.209103876G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:364:0:0,0:168,196:364,0:0:2,0:41.9:1:36.1:1:1:0:60:90:1:0:0.1	0/1:277:3:1,2:132,142:274,3:0.0108:2,2:28:1:24.3:1:1:1.85516:60:2:0.0075:0:1.7
    878. 

  878. 2	209103969	209103969	-	A	intronic	IDH1	.	.	.	0.0003	.	.	.	.	.	.	.	.	rs751745975	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114582203	COCA-CN|1|321|0.00311526	0.25	38	171	2	209103969	.	G	GA	38	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=128;VD=2;AF=0.0156;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.18244;SOR=inf;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding||8/9|NM_001282386.1:c.992-13dup|||||||rs139521409||-1||EntrezGene||||||2:g.209103977dup|4.055e-05|0|0|9.996e-05|0.0001105|0|5.405e-05|0.0001655|0|0.0001655|gnomAD_OTH|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding||8/9|NM_001282387.1:c.992-13dup|||||||rs139521409||-1||EntrezGene||YES||||2:g.209103977dup|4.055e-05|0|0|9.996e-05|0.0001105|0|5.405e-05|0.0001655|0|0.0001655|gnomAD_OTH|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding||8/9|NM_005896.4:c.992-13dup|||||||rs139521409||-1||EntrezGene||||||2:g.209103977dup|4.055e-05|0|0|9.996e-05|0.0001105|0|5.405e-05|0.0001655|0|0.0001655|gnomAD_OTH|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:128:2:0,2:30,91:121,2:0.0156:2,0:38.7:1:38.7:0:1:0:62.8:4:0.018:0:0	0/0:171:0:0,0:51,118:169,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    879. 

  879. 2	209103975	209103975	A	G	intronic	IDH1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	161	2	209103975	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=110;VD=0;AF=0;SHIFT3=0;MSI=8;MSILEN=1;SSF=0.35206;SOR=0;LSEQ=AAGCTAAAAGAGGGGAAAAA;RSEQ=AACACAACACTCCAATCATC;CSQ=G|intron_variant|MODIFIER|IDH1|3417|Transcript|NM_001282386.1|protein_coding||8/9|NM_001282386.1:c.992-18T>C|||||||||-1||EntrezGene||||||2:g.209103975A>G||||||||||||||,G|intron_variant|MODIFIER|IDH1|3417|Transcript|NM_001282387.1|protein_coding||8/9|NM_001282387.1:c.992-18T>C|||||||||-1||EntrezGene||YES||||2:g.209103975A>G||||||||||||||,G|intron_variant|MODIFIER|IDH1|3417|Transcript|NM_005896.4|protein_coding||8/9|NM_005896.4:c.992-18T>C|||||||||-1||EntrezGene||||||2:g.209103975A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:110:0:0,0:27,83:110,0:0:2,0:30.5:1:36.3:1:1:0:60:109:1:0:0.2	0/1:161:2:1,1:46,113:159,2:0.0124:2,2:36:1:37:0:0.49992:2.44:60:4:0.0124:0:1
    880. 

  880. 2	209106825	209106825	T	C	exonic	IDH1	.	nonsynonymous SNV	IDH1:NM_001282386:exon7:c.A743G:p.H248R,IDH1:NM_001282387:exon7:c.A743G:p.H248R,IDH1:NM_005896:exon7:c.A743G:p.H248R	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.97	0.706	D	0.000	0.843	D	1	0.810	D	4.43	0.988	H	-0.64	0.721	T	-7.24	0.943	D	0.924	0.919	0.756	0.939	D	0.711	0.901	D	0.244	0.889	D	5.847	0.801	27.3	0.998	0.927	0.974	0.746	D	c	1.081	0.997	1.000	0.747	0.707	0.730	0	6.17	0.997	7.941	0.871	1.061	0.807	1.000	0.715	0.988	0.529	16.822	0.856	Isopropylmalate dehydrogenase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	184	2	209106825	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=859;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03098;SOR=0;LSEQ=CCATGTCGTCGATGAGCCTA;RSEQ=GCTCATACCAGATCTTTTGA;CSQ=C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282386.1|protein_coding|7/10||NM_001282386.1:c.743A>G|NP_001269315.1:p.His248Arg|949|743|248|H/R|cAt/cGt|||-1||EntrezGene||||||2:g.209106825T>C||||||||||||||,C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282387.1|protein_coding|7/10||NM_001282387.1:c.743A>G|NP_001269316.1:p.His248Arg|1106|743|248|H/R|cAt/cGt|||-1||EntrezGene||YES||||2:g.209106825T>C||||||||||||||,C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_005896.4|protein_coding|7/10||NM_005896.4:c.743A>G|NP_005887.2:p.His248Arg|966|743|248|H/R|cAt/cGt|||-1||EntrezGene||||||2:g.209106825T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:859:0:0,0:336,522:858,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:184:2:1,1:78,104:182,2:0.0109:2,2:44.5:1:37:0:1:1.33:60:4:0.0112:0:1
    881. 

  881. 2	209106886	209106887	AA	-	intronic	IDH1	.	.	.	0.0042	0.0001	0	0	0	0.0025	0	0	0	rs530619587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	224	122	2	209106885	.	TAA	T	224	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=331;VD=0;AF=0;SHIFT3=2;MSI=4;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTGCCTGGGAAACAAAAGG;RSEQ=AAGAGAATAATAATAAAGAA;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding||6/9|NM_001282386.1:c.699-18_699-17del|||||||rs530619587||-1||EntrezGene||||||2:g.209106888_209106889del|0.0002708|0|0|0|0.003046|0|0|0.0003267|0.0003266|0.004|EAS|||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding||6/9|NM_001282387.1:c.699-18_699-17del|||||||rs530619587||-1||EntrezGene||YES||||2:g.209106888_209106889del|0.0002708|0|0|0|0.003046|0|0|0.0003267|0.0003266|0.004|EAS|||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding||6/9|NM_005896.4:c.699-18_699-17del|||||||rs530619587||-1||EntrezGene||||||2:g.209106888_209106889del|0.0002708|0|0|0|0.003046|0|0|0.0003267|0.0003266|0.004|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:331:0:0,0:74,257:331,0:0:2,0:25.2:1:35.9:1:1:0:60:40.375:1:0:0.1	1/0:122:68:20,48:23,31:54,68:0.5574:2,2:35.6:1:36.9:1:0.18145:1.77211:60:136:0.5714:0.082:0.2
    882. 

  882. 2	209108327	209108327	T	C	exonic	IDH1	.	synonymous SNV	IDH1:NM_001282386:exon6:c.A522G:p.E174E,IDH1:NM_001282387:exon6:c.A522G:p.E174E,IDH1:NM_005896:exon6:c.A522G:p.E174E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	164	2	209108327	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.55484;SOR=0;LSEQ=CCCATGGCAACACCACCACC;RSEQ=TCTGTAGAGGAGAAGCCAGT;CSQ=C|splice_region_variant&synonymous_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding|6/10||NM_001282386.1:c.522A>G|NP_001269315.1:p.Glu174%3D|728|522|174|E|gaA/gaG|||-1||EntrezGene||||||2:g.209108327T>C||||||||||||||,C|splice_region_variant&synonymous_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding|6/10||NM_001282387.1:c.522A>G|NP_001269316.1:p.Glu174%3D|885|522|174|E|gaA/gaG|||-1||EntrezGene||YES||||2:g.209108327T>C||||||||||||||,C|splice_region_variant&synonymous_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding|6/10||NM_005896.4:c.522A>G|NP_005887.2:p.Glu174%3D|745|522|174|E|gaA/gaG|||-1||EntrezGene||||||2:g.209108327T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:56:0:0,0:25,31:56,0:0:2,0:36.9:1:35.2:1:1:0:60:17.667:1:0:0.1	0/1:164:2:1,1:60,101:161,2:0.0122:2,2:51:1:37:0:1:1.68:60:4:0.0127:0:1
    883. 

  883. 2	209110141	209110141	G	A	exonic	IDH1	.	nonsynonymous SNV	IDH1:NM_001282386:exon5:c.C422T:p.A141V,IDH1:NM_001282387:exon5:c.C422T:p.A141V,IDH1:NM_005896:exon5:c.C422T:p.A141V	.	.	.	.	.	.	.	.	.	.	.	0.026	0.912	D	0.177	0.273	B	0.029	0.203	B	0.000	0.843	D	1	0.810	D	4.385	0.986	H	-0.48	0.703	T	-3.43	0.721	D	0.807	0.800	0.146	0.850	D	0.537	0.829	D	0.268	0.898	D	5.112	0.689	25.3	0.998	0.925	0.995	0.970	D	c	0.606	0.665	1.000	0.747	0.732	0.924	0	5.66	0.872	9.602	0.976	1.048	0.713	1.000	0.715	1.000	0.888	19.740	0.962	Isopropylmalate dehydrogenase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	187	2	209110141	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=21;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.80783;SOR=0;LSEQ=CAGGAACAACAAAATCAGTT;RSEQ=CTCTGTACTGTGTAGAGGGG;CSQ=A|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282386.1|protein_coding|5/10||NM_001282386.1:c.422C>T|NP_001269315.1:p.Ala141Val|628|422|141|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.209110141G>A||||||||||||||,A|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282387.1|protein_coding|5/10||NM_001282387.1:c.422C>T|NP_001269316.1:p.Ala141Val|785|422|141|A/V|gCa/gTa|||-1||EntrezGene||YES||||2:g.209110141G>A||||||||||||||,A|missense_variant|MODERATE|IDH1|3417|Transcript|NM_005896.4|protein_coding|5/10||NM_005896.4:c.422C>T|NP_005887.2:p.Ala141Val|645|422|141|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.209110141G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:21:0:0,0:9,12:21,0:0:2,0:43:1:33.4:1:1:0:60:9.5:1:0:0	0/1:187:2:1,1:70,114:184,2:0.0107:2,2:19:1:37:0:1:1.62:60:4:0.011:0:1
    884. 

  884. 2	209113229	209113229	T	C	exonic	IDH1	.	nonsynonymous SNV	IDH1:NM_001282386:exon4:c.A278G:p.K93R,IDH1:NM_001282387:exon4:c.A278G:p.K93R,IDH1:NM_005896:exon4:c.A278G:p.K93R	.	.	.	.	.	.	.	.	.	.	.	0.368	0.128	T	0.001	0.067	B	0.005	0.104	B	0.000	0.843	D	1.000	0.548	D	0.975	0.246	L	-0.73	0.731	T	-1.22	0.309	N	0.078	0.168	-0.827	0.536	T	0.221	0.584	T	0.013	0.316	T	1.947	0.295	15.88	0.996	0.724	0.886	0.483	D	c	-0.134	0.077	1.000	0.747	0.707	0.730	0	5.57	0.840	4.054	0.569	0.964	0.580	1.000	0.715	1.000	0.888	15.718	0.773	Isopropylmalate dehydrogenase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	313	2	209113229	.	T	C	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=933;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00393;SOR=0;LSEQ=GTATGGTGCCATTTGGTGAT;RSEQ=TCCACATTTGTTTCAACTTG;CSQ=C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282386.1|protein_coding|4/10||NM_001282386.1:c.278A>G|NP_001269315.1:p.Lys93Arg|484|278|93|K/R|aAa/aGa|||-1||EntrezGene||||||2:g.209113229T>C||||||||||||||,C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282387.1|protein_coding|4/10||NM_001282387.1:c.278A>G|NP_001269316.1:p.Lys93Arg|641|278|93|K/R|aAa/aGa|||-1||EntrezGene||YES||||2:g.209113229T>C||||||||||||||,C|missense_variant|MODERATE|IDH1|3417|Transcript|NM_005896.4|protein_coding|4/10||NM_005896.4:c.278A>G|NP_005887.2:p.Lys93Arg|501|278|93|K/R|aAa/aGa|||-1||EntrezGene||||||2:g.209113229T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:933:0:0,0:480,452:932,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:313:4:2,2:141,168:309,4:0.0128:2,2:47.2:1:37:0:1:1.19:60:8:0.013:0:1
    885. 

  885. 2	209116234	209116234	T	G	exonic	IDH1	.	nonsynonymous SNV	IDH1:NM_001282386:exon3:c.A42C:p.Q14H,IDH1:NM_001282387:exon3:c.A42C:p.Q14H,IDH1:NM_005896:exon3:c.A42C:p.Q14H	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	0.974	0.559	D	0.661	0.510	P	0.000	0.843	D	1	0.810	D	1.505	0.383	L	-0.34	0.685	T	-1.23	0.412	N	0.789	0.804	-0.670	0.618	T	0.229	0.595	T	0.038	0.582	D	5.365	0.727	25.9	0.997	0.795	0.934	0.578	D	c	0.220	0.252	1.000	0.747	0.719	0.830	0	4.32	0.507	1.156	0.311	0.964	0.580	1.000	0.715	1.000	0.888	9.299	0.368	Isopropylmalate dehydrogenase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	158	2	209116234	.	T	G	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=96;VD=3;AF=0.0312;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05294;SOR=inf;LSEQ=ATTCGTGTCATTTCATCTCC;RSEQ=TGCATCTCTACCACAGAACC;CSQ=G|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282386.1|protein_coding|3/10||NM_001282386.1:c.42A>C|NP_001269315.1:p.Gln14His|248|42|14|Q/H|caA/caC|||-1||EntrezGene||||||2:g.209116234T>G||||||||||||||,G|missense_variant|MODERATE|IDH1|3417|Transcript|NM_001282387.1|protein_coding|3/10||NM_001282387.1:c.42A>C|NP_001269316.1:p.Gln14His|405|42|14|Q/H|caA/caC|||-1||EntrezGene||YES||||2:g.209116234T>G||||||||||||||,G|missense_variant|MODERATE|IDH1|3417|Transcript|NM_005896.4|protein_coding|3/10||NM_005896.4:c.42A>C|NP_005887.2:p.Gln14His|265|42|14|Q/H|caA/caC|||-1||EntrezGene||||||2:g.209116234T>G||||||||||||||,G|upstream_gene_variant|MODIFIER|IDH1-AS1|100507475|Transcript|NR_046452.1|lncRNA|||||||||||3723|1||EntrezGene||YES||||2:g.209116234T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:96:3:2,1:32,61:93,3:0.0312:2,2:31.7:1:28.3:1:0.28532:3.76:60:2:0.022:0:1	0/0:158:0:0,0:80,78:158,0:0:2,0:38.5:1:34.6:1:1:0:60:18.75:1:0:0.1
    886. 

  886. 2	209116255	209116255	G	T	exonic	IDH1	.	synonymous SNV	IDH1:NM_001282386:exon3:c.C21A:p.G7G,IDH1:NM_001282387:exon3:c.C21A:p.G7G,IDH1:NM_005896:exon3:c.C21A:p.G7G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	150	2	209116255	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=77;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.43566;SOR=0;LSEQ=TGCATCTCTACCACAGAACC;RSEQ=CCACTGATTTTTTTGGACAT;CSQ=T|synonymous_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding|3/10||NM_001282386.1:c.21C>A|NP_001269315.1:p.Gly7%3D|227|21|7|G|ggC/ggA|COSV61620070||-1||EntrezGene||||||2:g.209116255G>T|||||||||||||1|1,T|synonymous_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding|3/10||NM_001282387.1:c.21C>A|NP_001269316.1:p.Gly7%3D|384|21|7|G|ggC/ggA|COSV61620070||-1||EntrezGene||YES||||2:g.209116255G>T|||||||||||||1|1,T|synonymous_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding|3/10||NM_005896.4:c.21C>A|NP_005887.2:p.Gly7%3D|244|21|7|G|ggC/ggA|COSV61620070||-1||EntrezGene||||||2:g.209116255G>T|||||||||||||1|1,T|upstream_gene_variant|MODIFIER|IDH1-AS1|100507475|Transcript|NR_046452.1|lncRNA||||||||||COSV61620070|3702|1||EntrezGene||YES||||2:g.209116255G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:77:0:0,0:27,50:77,0:0:2,0:29.6:1:35.4:1:1:0:60:24.667:1:0:0.1	0/1:150:2:1,1:63,85:148,2:0.0133:2,2:57:1:37:0:1:1.35:60:4:0.014:0:1
    887. 

  887. 2	209116299	209116299	-	A	intronic	IDH1	.	.	.	0.15	0.0446	0.1395	0.0087	0	0.0006	0.0018	0.0010	0.0082	rs139018716	rs139018716	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112122018	BTCA-SG|2|71|0.028169	0.25	32	107	2	209116299	.	G	GA	32	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=24;VD=0;AF=0;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.666;SOR=0;LSEQ=GACTTCAATAAACCTAAAAA;RSEQ=AAAAAAAAAATACATGCCTT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282386.1|protein_coding||2/9|NM_001282386.1:c.-16-9dup|||||||rs139018716||-1||EntrezGene||||||2:g.209116309dup|0.01538|0.1599|0.01175|0.001892|0.0009447|0.007985|0.002217|0.007307|0.003043|0.1599|gnomAD_AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_001282387.1|protein_coding||2/9|NM_001282387.1:c.-16-9dup|||||||rs139018716||-1||EntrezGene||YES||||2:g.209116309dup|0.01538|0.1599|0.01175|0.001892|0.0009447|0.007985|0.002217|0.007307|0.003043|0.1599|gnomAD_AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|IDH1|3417|Transcript|NM_005896.4|protein_coding||2/9|NM_005896.4:c.-16-9dup|||||||rs139018716||-1||EntrezGene||||||2:g.209116309dup|0.01538|0.1599|0.01175|0.001892|0.0009447|0.007985|0.002217|0.007307|0.003043|0.1599|gnomAD_AFR|||,A|upstream_gene_variant|MODIFIER|IDH1-AS1|100507475|Transcript|NR_046452.1|lncRNA||||||||||rs139018716|3657|1||EntrezGene||YES||||2:g.209116309dup|0.01538|0.1599|0.01175|0.001892|0.0009447|0.007985|0.002217|0.007307|0.003043|0.1599|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:24:0:0,0:7,17:24,0:0:2,0:31.2:1:33.8:1:1:0:60:11:1:0:0.2	0/1:107:2:1,1:32,66:98,2:0.0187:2,2:43.5:1:32.9:1:1:2.05:63.6:4:0.0227:0:0.5
    888. 

  888. 2	212248754	212248754	A	-	exonic	ERBB4	.	frameshift deletion	ERBB4:NM_001042599:exon27:c.3465delT:p.F1155Lfs*33,ERBB4:NM_005235:exon28:c.3513delT:p.F1171Lfs*33	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	255	2	212248753	.	CA	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=195;VD=2;AF=0.0103;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.18723;SOR=inf;LSEQ=TCCATTTTTTCTCCGAGAAA;RSEQ=AAAGGGTTCTCCTCCACTGG;CSQ=-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|27/27||NM_001042599.1:c.3465del|NP_001036064.1:p.Phe1155LeufsTer33|3563|3465|1155|F/X|ttT/tt|||-1||EntrezGene||||||2:g.212248757del||||||||||||||,-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_005235.3|protein_coding|28/28||NM_005235.3:c.3513del|NP_005226.1:p.Phe1171LeufsTer33|3785|3513|1171|F/X|ttT/tt|||-1||EntrezGene||YES||||2:g.212248757del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:195:2:1,1:53,140:193,2:0.0103:2,2:48.5:1:37:0:0.47819:2.63:60:4:0.0104:0:0	0/0:255:0:0,0:79,176:255,0:0:2,0:36.7:1:36.7:1:1:0:60:254:1:0:0.1
    889. 

  889. 2	212248762	212248762	T	C	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon27:c.A3457G:p.N1153D,ERBB4:NM_005235:exon28:c.A3505G:p.N1169D	.	.	.	.	.	.	.	.	.	.	.	0.06	0.373	T	0.998	0.715	D	0.991	0.782	D	0.000	0.843	N	1.000	0.524	D	2.38	0.688	M	-0.9	0.750	T	-1.8	0.425	N	0.246	0.304	-0.071	0.808	T	0.482	0.802	T	0.067	0.700	D	3.796	0.513	23.4	0.997	0.797	0.983	0.809	D	c	0.626	0.618	0.037	0.143	0.554	0.246	0	4.62	0.568	7.608	0.820	1.061	0.807	1.000	0.715	1.000	0.888	11.735	0.508	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	236	2	212248762	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=165;VD=2;AF=0.0121;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.1687;SOR=inf;LSEQ=TCTCCGAGAAACAAAAGGGT;RSEQ=CTCCTCCACTGGATTCAGGT;CSQ=C|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|27/27||NM_001042599.1:c.3457A>G|NP_001036064.1:p.Asn1153Asp|3555|3457|1153|N/D|Aac/Gac|||-1||EntrezGene||||||2:g.212248762T>C||||||||||||||,C|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|28/28||NM_005235.3:c.3505A>G|NP_005226.1:p.Asn1169Asp|3777|3505|1169|N/D|Aac/Gac|||-1||EntrezGene||YES||||2:g.212248762T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:165:2:1,1:40,123:163,2:0.0121:2,2:63:1:37:0:0.43636:3.05:60:4:0.0123:0:1	0/0:236:0:0,0:70,166:236,0:0:2,0:37:1:36.6:1:1:0:60:235:1:0:0.1
    890. 

  890. 2	212251549	212251549	G	T	intronic	ERBB4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	96	2	212251549	.	G	T	38	p8	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=153;VD=3;AF=0.0196;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.23023;SOR=inf;LSEQ=ATGGAAGTGAACTTCGAATG;RSEQ=CGATCGTTTCTGAATAATCA;CSQ=T|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||26/26|NM_001042599.1:c.3433+29C>A|||||||||-1||EntrezGene||||||2:g.212251549G>T||||||||||||||,T|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_005235.3|protein_coding||27/27|NM_005235.3:c.3481+29C>A|||||||||-1||EntrezGene||YES||||2:g.212251549G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:153:3:2,1:104,46:150,3:0.0196:2,2:7.7:1:24.3:1:1:1.1295:60:2:0.0134:0:2	0/0:96:0:0,0:74,22:96,0:0:2,0:35.2:1:36:1:1:0:60:95:1:0:0.1
    891. 

  891. 2	212251555	212251555	G	A	intronic	ERBB4	.	.	.	0.0003	.	.	.	.	.	.	.	.	rs753460430	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61528056;OCCURENCE=1(oesophagus)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU41488879	ESCA-CN|1|332|0.00301205	0.25	37	109	2	212251555	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=168;VD=2;AF=0.0119;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.36698;SOR=inf;LSEQ=GTGAACTTCGAATGGCGATC;RSEQ=TTTCTGAATAATCAGTTCAT;CSQ=A|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||26/26|NM_001042599.1:c.3433+23C>T|||||||rs753460430&COSV61528056||-1||EntrezGene||||||2:g.212251555G>A|3.202e-05|0|0.0002024|0|5.438e-05|0|0|0|0|0.0002024|gnomAD_AMR||0&1|0&1,A|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_005235.3|protein_coding||27/27|NM_005235.3:c.3481+23C>T|||||||rs753460430&COSV61528056||-1||EntrezGene||YES||||2:g.212251555G>A|3.202e-05|0|0.0002024|0|5.438e-05|0|0|0|0|0.0002024|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:168:2:1,1:114,52:166,2:0.0119:2,2:49:1:37:0:0.53272:2.18107:60:4:0.0121:0:1	0/0:109:0:0,0:84,25:109,0:0:2,0:34.9:1:36.2:1:1:0:60:108:1:0:0
    892. 

  892. 2	212285340	212285343	AAAG	-	intronic	ERBB4	.	.	.	0.41	0.1128	0.3437	0.0919	0.0199	0.0816	0.0089	0.0159	0.0235	rs138150601	rs138150601	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU113934974	COCA-CN|1|321|0.00311526	0.25	85	147	2	212285339	.	AAAAG	A	85	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=9;VD=5;AF=0.5556;SHIFT3=5;MSI=4;MSILEN=1;SSF=0;SOR=inf;LSEQ=CTTCATACGATCATCACCCT;RSEQ=AAAGATTGCCCATCAGACAC;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||24/26|NM_001042599.1:c.2965-7_2965-4del|||||||rs60420993||-1||EntrezGene||||||2:g.212285345_212285348del|0.05321|0.3612|0.08901|0.01351|0.08135|0.004855|0.01725|0.03617|0.01699|0.413|AFR|||,-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding||24/27|NM_005235.3:c.2965-7_2965-4del|||||||rs60420993||-1||EntrezGene||YES||||2:g.212285345_212285348del|0.05321|0.3612|0.08901|0.01351|0.08135|0.004855|0.01725|0.03617|0.01699|0.413|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:9:5:2,3:2,2:4,5:0.5556:2,2:27.6:1:37:1:1:1.43328:60:10:0.5556:0.1111:0	0/0:147:0:0,0:52,95:147,0:0:2,0:39.2:1:35.4:1:1:0:60:72.5:1:0:0
    893. 

  893. 2	212289001	212289001	G	A	exonic	ERBB4	.	synonymous SNV	ERBB4:NM_001042599:exon23:c.C2745T:p.T915T,ERBB4:NM_005235:exon23:c.C2745T:p.T915T	0.007	0.0040	0.0013	0.0048	0	0	0.0034	0.0062	0.0031	rs75536447	rs75536447	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV61495356;OCCURENCE=1(skin),6(prostate)	707997	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	1	.	.	0.25	37	170	2	212289001	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.88183;SOR=0;LSEQ=TCATAGGGTTTTCCTCCAAA;RSEQ=GTCATCAGTTCCCATATAGT;CSQ=A|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|23/27||NM_001042599.1:c.2745C>T|NP_001036064.1:p.Thr915%3D|2843|2745|915|T|acC/acT|rs75536447&COSV61495356||-1||EntrezGene||||||2:g.212289001G>A|0.003578|0.0009236|0.001046|0.002483|0|0.003054|0.006208|0.003924|0.0008825|0.007|EUR|benign|0&1|1&1,A|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding|23/28||NM_005235.3:c.2745C>T|NP_005226.1:p.Thr915%3D|3017|2745|915|T|acC/acT|rs75536447&COSV61495356||-1||EntrezGene||YES||||2:g.212289001G>A|0.003578|0.0009236|0.001046|0.002483|0|0.003054|0.006208|0.003924|0.0008825|0.007|EUR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:4,7:11,0:0:2,0:24.9:1:37:0:1:0:60:22:1:0:0.3	0/1:170:2:1,1:58,110:168,2:0.0118:2,2:55.5:1:37:0:1:1.89:60:4:0.0118:0:1
    894. 

  894. 2	212295719	212295719	G	A	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon21:c.C2594T:p.A865V,ERBB4:NM_005235:exon21:c.C2594T:p.A865V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.992	0.818	D	0.000	0.843	D	1	0.810	D	2.19	0.618	M	-0.41	0.694	T	-3.56	0.688	D	0.981	0.984	0.085	0.839	D	0.511	0.816	D	0.110	0.788	D	4.272	0.572	24.0	0.999	0.979	0.992	0.926	D	c	0.798	0.727	1.000	0.747	0.487	0.133	0	5.19	0.713	9.964	0.990	1.048	0.713	1.000	0.715	0.948	0.423	19.063	0.931	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU128861760	GACA-JP|1|585|0.0017094	0.25	37	215	2	212295719	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=40;VD=2;AF=0.05;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.02409;SOR=inf;LSEQ=CATCTCCTTCCAAGAGTCTG;RSEQ=CTAGCCCAAAATCTGTGATT;CSQ=A|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|21/27||NM_001042599.1:c.2594C>T|NP_001036064.1:p.Ala865Val|2692|2594|865|A/V|gCc/gTc|||-1||EntrezGene||||||2:g.212295719G>A||||||||||||||,A|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|21/28||NM_005235.3:c.2594C>T|NP_005226.1:p.Ala865Val|2866|2594|865|A/V|gCc/gTc|||-1||EntrezGene||YES||||2:g.212295719G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:40:2:1,1:21,17:38,2:0.05:2,2:22:1:37:0:1:1.22874:60:4:0.05:0:1	0/0:215:0:0,0:125,90:215,0:0:2,0:40:1:36.2:1:1:0:60:52.75:1:0:0.1
    895. 

  895. 2	212295779	212295779	G	A	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon21:c.C2534T:p.A845V,ERBB4:NM_005235:exon21:c.C2534T:p.A845V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.991	0.637	D	0.665	0.682	P	0.000	0.843	D	1	0.810	D	3.835	0.958	H	-0.05	0.634	T	-3.52	0.684	D	0.969	0.969	0.524	0.909	D	0.601	0.858	D	0.179	0.855	D	6.720	0.918	32	0.999	0.988	0.992	0.925	D	c	1.000	0.913	1.000	0.747	0.487	0.133	0	5.17	0.707	9.959	0.990	1.048	0.713	1.000	0.715	0.997	0.653	19.028	0.929	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	224	2	212295779	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=2;AF=0.0476;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02443;SOR=inf;LSEQ=TCACTAAGACATTACGGGCT;RSEQ=CCAAATCCCGATGAACGAGT;CSQ=A|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|21/27||NM_001042599.1:c.2534C>T|NP_001036064.1:p.Ala845Val|2632|2534|845|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.212295779G>A||||||||||||||,A|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|21/28||NM_005235.3:c.2534C>T|NP_005226.1:p.Ala845Val|2806|2534|845|A/V|gCa/gTa|||-1||EntrezGene||YES||||2:g.212295779G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:42:2:1,1:18,22:40,2:0.0476:2,2:48:0:37:0:1:1.22:60:4:0.0476:0:1	0/0:224:0:0,0:108,116:224,0:0:2,0:38.5:1:36.3:1:1:0:60:111:1:0:0.4
    896. 

  896. 2	212426639	212426639	G	-	exonic	ERBB4	.	frameshift deletion	ERBB4:NM_001042599:exon20:c.2476delC:p.Q826Rfs*2,ERBB4:NM_005235:exon20:c.2476delC:p.Q826Rfs*2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	291	2	212426638	.	TG	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=70;VD=2;AF=0.0286;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.03717;SOR=inf;LSEQ=AGGCACTTACCTTAGCTATC;RSEQ=GACACACCAGTTAAGCAGCA;CSQ=-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|20/27||NM_001042599.1:c.2476del|NP_001036064.1:p.Gln826ArgfsTer2|2574|2476|826|Q/X|Cag/ag|||-1||EntrezGene||||||2:g.212426640del||||||||||||||,-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_005235.3|protein_coding|20/28||NM_005235.3:c.2476del|NP_005226.1:p.Gln826ArgfsTer2|2748|2476|826|Q/X|Cag/ag|||-1||EntrezGene||YES||||2:g.212426640del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:70:2:1,1:48,20:68,2:0.0286:2,2:42:1:37:0:0.51304:2.36645:60:4:0.0286:0:0	0/0:291:0:0,0:184,107:291,0:0:2,0:36.4:1:36.4:1:1:0:60:144.5:1:0:0.1
    897. 

  897. 2	212426708	212426708	A	T	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon20:c.T2407A:p.C803S,ERBB4:NM_005235:exon20:c.T2407A:p.C803S	.	.	.	.	.	.	.	.	.	.	.	0.238	0.178	T	0.832	0.899	P	0.498	0.807	P	0.000	0.843	D	1	0.810	D	-1.3	0.007	N	0.46	0.563	T	-5.38	0.849	D	0.915	0.910	-0.619	0.641	T	0.113	0.404	T	0.052	0.650	D	4.566	0.612	24.4	0.993	0.572	0.988	0.874	D	c	0.215	0.379	1.000	0.420	0.554	0.246	0	5.12	0.693	9.325	0.960	1.199	0.960	1.000	0.715	0.983	0.502	15.232	0.730	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	386	2	212426708	.	A	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.06825;SOR=inf;LSEQ=GTGGACATACTCCAACAGGC;RSEQ=GCCATGGGGCATAAGTTGAG;CSQ=T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|20/27||NM_001042599.1:c.2407T>A|NP_001036064.1:p.Cys803Ser|2505|2407|803|C/S|Tgc/Agc|||-1||EntrezGene||||||2:g.212426708A>T||||||||||||||,T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|20/28||NM_005235.3:c.2407T>A|NP_005226.1:p.Cys803Ser|2679|2407|803|C/S|Tgc/Agc|||-1||EntrezGene||YES||||2:g.212426708A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:70,65:135,2:0.0146:2,2:32:0:37:0:1:1.07632:60:4:0.0146:0:1	0/0:386:0:0,0:191,195:386,0:0:2,0:38.4:1:36.2:1:1:0:60:41.889:1:0:0.1
    898. 

  898. 2	212484002	212484002	T	C	splicing	ERBB4	NM_005235:exon19:c.2203-2A>G;NM_001042599:exon19:c.2203-2A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.190	0.562	23.8	0.992	0.556	0.983	0.812	D	c	1.014	0.824	1.000	0.437	0.074	0.012	0	4.91	0.638	7.756	0.839	1.061	0.807	1.000	0.715	0.893	0.376	14.494	0.671	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	95	2	212484002	.	T	C	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.95898;SOR=0;LSEQ=CTTCAGGTACCCAAATACCC;RSEQ=TTGGGGAAAAAAATTTACAT;CSQ=C|splice_acceptor_variant|HIGH|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||18/26|NM_001042599.1:c.2203-2A>G|||||||||-1||EntrezGene||||||2:g.212484002T>C||||||||||||||,C|splice_acceptor_variant|HIGH|ERBB4|2066|Transcript|NM_005235.3|protein_coding||18/27|NM_005235.3:c.2203-2A>G|||||||||-1||EntrezGene||YES||||2:g.212484002T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:12:1:31:1:1:0:60:4:1:0:1	0/1:95:2:1,1:34,59:93,2:0.0211:2,2:42:1:37:0:1:1.72:60:4:0.0217:0:1
    899. 

  899. 2	212488662	212488662	A	-	exonic	ERBB4	.	frameshift deletion	ERBB4:NM_001042599:exon18:c.2187delT:p.F729Lfs*16,ERBB4:NM_005235:exon18:c.2187delT:p.F729Lfs*16	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	181	2	212488661	.	CA	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=299;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.1417;SOR=0;LSEQ=ACTTACTTTATAAACCGTTC;RSEQ=AAAGCACCTGAGCCAAGGAC;CSQ=-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|18/27||NM_001042599.1:c.2187del|NP_001036064.1:p.Phe729LeufsTer16|2285|2187|729|F/X|ttT/tt|||-1||EntrezGene||||||2:g.212488665del||||||||||||||,-|frameshift_variant|HIGH|ERBB4|2066|Transcript|NM_005235.3|protein_coding|18/28||NM_005235.3:c.2187del|NP_005226.1:p.Phe729LeufsTer16|2459|2187|729|F/X|ttT/tt|||-1||EntrezGene||YES||||2:g.212488665del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:299:0:0,0:195,104:299,0:0:2,0:31.9:1:36.5:1:1:0:60:98.667:1:0:0.1	0/1:181:2:1,1:109,70:179,2:0.011:2,2:35.5:1:37:1:1:1.55317:60:4:0.011:0.0055:0
    900. 

  900. 2	212495192	212495192	T	C	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon17:c.A2074G:p.T692A,ERBB4:NM_005235:exon17:c.A2074G:p.T692A	.	.	.	.	.	.	.	.	.	.	.	0.241	0.176	T	0.999	0.764	D	0.996	0.832	D	0.000	0.843	D	1	0.810	D	2.135	0.597	M	-0.9	0.749	T	-2.05	0.470	N	0.658	0.711	-0.107	0.800	T	0.426	0.770	T	0.049	0.636	D	2.495	0.361	19.44	0.994	0.637	0.984	0.825	D	c	0.505	0.595	1.000	0.489	0.487	0.133	0	5.87	0.942	7.670	0.828	1.011	0.635	1.000	0.715	0.998	0.697	16.266	0.823	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	151	2	212495192	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=2;AF=0.1818;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.00422;SOR=inf;LSEQ=AAAGAAATACCTCACCTCTG;RSEQ=TTCCAAGAATCTTCTCAAGG;CSQ=C|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|17/27||NM_001042599.1:c.2074A>G|NP_001036064.1:p.Thr692Ala|2172|2074|692|T/A|Aca/Gca|||-1||EntrezGene||||||2:g.212495192T>C||||||||||||||,C|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|17/28||NM_005235.3:c.2074A>G|NP_005226.1:p.Thr692Ala|2346|2074|692|T/A|Aca/Gca|||-1||EntrezGene||YES||||2:g.212495192T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:11:2:1,1:6,3:9,2:0.1818:2,2:29:0:37:0:1:1.87089:60:4:0.1818:0:1	0/0:151:0:0,0:85,66:151,0:0:2,0:37.2:1:36.8:1:1:0:60:302:1:0:0.1
    901. 

  901. 2	212495337	212495337	A	-	intronic	ERBB4	.	.	.	0.13	0.0406	0.1253	0.0125	0.0125	0	0.0071	0.0015	0.0063	rs57466272	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU43225564	COCA-CN|1|321|0.00311526,BTCA-JP|2|239|0.0083682	0.5	95	121	2	212495336	.	GA	G	95	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=15;VD=2;AF=0.1333;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.21522;SOR=2.91564;LSEQ=AGTTCTGACAACCAGAATGA;RSEQ=AAAAAAAAAATAAAAAGTAT;CSQ=-|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||16/26|NM_001042599.1:c.1947-18del|||||||rs57466272&COSV104594385||-1||EntrezGene||||||2:g.212495347del|0.02427|0.1411|0.02545|0.01535|0.00964|0.01907|0.009336|0.02217|0.01284|0.1411|gnomAD_AFR||0&1|0&1,-|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_005235.3|protein_coding||16/27|NM_005235.3:c.1947-18del|||||||rs57466272&COSV104594385||-1||EntrezGene||YES||||2:g.212495347del|0.02427|0.1411|0.02545|0.01535|0.00964|0.01907|0.009336|0.02217|0.01284|0.1411|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:15:2:1,1:5,8:13,2:0.1333:2,2:51:0:37:0:1:1.55:60:4:0.1333:0:0	0/1:121:6:2,4:43,72:115,6:0.0496:2,2:30.3:1:37:0:1:1.19269:60:12:0.05:0:0
    902. 

  902. 2	212530161	212530161	G	C	exonic	ERBB4	.	synonymous SNV	ERBB4:NM_001042599:exon15:c.C1758G:p.G586G,ERBB4:NM_005235:exon15:c.C1758G:p.G586G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	261	2	212530161	.	G	C	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=2;AF=0.0213;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.06956;SOR=inf;LSEQ=CATTTTTCCACACAGTTTGG;RSEQ=CCATCTTTAAAATGAGAGCA;CSQ=C|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|15/27||NM_001042599.1:c.1758C>G|NP_001036064.1:p.Gly586%3D|1856|1758|586|G|ggC/ggG|COSV99629578||-1||EntrezGene||||||2:g.212530161G>C|||||||||||||1|1,C|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding|15/28||NM_005235.3:c.1758C>G|NP_005226.1:p.Gly586%3D|2030|1758|586|G|ggC/ggG|COSV99629578||-1||EntrezGene||YES||||2:g.212530161G>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:94:2:1,1:37,55:92,2:0.0213:2,2:47.5:1:31:1:1:1.48:60:4:0.022:0:1	0/0:261:0:0,0:92,168:260,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    903. 

  903. 2	212530180	212530180	C	T	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon15:c.G1739A:p.C580Y,ERBB4:NM_005235:exon15:c.G1739A:p.C580Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.25	0.981	H	-3.66	0.952	D	-10.1	0.989	D	0.956	0.953	1.103	0.998	D	0.947	0.983	D	0.473	0.947	D	6.476	0.893	30	0.998	0.892	0.993	0.944	D	c	1.018	0.907	1.000	0.747	0.487	0.133	0	4.94	0.645	7.899	0.859	0.935	0.490	1.000	0.715	0.998	0.697	18.546	0.910	Growth factor receptor cysteine-rich domain|Growth factor receptor domain 4	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	234	2	212530180	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=67;VD=2;AF=0.0299;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04897;SOR=inf;LSEQ=GGCCATCTTTAAAATGAGAG;RSEQ=ACTTTGTACAGTTGTCAGGA;CSQ=T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|15/27||NM_001042599.1:c.1739G>A|NP_001036064.1:p.Cys580Tyr|1837|1739|580|C/Y|tGc/tAc|||-1||EntrezGene||||||2:g.212530180C>T||||||||||||||,T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|15/28||NM_005235.3:c.1739G>A|NP_005226.1:p.Cys580Tyr|2011|1739|580|C/Y|tGc/tAc|||-1||EntrezGene||YES||||2:g.212530180C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:67:2:1,1:23,42:65,2:0.0299:2,2:28.5:1:37:0:1:1.81:60:4:0.0312:0:1	0/0:234:0:0,0:79,155:234,0:0:2,0:39:1:36:1:1:0:60:77:1:0:0.1
    904. 

  904. 2	212530218	212530218	-	A	intronic	ERBB4	.	.	.	0.004	0.0002	0	0.0012	0	0	0	0.0003	0	rs767387600	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	39	155	2	212530218	.	G	GA	39	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=40;VD=0;AF=0;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.63098;SOR=0;LSEQ=GGACCCTGAAATGTGAAAAC;RSEQ=AAAAAAAAAGAAAAAAGAAA;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||14/26|NM_001042599.1:c.1717-17dup|||||||rs759469301||-1||EntrezGene||||||2:g.212530227dup|0.0002515|0.0001348|0.0005107|0|0|4.969e-05|0.000237|0.0003781|0.0004529|0.003985|AA|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding||14/27|NM_005235.3:c.1717-17dup|||||||rs759469301||-1||EntrezGene||YES||||2:g.212530227dup|0.0002515|0.0001348|0.0005107|0|0|4.969e-05|0.000237|0.0003781|0.0004529|0.003985|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:40:0:0,0:14,26:40,0:0:2,0:38.7:1:30.9:1:1:0:60:4.714:1:0:0.1	0/1:155:2:0,2:37,107:144,2:0.0129:2,0:44.2:1:39:0:1:0:63.2:4:0.0142:0:0
    905. 

  905. 2	212537957	212537957	A	G	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon14:c.T1648C:p.S550P,ERBB4:NM_005235:exon14:c.T1648C:p.S550P	.	.	.	.	.	.	.	.	.	.	.	0.041	0.419	D	0.96	0.566	D	0.665	0.588	P	0.000	0.843	D	1	0.810	D	2.295	0.656	M	0.87	0.464	T	-3.13	0.639	D	0.831	0.819	-0.704	0.603	T	0.209	0.569	T	0.027	0.498	D	4.527	0.606	24.3	0.999	0.963	0.988	0.871	D	c	0.601	0.634	1.000	0.418	0.554	0.246	0	5.33	0.756	8.897	0.921	1.199	0.960	1.000	0.715	1.000	0.888	15.281	0.734	Growth factor receptor cysteine-rich domain|Growth factor receptor domain 4	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	309	2	212537957	.	A	G	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=185;VD=2;AF=0.0108;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.13977;SOR=inf;LSEQ=GTCACACTCCACACAGATGG;RSEQ=GCCATTCTCAAACTCCCGAA;CSQ=G|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|14/27||NM_001042599.1:c.1648T>C|NP_001036064.1:p.Ser550Pro|1746|1648|550|S/P|Tcc/Ccc|COSV104594376||-1||EntrezGene||||||2:g.212537957A>G|||||||||||||1|1,G|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|14/28||NM_005235.3:c.1648T>C|NP_005226.1:p.Ser550Pro|1920|1648|550|S/P|Tcc/Ccc|COSV104594376||-1||EntrezGene||YES||||2:g.212537957A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:185:2:1,1:94,89:183,2:0.0108:2,2:5:0:37:0:1:1.05589:60:4:0.011:0:1	0/0:309:0:0,0:135,174:309,0:0:2,0:39.1:1:36.8:1:1:0:60:308:1:0:0.1
    906. 

  906. 2	212566683	212566683	T	C	intronic	ERBB4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	161	2	212566683	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=21;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.78198;SOR=0;LSEQ=TGTTTTAAATGTCTGAGTAA;RSEQ=GTACTTACTACAATTTTCAG;CSQ=C|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||12/26|NM_001042599.1:c.1489+9A>G|||||||rs1234873121||-1||EntrezGene||||||2:g.212566683T>C|3.978e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|||,C|intron_variant|MODIFIER|ERBB4|2066|Transcript|NM_005235.3|protein_coding||12/27|NM_005235.3:c.1489+9A>G|||||||rs1234873121||-1||EntrezGene||YES||||2:g.212566683T>C|3.978e-06|0|0|0|0|0|0|0|3.266e-05|3.266e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:21:0:0,0:19,2:21,0:0:2,0:22:1:37:0:1:0:60:42:1:0:0.1	0/1:161:2:1,1:122,37:159,2:0.0124:2,2:44.5:1:37:0:0.41747:3.26691:60:4:0.0125:0:1
    907. 

  907. 2	212566777	212566777	A	G	exonic	ERBB4	.	synonymous SNV	ERBB4:NM_001042599:exon12:c.T1404C:p.Y468Y,ERBB4:NM_005235:exon12:c.T1404C:p.Y468Y	0.	.	.	.	.	.	.	.	.	rs772629122	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	747245	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	320	2	212566777	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12083;SOR=inf;LSEQ=GTCCAGTTAATGGTATGATA;RSEQ=TAACACAGGTTGCTGTTGTC;CSQ=G|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|12/27||NM_001042599.1:c.1404T>C|NP_001036064.1:p.Tyr468%3D|1502|1404|468|Y|taT/taC|rs772629122||-1||EntrezGene||||||2:g.212566777A>G|1.193e-05|0|5.782e-05|0|0|0|8.791e-06|0|0|5.782e-05|gnomAD_AMR|likely_benign||1,G|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding|12/28||NM_005235.3:c.1404T>C|NP_005226.1:p.Tyr468%3D|1676|1404|468|Y|taT/taC|rs772629122||-1||EntrezGene||YES||||2:g.212566777A>G|1.193e-05|0|5.782e-05|0|0|0|8.791e-06|0|0|5.782e-05|gnomAD_AMR|likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:114,55:169,2:0.0117:2,2:63:0:37:0:0.54902:2.06318:60:4:0.0118:0:1	0/0:320:0:0,0:188,132:320,0:0:2,0:37.1:1:36.5:1:1:0:60:159:1:0:0.1
    908. 

  908. 2	212568830	212568830	T	A	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon11:c.A1288T:p.S430C,ERBB4:NM_005235:exon11:c.A1288T:p.S430C	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	1.0	0.899	D	0.994	0.832	D	0.000	0.843	D	1	0.810	D	2.44	0.710	M	-1.35	0.800	T	-3.64	0.700	D	0.741	0.738	0.423	0.895	D	0.666	0.884	D	0.333	0.918	D	5.027	0.677	25.2	0.990	0.489	0.990	0.890	D	c	0.824	0.815	1.000	0.747	0.487	0.133	0	6.02	0.975	8.017	0.886	1.061	0.807	1.000	0.715	0.970	0.461	16.545	0.842	Leucine-rich repeat domain, L domain-like|Receptor L-domain	.	.	.	.	.	.	.	.	Likely pathogenic	0	0	0	0	0	1	1	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	165	2	212568830	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=20;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.79495;SOR=0;LSEQ=TTTAAACATATCCACTTACC;RSEQ=ATAGAGTACTCTTCCACCAA;CSQ=A|missense_variant&splice_region_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|11/27||NM_001042599.1:c.1288A>T|NP_001036064.1:p.Ser430Cys|1386|1288|430|S/C|Agt/Tgt|||-1||EntrezGene||||||2:g.212568830T>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|11/28||NM_005235.3:c.1288A>T|NP_005226.1:p.Ser430Cys|1560|1288|430|S/C|Agt/Tgt|||-1||EntrezGene||YES||||2:g.212568830T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:20:0:0,0:11,9:20,0:0:2,0:45.1:1:35.1:1:1:0:60:19:1:0:0	0/1:165:2:1,1:90,73:163,2:0.0121:2,2:30:0:37:0:1:1.2313:60:4:0.0126:0:1
    909. 

  909. 2	212570085	212570085	G	T	exonic	ERBB4	.	nonsynonymous SNV	ERBB4:NM_001042599:exon10:c.C1156A:p.P386T,ERBB4:NM_005235:exon10:c.C1156A:p.P386T	0.	.	.	.	.	.	.	.	.	rs762730624	.	0.024	0.491	D	1.0	0.899	D	0.999	0.971	D	0.000	0.843	D	1	0.810	D	2.87	0.836	M	0.93	0.441	T	-6.27	0.920	D	0.799	0.789	-0.361	0.733	T	0.327	0.696	T	0.117	0.797	D	6.044	0.832	28.0	0.998	0.903	0.995	0.971	D	c	0.913	0.876	1.000	0.747	0.554	0.283	0	5.33	0.756	9.960	0.990	0.994	0.605	1.000	0.715	0.999	0.750	19.362	0.944	Leucine-rich repeat domain, L domain-like|Receptor L-domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	148	2	212570085	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.66777;SOR=0;LSEQ=AAAGACGTTCAGTTTCTCTG;RSEQ=GTCTATGGCTTCAATTGCAT;CSQ=T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|10/27||NM_001042599.1:c.1156C>A|NP_001036064.1:p.Pro386Thr|1254|1156|386|P/T|Cca/Aca|rs762730624||-1||EntrezGene||||||2:g.212570085G>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE|||,T|missense_variant|MODERATE|ERBB4|2066|Transcript|NM_005235.3|protein_coding|10/28||NM_005235.3:c.1156C>A|NP_005226.1:p.Pro386Thr|1428|1156|386|P/T|Cca/Aca|rs762730624||-1||EntrezGene||YES||||2:g.212570085G>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:33:0:0,0:12,21:33,0:0:2,0:43.9:1:33.2:1:1:0:60:10:1:0:0.2	0/1:148:2:0,2:76,70:146,2:0.0135:2,0:24.5:1:31:1:0.23497:0:60:4:0.0142:0:5.5
    910. 

  910. 2	212615432	212615432	G	A	intronic	ERBB4	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	371	2	212615432	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=111;VD=2;AF=0.018;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05267;SOR=inf;LSEQ=ACTTATGGCAACGTCCACCT;RSEQ=CAGAACACGAAAAGGGAAAA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||4/26|NM_001042599.1:c.557-3C>T|||||||||-1||EntrezGene||||||2:g.212615432G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding||4/27|NM_005235.3:c.557-3C>T|||||||||-1||EntrezGene||YES||||2:g.212615432G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:111:2:1,1:40,69:109,2:0.018:2,2:26:0:37:0:1:1.72:60:4:0.0183:0:1	0/0:371:0:0,0:163,208:371,0:0:2,0:37.9:1:36.5:1:1:0:60:122.667:1:0:0.1
    911. 

  911. 2	212615440	212615440	C	T	intronic	ERBB4	.	.	.	0.0002	0.0001	0	0	0	0.0012	0.0006	0	0	rs370066248	rs370066248	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	356	2	212615440	.	C	T	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=106;VD=2;AF=0.0189;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05226;SOR=inf;LSEQ=CAACGTCCACCTGCAGAACA;RSEQ=GAAAAGGGAAAAAGGACATG;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding||4/26|NM_001042599.1:c.557-11G>A|||||||rs370066248||-1||EntrezGene||||||2:g.212615440C>T|3.977e-05|0|0|0|0.0001088|0.0002772|1.758e-05|0|0|0.0002772|gnomAD_FIN|||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding||4/27|NM_005235.3:c.557-11G>A|||||||rs370066248||-1||EntrezGene||YES||||2:g.212615440C>T|3.977e-05|0|0|0|0.0001088|0.0002772|1.758e-05|0|0|0.0002772|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:106:2:1,1:38,66:104,2:0.0189:2,2:50:0:31:1:1:1.73:60:4:0.019:0:2	0/0:356:0:0,0:149,207:356,0:0:2,0:37.4:1:36.1:1:1:0:60:177:1:0:0.1
    912. 

  912. 2	212812327	212812327	G	A	exonic	ERBB4	.	synonymous SNV	ERBB4:NM_001042599:exon3:c.C249T:p.V83V,ERBB4:NM_005235:exon3:c.C249T:p.V83V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	233	2	212812327	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=44;VD=2;AF=0.0455;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.02475;SOR=inf;LSEQ=GCCACTAACACGTAGCCTGT;RSEQ=ACTTCTCGAACAGACTGAAA;CSQ=A|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_001042599.1|protein_coding|3/27||NM_001042599.1:c.249C>T|NP_001036064.1:p.Val83%3D|347|249|83|V|gtC/gtT|||-1||EntrezGene||||||2:g.212812327G>A||||||||||||||,A|synonymous_variant|LOW|ERBB4|2066|Transcript|NM_005235.3|protein_coding|3/28||NM_005235.3:c.249C>T|NP_005226.1:p.Val83%3D|521|249|83|V|gtC/gtT|||-1||EntrezGene||YES||||2:g.212812327G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:44:2:1,1:21,21:42,2:0.0455:2,2:31.5:1:37:0:1:1:60:4:0.0455:0:1	0/0:233:0:0,0:108,125:233,0:0:2,0:39.5:1:36.3:1:1:0:60:57.25:1:0:0.1
    913. 

  913. 2	215593689	215593689	G	T	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282549:exon5:c.C506A:p.T169N,BARD1:NM_001282548:exon6:c.C635A:p.T212N,BARD1:NM_001282545:exon7:c.C692A:p.T231N,BARD1:NM_001282543:exon10:c.C1988A:p.T663N,BARD1:NM_000465:exon11:c.C2045A:p.T682N	.	.	.	.	.	.	.	.	.	.	.	0.28	0.155	T	0.0	0.026	B	0.001	0.040	B	0.121	0.190	N	1	0.090	N	-0.06	0.049	N	-0.7	0.728	T	0.01	0.069	N	0.044	0.024	-0.980	0.349	T	0.172	0.514	T	0.008	0.222	T	1.081	0.198	11.11	0.995	0.696	0.939	0.594	D	c	-0.518	-0.327	0.003	0.097	0.707	0.730	0	1.92	0.248	2.127	0.414	0.079	0.188	0.998	0.411	0.950	0.426	1.812	0.029	BRCT domain	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	31	323	2	215593689	.	G	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=2;AF=0.0107;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13399;SOR=inf;LSEQ=CCTTTGGATGGTGTTTGAAG;RSEQ=TTCCCCACAAATAGAAGTAG;CSQ=T|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|11/11||NM_000465.4:c.2045C>A|NP_000456.2:p.Thr682Asn|2159|2045|682|T/N|aCc/aAc|rs1559372592||-1||EntrezGene||YES||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|10/10||NM_001282543.2:c.1988C>A|NP_001269472.1:p.Thr663Asn|2102|1988|663|T/N|aCc/aAc|rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282545.2|protein_coding|7/7||NM_001282545.2:c.692C>A|NP_001269474.1:p.Thr231Asn|806|692|231|T/N|aCc/aAc|rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282548.2|protein_coding|6/6||NM_001282548.2:c.635C>A|NP_001269477.1:p.Thr212Asn|749|635|212|T/N|aCc/aAc|rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282549.2|protein_coding|5/5||NM_001282549.2:c.506C>A|NP_001269478.1:p.Thr169Asn|620|506|169|T/N|aCc/aAc|rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|10/10||NR_104212.2:n.2010C>A||2010|||||rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|9/9||NR_104215.2:n.1953C>A||1953|||||rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|10/10||NR_104216.2:n.1209C>A||1209|||||rs1559372592||-1||EntrezGene||||||2:g.215593689G>T|3.982e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:187:2:1,1:57,128:185,2:0.0107:2,2:44.5:1:31:1:0.52527:2.23:60:4:0.0108:0:1	0/0:323:0:0,0:122,201:323,0:0:2,0:35.9:1:36.3:1:1:0:60:79.75:1:0:0.1
    914. 

  914. 2	215595134	215595134	C	T	splicing	BARD1	NM_001282549:exon4:c.462+1G>A;NM_000465:exon10:c.2001+1G>A;NM_001282545:exon6:c.648+1G>A;NM_001282543:exon9:c.1944+1G>A;NM_001282548:exon5:c.591+1G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.641	0.769	26.6	0.993	0.602	0.993	0.948	D	c	1.184	1.048	1.000	0.747	0.322	0.047	0	5.77	0.910	6.509	0.734	0.935	0.490	1.000	0.715	1.000	0.888	19.983	0.973	.	.	.	.	517631	Familial_cancer_of_breast	MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_single_submitter	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	123	2	215595134	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.90879;SOR=0;LSEQ=GTTGTATTAAAAGAAAAATA;RSEQ=CAGCTGTTCTCTGTTGAGCC;CSQ=T|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding||10/10|NM_000465.4:c.2001+1G>A|||||||rs768490891||-1||EntrezGene||YES||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding||9/9|NM_001282543.2:c.1944+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282545.2|protein_coding||6/6|NM_001282545.2:c.648+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282548.2|protein_coding||5/5|NM_001282548.2:c.591+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282549.2|protein_coding||4/4|NM_001282549.2:c.462+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104212.2|misc_RNA||9/9|NR_104212.2:n.1966+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104215.2|misc_RNA||8/8|NR_104215.2:n.1909+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1,T|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104216.2|misc_RNA||9/9|NR_104216.2:n.1165+1G>A|||||||rs768490891||-1||EntrezGene||||||2:g.215595134C>T||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:4,2:6,0:0:2,0:16.3:1:37:0:1:0:60:12:1:0:0.3	0/1:123:2:1,1:71,50:121,2:0.0163:2,2:36:1:37:0:1:1.41585:60:4:0.0164:0:1
    915. 

  915. 2	215610450	215610450	A	T	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282548:exon3:c.T396A:p.S132R,BARD1:NM_001282545:exon4:c.T453A:p.S151R,BARD1:NM_001282543:exon7:c.T1749A:p.S583R,BARD1:NM_000465:exon8:c.T1806A:p.S602R	.	.	.	.	.	.	.	.	.	.	.	0.019	0.501	D	0.984	0.615	D	0.839	0.599	P	0.011	0.297	N	0.978	0.395	D	2.26	0.646	M	-1.3	0.796	T	-3.18	0.644	D	0.299	0.376	-0.191	0.779	T	0.494	0.808	T	0.093	0.761	D	5.373	0.728	25.9	0.996	0.731	0.750	0.364	D	c	0.160	0.078	0.002	0.092	0.651	0.465	0	1.18	0.200	1.246	0.322	0.177	0.246	1.000	0.715	0.990	0.544	7.715	0.277	BRCT domain	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	37	164	2	215610450	.	A	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=38;VD=2;AF=0.0526;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03463;SOR=inf;LSEQ=AATTCAAAATCCTCACCTGT;RSEQ=CTGTCAAACTCAGTATATTT;CSQ=T|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|8/11||NM_000465.4:c.1806T>A|NP_000456.2:p.Ser602Arg|1920|1806|602|S/R|agT/agA|||-1||EntrezGene||YES||||2:g.215610450A>T||||||||||||||,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|7/10||NM_001282543.2:c.1749T>A|NP_001269472.1:p.Ser583Arg|1863|1749|583|S/R|agT/agA|||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282545.2|protein_coding|4/7||NM_001282545.2:c.453T>A|NP_001269474.1:p.Ser151Arg|567|453|151|S/R|agT/agA|||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282548.2|protein_coding|3/6||NM_001282548.2:c.396T>A|NP_001269477.1:p.Ser132Arg|510|396|132|S/R|agT/agA|||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.365-15218T>A|||||||||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|7/10||NR_104212.2:n.1771T>A||1771|||||||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|6/9||NR_104215.2:n.1714T>A||1714|||||||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|7/10||NR_104216.2:n.970T>A||970|||||||-1||EntrezGene||||||2:g.215610450A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:38:2:1,1:23,13:36,2:0.0526:2,2:13:0:37:0:1:1.74146:60:4:0.0541:0:1	0/0:164:0:0,0:103,61:164,0:0:2,0:37.1:1:36.6:1:1:0:60:163:1:0:0.1
    916. 

  916. 2	215617169	215617169	A	G	splicing	BARD1	NM_000465:exon7:c.1677+2T>C;NM_001282545:exon3:c.324+2T>C;NM_001282543:exon6:c.1620+2T>C;NM_001282548:exon2:c.267+2T>C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.763	0.509	23.3	0.985	0.420	0.992	0.933	D	c	0.920	0.722	0.973	0.293	0.156	0.027	0	4.8	0.610	5.922	0.696	1.140	0.893	1.000	0.715	0.470	0.266	14.505	0.672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	116	2	215617169	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=3;SSF=0.69544;SOR=0;LSEQ=CCAAAGCTAAATCCATACTT;RSEQ=CTACTGAGCAGTGGCTAGCT;CSQ=G|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding||7/10|NM_000465.4:c.1677+2T>C|||||||||-1||EntrezGene||YES||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding||6/9|NM_001282543.2:c.1620+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282545.2|protein_coding||3/6|NM_001282545.2:c.324+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant|HIGH|BARD1|580|Transcript|NM_001282548.2|protein_coding||2/5|NM_001282548.2:c.267+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.365-21937T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104212.2|misc_RNA||6/9|NR_104212.2:n.1642+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104215.2|misc_RNA||5/8|NR_104215.2:n.1585+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||,G|splice_donor_variant&non_coding_transcript_variant|HIGH|BARD1|580|Transcript|NR_104216.2|misc_RNA||6/9|NR_104216.2:n.841+2T>C|||||||||-1||EntrezGene||||||2:g.215617169A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:12,11:23,0:0:2,0:23:1:37:0:1:0:60:46:1:0:0	0/1:116:2:1,1:80,34:114,2:0.0172:2,2:38:0:37:0:0.51424:2.33356:60:4:0.0172:0:1
    917. 

  917. 2	215632192	215632192	G	A	intronic	BARD1	.	.	.	0.45	0.3655	0.3481	0.2938	0.4073	0.3850	0.4501	0.3537	0.4131	rs5031011	rs5031011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53615058;OCCURENCE=2(haematopoietic_and_lymphoid_tissue)	250542	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU757044	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,COCA-CN|4|321|0.0124611	0.5	193	90	2	215632192	.	G	A	193	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=8;AF=0.3478;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.21598;SOR=0.61216;LSEQ=ATTTTAAAAATAATTTTTAC;RSEQ=TTGAACTACTTACACAGCAT;CSQ=A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_000465.4|protein_coding||6/10|NM_000465.4:c.1568+14C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||YES||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282543.2|protein_coding||5/9|NM_001282543.2:c.1511+14C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-14913C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-14913C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+24829C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA||5/9|NR_104212.2:n.1533+14C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA||4/8|NR_104215.2:n.1476+14C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||5/9|NR_104216.2:n.732+14C>T|||||||rs5031011&COSV53615058||-1||EntrezGene||||||2:g.215632192G>A|0.3569|0.3471|0.2866|0.3916|0.3664|0.4515|0.348|0.3397|0.3938|0.4515|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:23:8:7,1:11,4:15,8:0.3478:2,2:24.5:1:35.5:1:0.62139:2.45:60:16:0.3478:0:3.9	0/1:90:42:30,12:36,12:48,42:0.4667:2,2:37.3:1:35.8:1:0.81227:1.19756:60:41:0.4713:0:3.4
    918. 

  918. 2	215632255	215632256	CA	TG	exonic	BARD1	.	nonframeshift substitution	BARD1:NM_001282543:exon5:c.1461_1462delinsCA:p.V488M,BARD1:NM_000465:exon6:c.1518_1519delinsCA:p.V507M	0.37	.	.	.	.	.	.	.	.	rs386654966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	212134	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	234	162	2	215632255	.	CA	TG	234	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Complex;DP=68;VD=26;AF=0.3824;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.03354;SOR=0.56219;LSEQ=TAACAGCTTGACTATATCCA;RSEQ=TGCCCATTCTTGGCTGCATC;CSQ=TG|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|6/11||NM_000465.4:c.1518_1519inv|NP_000456.2:p.Val507Met|1632-1633|1518-1519|506-507|HV/HM|caTGtg/caCAtg|rs386654966||-1||EntrezGene||YES||||2:g.215632255_215632256inv||||||||||||||1,TG|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|5/10||NM_001282543.2:c.1461_1462inv|NP_001269472.1:p.Val488Met|1575-1576|1461-1462|487-488|HV/HM|caTGtg/caCAtg|rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-14977_216-14976inv|||||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-14977_159-14976inv|||||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+24765_364+24766inv|||||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|5/10||NR_104212.2:n.1483_1484inv||1483-1484|||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|4/9||NR_104215.2:n.1426_1427inv||1426-1427|||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1,TG|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|5/10||NR_104216.2:n.682_683inv||682-683|||||rs386654966||-1||EntrezGene||||||2:g.215632255_215632256inv||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:68:26:17,9:24,18:42,26:0.3824:2,2:35.3:1:36.8:1:0.61237:1.41:60:52:0.3824:0:1.7	1/0:162:85:49,36:41,35:76,85:0.5247:2,2:37.1:1:36.6:1:0.75064:1.16:60:170:0.5312:0.0247:1.6
    919. 

  919. 2	215632256	215632256	A	G	exonic	BARD1	.	synonymous SNV	BARD1:NM_001282543:exon5:c.T1461C:p.H487H,BARD1:NM_000465:exon6:c.T1518C:p.H506H	0.95	0.7658	0.6055	0.7883	0.7848	0.9543	0.8947	0.8028	0.8286	rs2070093	rs2070093	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53617490;OCCURENCE=1(urinary_tract)	181790	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU31491380	COCA-CN|5|321|0.0155763	0.5	234	162	2	215632256	.	A	G	234	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=67;VD=41;AF=0.6119;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08057;SOR=1.57377;LSEQ=AACAGCTTGACTATATCCAC;RSEQ=TGCCCATTCTTGGCTGCATC;CSQ=G|synonymous_variant|LOW|BARD1|580|Transcript|NM_000465.4|protein_coding|6/11||NM_000465.4:c.1518T>C|NP_000456.2:p.His506%3D|1632|1518|506|H|caT/caC|rs2070093&COSV53617490||-1||EntrezGene||YES||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|synonymous_variant|LOW|BARD1|580|Transcript|NM_001282543.2|protein_coding|5/10||NM_001282543.2:c.1461T>C|NP_001269472.1:p.His487%3D|1575|1461|487|H|caT/caC|rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-14977T>C|||||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-14977T>C|||||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+24765T>C|||||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|5/10||NR_104212.2:n.1483T>C||1483|||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|4/9||NR_104215.2:n.1426T>C||1426|||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|5/10||NR_104216.2:n.682T>C||682|||||rs2070093&COSV53617490||-1||EntrezGene||||||2:g.215632256A>G|0.8169|0.597|0.8158|0.827|0.9535|0.8925|0.8062|0.7931|0.8408|0.9535|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:67:41:23,18:0,0:0,41:0.6119:0,2:34.4:1:36.7:1:1:0:60:82:1:0:1.1	1/0:162:81:43,38:0,0:0,81:0.5:0,2:37.7:1:37:0:1:0:60:162:1:0:1.2
    920. 

  920. 2	215632366	215632366	T	A	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon5:c.A1351T:p.N451Y,BARD1:NM_000465:exon6:c.A1408T:p.N470Y	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	1.0	0.899	D	0.99	0.782	D	0.000	0.559	D	0.998	0.448	D	-0.335	0.035	N	-0.08	0.639	T	-5.6	0.866	D	0.441	0.498	-0.518	0.680	T	0.243	0.611	T	0.052	0.650	D	6.545	0.901	31	0.984	0.411	0.981	0.798	D	c	0.463	0.514	1.000	0.747	0.732	0.924	0	5.38	0.772	7.128	0.767	1.011	0.635	1.000	0.715	0.998	0.697	15.672	0.769	Ankyrin repeat-containing domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	150	2	215632366	.	T	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=2;AF=0.0317;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0865;SOR=inf;LSEQ=TACCTTCAGGTGCCCATGAT;RSEQ=GCAAGCTTCATGCTAATTAA;CSQ=A|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|6/11||NM_000465.4:c.1408A>T|NP_000456.2:p.Asn470Tyr|1522|1408|470|N/Y|Aat/Tat|||-1||EntrezGene||YES||||2:g.215632366T>A||||||||||||||,A|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|5/10||NM_001282543.2:c.1351A>T|NP_001269472.1:p.Asn451Tyr|1465|1351|451|N/Y|Aat/Tat|||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-15087A>T|||||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-15087A>T|||||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+24655A>T|||||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|5/10||NR_104212.2:n.1373A>T||1373|||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|4/9||NR_104215.2:n.1316A>T||1316|||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|5/10||NR_104216.2:n.572A>T||572|||||||-1||EntrezGene||||||2:g.215632366T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:63:2:1,1:24,37:61,2:0.0317:2,2:20:0:37:0:1:1.53:60:4:0.0317:0:2	0/0:150:0:0,0:49,101:150,0:0:2,0:39.2:1:36.4:1:1:0:60:149:1:0:0.4
    921. 

  921. 2	215633993	215633993	T	C	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon4:c.A1301G:p.D434G,BARD1:NM_000465:exon5:c.A1358G:p.D453G	.	.	.	.	.	.	.	.	.	.	.	0.011	0.555	D	0.998	0.899	D	0.986	0.790	D	0.000	0.843	D	1.000	0.530	D	3.29	0.905	M	-0.74	0.732	T	-4.21	0.757	D	0.906	0.908	0.396	0.890	D	0.618	0.865	D	0.135	0.818	D	6.502	0.896	31	0.999	0.957	0.987	0.853	D	c	0.787	0.721	1.000	0.448	0.732	0.924	0	5.01	0.663	7.117	0.766	0.964	0.580	1.000	0.715	0.998	0.697	15.027	0.712	Ankyrin repeat-containing domain	.	.	ID=COSV53619906;OCCURENCE=1(biliary_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	102	2	215633993	.	T	C	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.96173;SOR=0;LSEQ=CATGGTCTTTAACATTTGGA;RSEQ=CACTTCCATTTTGTAAAAGG;CSQ=C|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|5/11||NM_000465.4:c.1358A>G|NP_000456.2:p.Asp453Gly|1472|1358|453|D/G|gAt/gGt|COSV53619906||-1||EntrezGene||YES||||2:g.215633993T>C|||||||||||||1|1,C|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|4/10||NM_001282543.2:c.1301A>G|NP_001269472.1:p.Asp434Gly|1415|1301|434|D/G|gAt/gGt|COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-16714A>G|||||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-16714A>G|||||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+23028A>G|||||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|4/10||NR_104212.2:n.1323A>G||1323|||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|3/9||NR_104215.2:n.1266A>G||1266|||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|4/10||NR_104216.2:n.522A>G||522|||||COSV53619906||-1||EntrezGene||||||2:g.215633993T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:36.5:1:37:0:1:0:60:4:1:0:0	0/1:102:2:1,1:49,51:100,2:0.0196:2,2:23.5:1:37:0:1:1.04:60:4:0.0196:0:1.5
    922. 

  922. 2	215634055	215634055	C	T	intronic	BARD1	.	.	.	0.48	0.3855	0.3717	0.3110	0.4267	0.3835	0.4670	0.3754	0.4284	rs6704780	rs6704780	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53612311;OCCURENCE=2(haematopoietic_and_lymphoid_tissue)	250543	Hereditary_cancer-predisposing_syndrome|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU757049	COCA-CN|4|321|0.0124611	0.25	173	66	2	215634055	.	C	T	173	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.61194;SOR=0;LSEQ=CCCTAGAAAAATGAACAAAA;RSEQ=GGAAATTAAAAAGCATTAAG;CSQ=T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_000465.4|protein_coding||4/10|NM_000465.4:c.1315-19G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||YES||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282543.2|protein_coding||3/9|NM_001282543.2:c.1258-19G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.216-16776G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-16776G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+22966G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA||3/9|NR_104212.2:n.1280-19G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA||2/8|NR_104215.2:n.1223-19G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.479-19G>A|||||||rs6704780&COSV53612311||-1||EntrezGene||||||2:g.215634055C>T|0.3734|0.3747|0.2939|0.4151|0.3659|0.4688|0.3702|0.3552|0.4006|0.4688|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:68:0:37:0:1:0:60:2:1:0:0	0/1:66:26:6,20:17,23:40,26:0.3939:2,2:44.4:1:37:0:0.1217:2.43078:60:52:0.3939:0:1.1
    923. 

  923. 2	215645313	215645313	C	T	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon3:c.G1228A:p.E410K,BARD1:NM_000465:exon4:c.G1285A:p.E429K	.	.	.	.	.	.	.	.	.	rs878853998	.	0.004	0.654	D	0.989	0.609	D	0.982	0.739	D	0.000	0.843	D	1.000	0.548	D	0.275	0.100	N	-0.14	0.650	T	-3.11	0.636	D	0.845	0.850	-0.456	0.702	T	0.224	0.589	T	0.062	0.687	D	7.452	0.951	34	0.998	0.879	0.969	0.715	D	c	0.363	0.452	1.000	0.473	0.563	0.310	0	5.24	0.728	5.138	0.644	0.935	0.490	1.000	0.715	1.000	0.888	18.818	0.920	Ankyrin repeat-containing domain	.	.	.	238633	Familial_cancer_of_breast	MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	209	2	215645313	.	C	T	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=120;VD=2;AF=0.0167;SHIFT3=3;MSI=2;MSILEN=2;SSF=0.13233;SOR=inf;LSEQ=AGCAATATGGAGCAAAGTCT;RSEQ=TCCTCTATGATTTCTTTTCA;CSQ=T|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.1285G>A|NP_000456.2:p.Glu429Lys|1399|1285|429|E/K|Gag/Aag|rs878853998||-1||EntrezGene||YES||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.1228G>A|NP_001269472.1:p.Glu410Lys|1342|1228|410|E/K|Gag/Aag|rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16472G>A|||||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-28034G>A|||||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11708G>A|||||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.1250G>A||1250|||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.1193G>A||1193|||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.479-11277G>A|||||||rs878853998||-1||EntrezGene||||||2:g.215645313C>T||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:120:2:1,1:83,35:118,2:0.0167:2,2:6:0:37:0:0.51176:2.35233:60:4:0.0169:0:1	0/0:209:0:0,0:132,77:209,0:0:2,0:36.7:1:36.8:1:1:0:60:418:1:0:0
    924. 

  924. 2	215645345	215645345	G	T	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon3:c.C1196A:p.P399H,BARD1:NM_000465:exon4:c.C1253A:p.P418H	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	1.0	0.899	D	0.994	0.807	D	0.000	0.463	D	1	0.090	N	2.455	0.715	M	-0.05	0.634	T	-2.74	0.582	D	0.224	0.314	-0.544	0.670	T	0.395	0.748	T	0.035	0.563	D	3.097	0.432	22.5	0.994	0.620	0.861	0.451	D	c	0.343	0.234	0.535	0.212	0.672	0.522	0	4.35	0.513	3.703	0.543	0.980	0.597	0.994	0.380	0.004	0.083	12.969	0.577	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	240	2	215645345	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=198;VD=2;AF=0.0101;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.20379;SOR=inf;LSEQ=TTCTTTTCACAGCCATATTG;RSEQ=GCAACAGCTTCATTGCTGAG;CSQ=T|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.1253C>A|NP_000456.2:p.Pro418His|1367|1253|418|P/H|cCc/cAc|||-1||EntrezGene||YES||||2:g.215645345G>T||||||||||||||,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.1196C>A|NP_001269472.1:p.Pro399His|1310|1196|399|P/H|cCc/cAc|||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16440C>A|||||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-28066C>A|||||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11676C>A|||||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.1218C>A||1218|||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.1161C>A||1161|||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.479-11309C>A|||||||||-1||EntrezGene||||||2:g.215645345G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:198:2:1,1:133,63:196,2:0.0101:2,2:25:1:37:0:0.5431:2.10246:60:4:0.0103:0:1.5	0/0:240:0:0,0:140,100:240,0:0:2,0:38.9:1:36.3:1:1:0:60:47:1:0:0.1
    925. 

  925. 2	215645464	215645464	C	G	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon3:c.G1077C:p.R359S,BARD1:NM_000465:exon4:c.G1134C:p.R378S	0.69	0.5519	0.4006	0.4376	0.5894	0.3851	0.6827	0.6283	0.6214	rs2229571	rs2229571	0.174	0.225	T	0.024	0.188	B	0.005	0.162	B	0.079	0.210	N	1	0.090	P	1.67	0.430	L	-0.67	0.725	T	-0.31	0.121	N	0.117	0.354	-0.921	0.454	T	0.000	0.000	T	.	.	.	0.673	0.158	8.652	0.897	0.184	0.121	0.168	N	c	-1.031	-1.061	0.007	0.115	0.672	0.522	0	-1.03	0.095	-0.395	0.073	0.935	0.490	0.000	0.063	0.050	0.164	2.531	0.044	.	ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000229267.2|ENSG00000138376.6|ENSG00000229267.2|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6	Adipose_Subcutaneous|Artery_Aorta|Artery_Tibial|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Cells_Transformed_fibroblasts|Heart_Left_Ventricle|Lung|Muscle_Skeletal|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Thyroid	ID=COSV53612030;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue),1(lung)	152483	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	1	0	1	0	MU152809	LICA-CN|2|402|0.00497512,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	269	331	2	215645464	.	C	G	269	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=369;VD=169;AF=0.458;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.3547;SOR=1.07061;LSEQ=TCGGACATGTTACTGTTTTT;RSEQ=CTCCCTGATGTACCACCAAC;CSQ=G|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.1134G>C|NP_000456.2:p.Arg378Ser|1248|1134|378|R/S|agG/agC|rs2229571&CM076014&COSV53612030||-1||EntrezGene||YES||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.1077G>C|NP_001269472.1:p.Arg359Ser|1191|1077|359|R/S|agG/agC|rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16321G>C|||||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-28185G>C|||||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11557G>C|||||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.1099G>C||1099|||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.1042G>C||1042|||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1,G|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.479-11428G>C|||||||rs2229571&CM076014&COSV53612030||-1||EntrezGene||||||2:g.215645464C>G|0.5436|0.3976|0.4125|0.5851|0.3645|0.6927|0.6166|0.5539|0.4846|0.6927|gnomAD_FIN|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:369:169:92,77:100,100:200,169:0.458:2,2:35.2:1:36.4:1:0.40482:1.19:60:83.5:0.4588:0:1.1	0/1:331:146:77,69:102,83:185,146:0.4411:2,2:38.2:1:36.3:1:0.73905:1.10091:60:145:0.4394:0:1.1
    926. 

  926. 2	215645545	215645545	C	G	exonic	BARD1	.	synonymous SNV	BARD1:NM_001282543:exon3:c.G996C:p.T332T,BARD1:NM_000465:exon4:c.G1053C:p.T351T	0.24	0.1838	0.1721	0.2053	0.2148	0.1391	0.1418	0.2041	0.1748	rs2070096	rs2070096	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53608946;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue),1(lung)	151739	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU154678	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.25	272	352	2	215645545	.	C	G	272	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=369;VD=178;AF=0.4824;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGTATATTTTCTGAGGGCAC;RSEQ=GTTTGCTTAACAAAATCTCC;CSQ=G|synonymous_variant|LOW|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.1053G>C|NP_000456.2:p.Thr351%3D|1167|1053|351|T|acG/acC|rs2070096&COSV53608946||-1||EntrezGene||YES||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|synonymous_variant|LOW|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.996G>C|NP_001269472.1:p.Thr332%3D|1110|996|332|T|acG/acC|rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16240G>C|||||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.159-28266G>C|||||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11476G>C|||||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.1018G>C||1018|||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.961G>C||961|||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1,G|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11476G>C|||||||rs2070096&COSV53608946||-1||EntrezGene||||||2:g.215645545C>G|0.2061|0.1623|0.2302|0.2429|0.162|0.1286|0.2135|0.2136|0.2426|0.2444|SAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:369:178:71,107:90,101:191,178:0.4824:2,2:36.5:1:36.4:1:0.17309:1.34182:60:177:0.4849:0:1.1	0/0:352:0:0,0:171,181:352,0:0:2,0:40.4:1:36.5:1:1:0:60:175:1:0:0.2
    927. 

  927. 2	215645740	215645740	T	C	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon3:c.A801G:p.I267M,BARD1:NM_000465:exon4:c.A858G:p.I286M	0.	.	.	.	.	.	.	.	.	rs772845446	.	0.144	0.252	T	0.93	0.498	P	0.459	0.446	P	0.048	0.233	N	1.000	0.090	N	2.38	0.688	M	-0.75	0.733	T	-0.99	0.262	N	0.057	0.112	-0.797	0.554	T	0.234	0.600	T	0.020	0.422	T	2.282	0.335	18.05	0.988	0.464	0.052	0.109	N	c	-0.524	-0.700	0.015	0.127	0.563	0.310	0	-4.53	0.032	-0.662	0.054	1.061	0.807	0.000	0.063	0.993	0.574	0.256	0.002	.	.	.	.	616562	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	37	383	2	215645740	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=156;VD=2;AF=0.0128;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.08338;SOR=inf;LSEQ=CTCTTAGTGTCTGGAGACTC;RSEQ=ATTTGCTCAGCCAATGGTAA;CSQ=C|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.858A>G|NP_000456.2:p.Ile286Met|972|858|286|I/M|atA/atG|rs772845446||-1||EntrezGene||YES||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.801A>G|NP_001269472.1:p.Ile267Met|915|801|267|I/M|atA/atG|rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16045A>G|||||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28396A>G|||||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11281A>G|||||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.823A>G||823|||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.766A>G||766|||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1,C|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11281A>G|||||||rs772845446||-1||EntrezGene||||||2:g.215645740T>C|4.013e-06|0|0|0|0|0|8.879e-06|0|0|8.879e-06|gnomAD_NFE|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:156:2:1,1:84,70:154,2:0.0128:2,2:51.5:1:37:0:1:1.19859:60:4:0.0132:0:1	0/0:383:0:0,0:206,176:382,0:0:2,0:36.6:1:36:1:1:0:60:46.75:1:0:0.1
    928. 

  928. 2	215645745	215645745	G	A	exonic	BARD1	.	stopgain	BARD1:NM_001282543:exon3:c.C796T:p.Q266X,BARD1:NM_000465:exon4:c.C853T:p.Q285X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.027	0.259	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.922	0.971	37	0.998	0.910	0.924	0.554	D	c	0.888	0.739	0.098	0.163	0.563	0.310	0	4.68	0.582	3.625	0.537	1.048	0.713	0.941	0.324	0.990	0.544	15.758	0.777	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	385	2	215645745	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=158;VD=2;AF=0.0127;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.08429;SOR=inf;LSEQ=AGTGTCTGGAGACTCTATTT;RSEQ=CTCAGCCAATGGTAAAGAGA;CSQ=A|stop_gained|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.853C>T|NP_000456.2:p.Gln285Ter|967|853|285|Q/*|Caa/Taa|||-1||EntrezGene||YES||||2:g.215645745G>A||||||||||||||,A|stop_gained|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.796C>T|NP_001269472.1:p.Gln266Ter|910|796|266|Q/*|Caa/Taa|||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16040C>T|||||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28391C>T|||||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11276C>T|||||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.818C>T||818|||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.761C>T||761|||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11276C>T|||||||||-1||EntrezGene||||||2:g.215645745G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:158:2:1,1:87,69:156,2:0.0127:2,2:7:0:37:0:1:1.259:60:4:0.0128:0:1	0/0:385:0:0,0:207,178:385,0:0:2,0:37:1:36.2:1:1:0:60:41.778:1:0:0.1
    929. 

  929. 2	215645753	215645753	A	T	exonic	BARD1	.	stopgain	BARD1:NM_001282543:exon3:c.T788A:p.L263X,BARD1:NM_000465:exon4:c.T845A:p.L282X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.057	0.225	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.583	0.985	39	0.991	0.515	0.766	0.373	D	c	0.714	0.532	0.029	0.139	0.707	0.730	0	4.45	0.532	3.357	0.517	1.199	0.960	0.155	0.235	0.998	0.697	10.366	0.430	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	387	2	215645753	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=167;VD=2;AF=0.012;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.09049;SOR=inf;LSEQ=GAGACTCTATTTGCTCAGCC;RSEQ=ATGGTAAAGAGACTTCAGTT;CSQ=T|stop_gained|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.845T>A|NP_000456.2:p.Leu282Ter|959|845|282|L/*|tTg/tAg|||-1||EntrezGene||YES||||2:g.215645753A>T||||||||||||||,T|stop_gained|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.788T>A|NP_001269472.1:p.Leu263Ter|902|788|263|L/*|tTg/tAg|||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+16032T>A|||||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28383T>A|||||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11268T>A|||||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.810T>A||810|||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.753T>A||753|||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11268T>A|||||||||-1||EntrezGene||||||2:g.215645753A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:167:2:1,1:91,74:165,2:0.012:2,2:53:1:37:0:1:1.22819:60:4:0.0122:0:1	0/0:387:0:0,0:201,184:385,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    930. 

  930. 2	215645807	215645807	C	-	exonic	BARD1	.	frameshift deletion	BARD1:NM_001282543:exon3:c.734delG:p.G245Afs*3,BARD1:NM_000465:exon4:c.791delG:p.G264Afs*3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	405	2	215645806	.	GC	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=192;VD=2;AF=0.0104;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.10307;SOR=inf;LSEQ=CATTCAGATTCTGTCAAGGA;RSEQ=CACTTGCTAGTAAGTCTATT;CSQ=-|frameshift_variant|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.791del|NP_000456.2:p.Gly264AlafsTer3|905|791|264|G/X|gGc/gc|COSV53608844||-1||EntrezGene||YES||||2:g.215645808del|||||||||||||1|1,-|frameshift_variant|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.734del|NP_001269472.1:p.Gly245AlafsTer3|848|734|245|G/X|gGc/gc|COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+15978del|||||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28329del|||||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11214del|||||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.756del||756|||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.699del||699|||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1,-|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11214del|||||||COSV53608844||-1||EntrezGene||||||2:g.215645808del|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:192:2:1,1:105,85:190,2:0.0104:2,2:8:1:37:1:1:1.23392:60:4:0.0105:0.0052:0	0/0:405:0:0,0:191,212:403,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    931. 

  931. 2	215645991	215645991	C	A	exonic	BARD1	.	stopgain	BARD1:NM_001282543:exon3:c.G550T:p.G184X,BARD1:NM_000465:exon4:c.G607T:p.G203X	.	.	.	.	.	.	.	.	.	rs730881415	.	.	.	.	.	.	.	.	.	.	0.624	0.058	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.924	0.292	15.73	0.761	0.110	0.085	0.142	N	c	-0.953	-1.312	0.124	0.170	0.719	0.830	0	-4.6	0.031	-0.480	0.066	-1.698	0.008	0.000	0.063	0.033	0.150	8.351	0.313	.	.	.	.	179964	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Pathogenic	Pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	190	2	215645991	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=253;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1834;SOR=0;LSEQ=TTTCTTTTTTTGCTTTTTTC;RSEQ=AGATCTTGCAGAAGCCTTTT;CSQ=A|stop_gained|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.607G>T|NP_000456.2:p.Gly203Ter|721|607|203|G/*|Gga/Tga|rs730881415&CM1617018||-1||EntrezGene||YES||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|stop_gained|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.550G>T|NP_001269472.1:p.Gly184Ter|664|550|184|G/*|Gga/Tga|rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+15794G>T|||||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28145G>T|||||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11030G>T|||||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.572G>T||572|||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.515G>T||515|||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11030G>T|||||||rs730881415&CM1617018||-1||EntrezGene||||||2:g.215645991C>A||||||||||||pathogenic||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:253:0:0,0:117,136:253,0:0:2,0:34.9:1:34.9:1:1:0:60:17.071:1:0:0.1	0/1:190:2:1,1:97,90:187,2:0.0105:2,2:59.5:1:37:0:1:1.07733:60:4:0.0109:0:1
    932. 

  932. 2	215646008	215646008	T	-	exonic	BARD1	.	frameshift deletion	BARD1:NM_001282543:exon3:c.533delA:p.K178Rfs*15,BARD1:NM_000465:exon4:c.590delA:p.K197Rfs*15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	52	212	2	215646007	.	CT	C	52	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=258;VD=3;AF=0.0116;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.16454;SOR=inf;LSEQ=TTTCCAGATCTTGCAGAAGC;RSEQ=TTTTAGCCCTCTCAGAAACA;CSQ=-|frameshift_variant|HIGH|BARD1|580|Transcript|NM_000465.4|protein_coding|4/11||NM_000465.4:c.590del|NP_000456.2:p.Lys197ArgfsTer15|704|590|197|K/X|aAg/ag|||-1||EntrezGene||YES||||2:g.215646012del||||||||||||||,-|frameshift_variant|HIGH|BARD1|580|Transcript|NM_001282543.2|protein_coding|3/10||NM_001282543.2:c.533del|NP_001269472.1:p.Lys178ArgfsTer15|647|533|178|K/X|aAg/ag|||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+15777del|||||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+28128del|||||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding||3/4|NM_001282549.2:c.364+11013del|||||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|3/10||NR_104212.2:n.555del||555|||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|2/9||NR_104215.2:n.498del||498|||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA||3/9|NR_104216.2:n.478+11013del|||||||||-1||EntrezGene||||||2:g.215646012del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:258:3:1,2:114,141:255,3:0.0116:2,2:68.7:1:33:1:1:1.61413:60:6:0.0121:0:0	0/0:212:0:0,0:116,96:212,0:0:2,0:39.2:1:34.8:1:1:0:60:22.556:1:0:0.1
    933. 

  933. 2	215657035	215657035	T	C	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_001282543:exon2:c.A293G:p.D98G,BARD1:NM_000465:exon3:c.A350G:p.D117G,BARD1:NM_001282549:exon3:c.A350G:p.D117G	.	.	.	.	.	.	.	.	.	rs876658241	.	0.407	0.102	T	0.002	0.090	B	0.001	0.040	B	0.063	0.221	N	1	0.090	N	1.225	0.308	L	-0.73	0.731	T	-1.28	0.322	N	0.147	0.179	-0.955	0.401	T	0.209	0.569	T	0.013	0.326	T	0.494	0.141	7.384	0.956	0.269	0.026	0.070	N	c	-0.819	-0.803	0.868	0.253	0.707	0.730	0	2.92	0.329	0.032	0.135	0.964	0.580	0.000	0.063	0.750	0.322	9.219	0.363	Zinc finger, RING/FYVE/PHD-type	.	.	.	232430	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	113	2	215657035	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.80356;SOR=0;LSEQ=TCTTACCTGACAGCTCATTG;RSEQ=CATGTAGCAAATTTCGAAGC;CSQ=C|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|3/11||NM_000465.4:c.350A>G|NP_000456.2:p.Asp117Gly|464|350|117|D/G|gAc/gGc|rs876658241||-1||EntrezGene||YES||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|2/10||NM_001282543.2:c.293A>G|NP_001269472.1:p.Asp98Gly|407|293|98|D/G|gAc/gGc|rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+4750A>G|||||||rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+17101A>G|||||||rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282549.2|protein_coding|3/5||NM_001282549.2:c.350A>G|NP_001269478.1:p.Asp117Gly|464|350|117|D/G|gAc/gGc|rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA||2/9|NR_104212.2:n.329+4750A>G|||||||rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA||1/8|NR_104215.2:n.273-10802A>G|||||||rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1,C|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|3/10||NR_104216.2:n.464A>G||464|||||rs876658241||-1||EntrezGene||||||2:g.215657035T>C|7.969e-06|0|5.807e-05|0|0|0|0|0|0|5.807e-05|gnomAD_AMR|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:13:0:0,0:8,5:13,0:0:2,0:25.5:1:37:0:1:0:60:26:1:0:0.2	0/1:113:2:1,1:65,46:111,2:0.0177:2,2:31.5:1:37:0:1:1.40862:60:4:0.0177:0:1
    934. 

  934. 2	215657183	215657183	A	-	intronic	BARD1	.	.	.	0.5	0.3164	0.3335	0.3605	0.3130	0.2098	0.2949	0.3181	0.3190	rs56130510	rs56130510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	151721	Breast_neoplasm|Malignant_tumor_of_breast|Hereditary_cancer-predisposing_syndrome	Human_Phenotype_Ontology:HP:0010623,Human_Phenotype_Ontology:HP:0100013,MONDO:MONDO:0021100,MeSH:D001943,MedGen:C1458155,SNOMED_CT:126926005|MONDO:MONDO:0007254,MedGen:C0006142,SNOMED_CT:254837009|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	131	51	2	215657182	.	TA	T	131	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=2;VD=0;AF=0;SHIFT3=15;MSI=16;MSILEN=1;SSF=0.56604;SOR=0;LSEQ=CACAATTACTTTAAAATAAT;RSEQ=AAAAAAAAAAAAAAAGCAAC;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|BARD1|580|Transcript|NM_000465.4|protein_coding||2/10|NM_000465.4:c.216-14del|||||||rs56130510&COSV53615638||-1||EntrezGene||YES||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|BARD1|580|Transcript|NM_001282543.2|protein_coding||1/9|NM_001282543.2:c.159-14del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding||2/6|NM_001282545.2:c.215+4602del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+16953del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|BARD1|580|Transcript|NM_001282549.2|protein_coding||2/4|NM_001282549.2:c.216-14del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA||2/9|NR_104212.2:n.329+4602del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA||1/8|NR_104215.2:n.273-10950del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1,-|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|BARD1|580|Transcript|NR_104216.2|misc_RNA||2/9|NR_104216.2:n.330-14del|||||||rs56130510&COSV53615638||-1||EntrezGene||||||2:g.215657198del|0.4229|0.4262|0.4157|0.4309|0.4512|0.4035|0.4183|0.4249|0.4341|0.499|SAS|uncertain_significance&benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,0:1,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:51:13:5,8:13,25:38,13:0.2549:2,2:40.9:1:35.5:1:1:1.2:60:12:0.24:0.0392:1
    935. 

  935. 2	215661788	215661788	C	T	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_000465:exon2:c.G212A:p.C71Y,BARD1:NM_001282545:exon2:c.G212A:p.C71Y,BARD1:NM_001282549:exon2:c.G212A:p.C71Y	.	.	.	.	.	.	.	.	.	.	.	0.004	0.912	D	0.996	0.670	D	0.831	0.578	P	0.000	0.843	D	1.000	0.810	D	4.44	0.988	H	-5.71	0.993	D	-7.17	0.941	D	0.978	0.991	1.036	0.978	D	0.986	0.996	D	0.820	0.986	D	5.589	0.761	26.5	0.932	0.223	0.954	0.643	D	c	0.825	0.725	1.000	0.747	0.706	0.609	0	5.68	0.880	4.841	0.623	0.892	0.403	1.000	0.715	0.996	0.625	19.773	0.964	Zinc finger, RING-type|Zinc finger, RING-type, conserved site|Zinc finger, RING/FYVE/PHD-type;Zinc finger, RING/FYVE/PHD-type	.	.	.	966623	Familial_cancer_of_breast	MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_single_submitter	Pathogenic	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	135	2	215661788	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.89087;SOR=0;LSEQ=AAACCGTAATTACTTACCTA;RSEQ=AGAAGATGTGCTCACATCCT;CSQ=T|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|2/11||NM_000465.4:c.212G>A|NP_000456.2:p.Cys71Tyr|326|212|71|C/Y|tGt/tAt|CM1512788||-1||EntrezGene||YES||||2:g.215661788C>T||||||||||||||1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282543.2|protein_coding||1/9|NM_001282543.2:c.159-4619G>A|||||||CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282545.2|protein_coding|2/7||NM_001282545.2:c.212G>A|NP_001269474.1:p.Cys71Tyr|326|212|71|C/Y|tGt/tAt|CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|intron_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding||1/5|NM_001282548.2:c.158+12348G>A|||||||CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282549.2|protein_coding|2/5||NM_001282549.2:c.212G>A|NP_001269478.1:p.Cys71Tyr|326|212|71|C/Y|tGt/tAt|CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|2/10||NR_104212.2:n.326G>A||326|||||CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|intron_variant&non_coding_transcript_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA||1/8|NR_104215.2:n.272+12348G>A|||||||CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1,T|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|2/10||NR_104216.2:n.326G>A||326|||||CM1512788||-1||EntrezGene||||||2:g.215661788C>T||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:33.6:1:32.2:1:1:0:60:7:1:0:0	0/1:135:2:1,1:69,64:133,2:0.0148:2,2:37.5:1:37:0:1:1.0775:60:4:0.015:0:1
    936. 

  936. 2	215674224	215674224	G	A	exonic	BARD1	.	nonsynonymous SNV	BARD1:NM_000465:exon1:c.C70T:p.P24S,BARD1:NM_001282543:exon1:c.C70T:p.P24S,BARD1:NM_001282545:exon1:c.C70T:p.P24S,BARD1:NM_001282548:exon1:c.C70T:p.P24S,BARD1:NM_001282549:exon1:c.C70T:p.P24S	0.49	0.3408	0.2121	0.4141	0.41	0.3779	0.4177	0.3819	0.4378	rs1048108	rs1048108	0.184	0.912	T	0.002	0.090	B	0.005	0.104	B	0.000	0.447	D	0.608	0.588	P	1.195	0.303	L	-0.72	0.849	T	-1.19	0.303	N	0.109	0.117	-1.043	0.165	T	0.000	0.000	T	.	.	.	1.242	0.214	11.97	0.997	0.825	0.263	0.227	N	c	-0.507	-0.404	1.000	0.747	0.442	0.072	0	3.1	0.346	0.990	0.290	0.880	0.385	0.726	0.286	0.116	0.195	5.315	0.151	.	ENSG00000138376.6|ENSG00000138376.6|ENSG00000229267.2|ENSG00000229267.2|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6|ENSG00000138376.6	Adipose_Subcutaneous|Artery_Aorta|Cells_EBV-transformed_lymphocytes|Cells_Transformed_fibroblasts|Heart_Atrial_Appendage|Heart_Left_Ventricle|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Testis|Thyroid	ID=COSV53608734;OCCURENCE=3(lung),1(thyroid),1(large_intestine)	181856	Hereditary_cancer-predisposing_syndrome|Familial_cancer_of_breast|not_specified	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	1	0	MU152818	LICA-CN|1|402|0.00248756,LUSC-KR|3|170|0.0176471,COCA-CN|4|321|0.0124611	0.5	285	68	2	215674224	.	G	A	285	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=445;VD=231;AF=0.5191;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.31598;SOR=0.85245;LSEQ=ACCATCCGGTTCCATGGCGG;RSEQ=CGCGGAACGAGGCTCGTTCC;CSQ=A|missense_variant|MODERATE|BARD1|580|Transcript|NM_000465.4|protein_coding|1/11||NM_000465.4:c.70C>T|NP_000456.2:p.Pro24Ser|184|70|24|P/S|Ccc/Tcc|rs1048108&CM076015&COSV53608734||-1||EntrezGene||YES||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282543.2|protein_coding|1/10||NM_001282543.2:c.70C>T|NP_001269472.1:p.Pro24Ser|184|70|24|P/S|Ccc/Tcc|rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282545.2|protein_coding|1/7||NM_001282545.2:c.70C>T|NP_001269474.1:p.Pro24Ser|184|70|24|P/S|Ccc/Tcc|rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282548.2|protein_coding|1/6||NM_001282548.2:c.70C>T|NP_001269477.1:p.Pro24Ser|184|70|24|P/S|Ccc/Tcc|rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|missense_variant|MODERATE|BARD1|580|Transcript|NM_001282549.2|protein_coding|1/5||NM_001282549.2:c.70C>T|NP_001269478.1:p.Pro24Ser|184|70|24|P/S|Ccc/Tcc|rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|1/10||NR_104212.2:n.184C>T||184|||||rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|1/9||NR_104215.2:n.184C>T||184|||||rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|1/10||NR_104216.2:n.184C>T||184|||||rs1048108&CM076015&COSV53608734||-1||EntrezGene||||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1,A|upstream_gene_variant|MODIFIER|LOC101928103|101928103|Transcript|NR_110292.1|lncRNA||||||||||rs1048108&CM076015&COSV53608734|729|1||EntrezGene||YES||||2:g.215674224G>A|0.3836|0.2213|0.4318|0.427|0.3576|0.4121|0.3775|0.3627|0.4088|0.4318|gnomAD_AMR|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:445:231:93,138:78,136:214,231:0.5191:2,2:37:1:36.4:1:0.43594:1.17:60:230:0.518:0:1.5	1/0:68:38:17,21:12,18:30,38:0.5588:2,2:36.6:1:34.7:1:0.80631:1.21:60:18:0.5455:0:1.5
    937. 

  937. 2	215674323	215674323	C	G	UTR5	BARD1	NM_001282549:c.-30G>C;NM_000465:c.-30G>C;NM_001282545:c.-30G>C;NM_001282543:c.-30G>C;NM_001282548:c.-30G>C	.	.	0.84	0.7473	0.7567	0.7976	0.7233	0.8290	0.7739	0.7243	0.75	rs1129804	rs1129804	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	287668	Familial_cancer_of_breast	MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:ORPHA227535,SNOMED_CT:254843006	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81750016	COCA-CN|5|321|0.0155763	0.75	199	21	2	215674323	.	C	G	199	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=102;VD=47;AF=0.4608;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCGGATGAAAGGCTCCTCG;RSEQ=AGAGCGGGAAGCAAGGAAGC;CSQ=G|5_prime_UTR_variant|MODIFIER|BARD1|580|Transcript|NM_000465.4|protein_coding|1/11||NM_000465.4:c.-30G>C||85|||||rs1129804||-1||EntrezGene||YES||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|5_prime_UTR_variant|MODIFIER|BARD1|580|Transcript|NM_001282543.2|protein_coding|1/10||NM_001282543.2:c.-30G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|5_prime_UTR_variant|MODIFIER|BARD1|580|Transcript|NM_001282545.2|protein_coding|1/7||NM_001282545.2:c.-30G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|5_prime_UTR_variant|MODIFIER|BARD1|580|Transcript|NM_001282548.2|protein_coding|1/6||NM_001282548.2:c.-30G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|5_prime_UTR_variant|MODIFIER|BARD1|580|Transcript|NM_001282549.2|protein_coding|1/5||NM_001282549.2:c.-30G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104212.2|misc_RNA|1/10||NR_104212.2:n.85G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104215.2|misc_RNA|1/9||NR_104215.2:n.85G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|non_coding_transcript_exon_variant|MODIFIER|BARD1|580|Transcript|NR_104216.2|misc_RNA|1/10||NR_104216.2:n.85G>C||85|||||rs1129804||-1||EntrezGene||||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1,G|upstream_gene_variant|MODIFIER|LOC101928103|101928103|Transcript|NR_110292.1|lncRNA||||||||||rs1129804|630|1||EntrezGene||YES||||2:g.215674323C>G|0.7339|0.7644|0.8147|0.7148|0.8037|0.7817|0.7082|0.7132|0.6635|0.8147|gnomAD_AMR|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:102:47:10,37:12,43:55,47:0.4608:2,2:35.3:1:35.9:1:1:1.03224:60:46:0.4646:0:3.1	1/1:21:21:2,19:0,0:0,21:1:0,2:30.8:1:34.5:1:1:0:60:9.5:1:0:2.9
    938. 

  938. 2	216212279	216212279	G	C	intronic	ATIC	.	.	.	1.	0.9255	0.9286	0.9200	0.8841	0.9963	0.8841	0.9276	0.9133	rs4673992	rs4673992	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81750181	COCA-CN|5|321|0.0155763	1	256	157	2	216212279	.	G	C	256	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=157;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGGATGGAAAACAGAAG;RSEQ=CTGCTAATCAAATACTAGAT;CSQ=C|intron_variant|MODIFIER|ATIC|471|Transcript|NM_004044.7|protein_coding||14/15|NM_004044.7:c.1503+615G>C|||||||rs4673992||1||EntrezGene||YES||||2:g.216212279G>C||||||||||1|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:157:157:84,73:0,0:0,157:1:0,2:40.1:1:36.3:1:1:0:60:77.5:1:0:1.4	1/1:157:157:93,64:0,0:0,157:1:0,2:35.7:1:35.2:1:1:0:60:21.429:1:0:1.2
    939. 

  939. 2	216212298	216212298	A	G	intronic	ATIC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	185	2	216212298	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=172;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.26784;SOR=0;LSEQ=GGCTGCTAATCAAATACTAG;RSEQ=TGGTCTTCTGAAGAGCCAAT;CSQ=G|intron_variant|MODIFIER|ATIC|471|Transcript|NM_004044.7|protein_coding||14/15|NM_004044.7:c.1503+634A>G|||||||||1||EntrezGene||YES||||2:g.216212298A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:172:0:0,0:88,84:172,0:0:2,0:42.1:1:35.7:1:1:0:60:20.5:1:0:1.3	0/1:185:2:1,1:99,84:183,2:0.0108:2,2:42.5:1:37:0:1:1.17752:60:4:0.0112:0:2
    940. 

  940. 2	216212332	216212332	T	-	intronic	ATIC	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU128857153	GACA-JP|1|585|0.0017094	0.25	37	214	2	216212331	.	GT	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=166;VD=2;AF=0.012;SHIFT3=5;MSI=6;MSILEN=1;SSF=0.19018;SOR=inf;LSEQ=GAGCCAATTGACTACCCTCA;RSEQ=TTTTTATTCAGGAGCAGGAA;CSQ=-|intron_variant|MODIFIER|ATIC|471|Transcript|NM_004044.7|protein_coding||14/15|NM_004044.7:c.1503+673del|||||||rs1488914000||1||EntrezGene||YES||||2:g.216212337del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:166:2:1,1:70,94:164,2:0.012:2,2:51:1:37:0:1:1.34:60:4:0.0121:0:4	0/0:214:0:0,0:109,105:214,0:0:2,0:41.6:1:36.2:1:1:0:60:70.333:1:0:0.9
    941. 

  941. 2	216212339	216212339	T	C	intronic	ATIC	.	.	.	0.49	0.2582	0.1226	0.3361	0.3940	0.2833	0.2735	0.3226	0.2755	rs4673993	rs4673993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52693378;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(lung)	227829	methotrexate_response_-_Efficacy	MedGen:CN236565	reviewed_by_expert_panel	drug_response	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13425296	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.25	229	212	2	216212339	.	T	C	229	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=167;VD=85;AF=0.509;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGACTACCCTCAGTTTTTTA;RSEQ=TCAGGAGCAGGAATCAACAT;CSQ=C|intron_variant|MODIFIER|ATIC|471|Transcript|NM_004044.7|protein_coding||14/15|NM_004044.7:c.1503+675T>C|||||||rs4673993&COSV52693378||1||EntrezGene||YES||||2:g.216212339T>C|0.3399|0.1176|0.3301|0.3459|0.3074|0.2743|0.3295|0.3267|0.4792|0.4908|SAS|drug_response|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:167:85:37,48:33,49:82,85:0.509:2,2:37.3:1:35.8:1:0.75407:1.14:60:84:0.506:0:1.8	0/0:212:0:0,0:104,108:212,0:0:2,0:42:1:36.5:1:1:0:60:105:1:0:0.8
    942. 

  942. 2	220437081	220437081	C	T	UTR5	INHA	NM_002191:c.-16C>T	.	.	0.25	0.1806	0.1338	0.2715	0.1921	0.2286	0.1982	0.1938	0.1725	rs35118453	rs35118453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV54727885;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	535724	not_provided	MedGen:CN517202	no_assertion_criteria_provided	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU648790	COCA-CN|3|321|0.00934579	0.25	157	0	2	220437081	.	C	T	157	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=23;AF=0.4894;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTGAGTTCCCCACTAG;RSEQ=AGGGCCAGGTGAGCTATGGT;CSQ=T|upstream_gene_variant|MODIFIER|OBSL1|23363|Transcript|NM_001173408.2|protein_coding||||||||||rs35118453&CR025436&COSV54727885|820|-1||EntrezGene||||||2:g.220437081C>T|0.1899|0.1342|0.2571|0.1714|0.1969|0.1981|0.2025|0.1933|0.0924|0.2571|gnomAD_AMR|uncertain_significance|0&0&1|1&1&1,T|upstream_gene_variant|MODIFIER|OBSL1|23363|Transcript|NM_001173431.2|protein_coding||||||||||rs35118453&CR025436&COSV54727885|820|-1||EntrezGene||||||2:g.220437081C>T|0.1899|0.1342|0.2571|0.1714|0.1969|0.1981|0.2025|0.1933|0.0924|0.2571|gnomAD_AMR|uncertain_significance|0&0&1|1&1&1,T|5_prime_UTR_variant|MODIFIER|INHA|3623|Transcript|NM_002191.4|protein_coding|1/2||NM_002191.4:c.-16C>T||50|||||rs35118453&CR025436&COSV54727885||1||EntrezGene||YES||||2:g.220437081C>T|0.1899|0.1342|0.2571|0.1714|0.1969|0.1981|0.2025|0.1933|0.0924|0.2571|gnomAD_AMR|uncertain_significance|0&0&1|1&1&1,T|upstream_gene_variant|MODIFIER|OBSL1|23363|Transcript|NM_015311.3|protein_coding||||||||||rs35118453&CR025436&COSV54727885|820|-1||EntrezGene||YES||||2:g.220437081C>T|0.1899|0.1342|0.2571|0.1714|0.1969|0.1981|0.2025|0.1933|0.0924|0.2571|gnomAD_AMR|uncertain_significance|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:47:23:11,12:11,13:24,23:0.4894:2,2:40.6:1:34.8:1:1:1.08:60:22:0.4783:0:1.2	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    943. 

  943. 2	225339005	225339005	G	A	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon15:c.C2066T:p.A689V,CUL3:NM_001257198:exon16:c.C2282T:p.A761V,CUL3:NM_003590:exon16:c.C2264T:p.A755V	.	.	.	.	.	.	.	.	.	.	.	0.057	0.390	T	0.985	0.637	D	0.687	0.604	P	0.000	0.843	D	1	0.810	D	2.505	0.732	M	-0.35	0.725	T	-2.08	0.491	N	0.651	0.669	0.187	0.857	D	0.526	0.824	D	0.121	0.803	D	4.370	0.585	24.1	0.998	0.906	0.987	0.860	D	c	0.787	0.754	1.000	0.420	0.706	0.609	0	4.76	0.600	9.602	0.976	0.953	0.551	1.000	0.715	1.000	0.888	15.996	0.799	Cullin protein, neddylation domain|Cullin, conserved site|Winged helix-turn-helix DNA-binding domain;Cullin protein, neddylation domain|Winged helix-turn-helix DNA-binding domain;Winged helix-turn-helix DNA-binding domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	162	2	225339005	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=40;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.64238;SOR=0;LSEQ=TGCGATCCTCAGGTGTTCGT;RSEQ=CCAAATATTCTCTCTCAATA;CSQ=A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|15/15||NM_001257197.2:c.2066C>T|NP_001244126.1:p.Ala689Val|2420|2066|689|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.225339005G>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|16/16||NM_001257198.2:c.2282C>T|NP_001244127.1:p.Ala761Val|2465|2282|761|A/V|gCa/gTa|||-1||EntrezGene||YES||||2:g.225339005G>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|16/16||NM_003590.5:c.2264C>T|NP_003581.1:p.Ala755Val|2618|2264|755|A/V|gCa/gTa|||-1||EntrezGene||||||2:g.225339005G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:40:0:0,0:20,20:40,0:0:2,0:42.6:1:36.7:1:1:0:60:80:1:0:0	0/1:162:2:1,1:83,77:160,2:0.0123:2,2:18:0:37:0:1:1.0774:60:4:0.0125:0:1
    944. 

  944. 2	225346646	225346646	T	C	exonic	CUL3	.	synonymous SNV	CUL3:NM_001257197:exon13:c.A1794G:p.Q598Q,CUL3:NM_001257198:exon14:c.A2010G:p.Q670Q,CUL3:NM_003590:exon14:c.A1992G:p.Q664Q	0.31	0.1837	0.2716	0.2285	0.1358	0.2708	0.1473	0.1309	0.1721	rs2070127	rs2070127	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52361484;OCCURENCE=1(stomach)	250580	Autosomal_dominant_pseudohypoaldosteronism_type_1|Pseudohypoaldosteronism_type_2E|not_specified	MONDO:MONDO:0008329,MedGen:C1449842,OMIM:177735,Orphanet:ORPHA171871|MONDO:MONDO:0013782,MedGen:C3469606,OMIM:614496,Orphanet:ORPHA300530|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU25439382	LICA-CN|1|402|0.00248756,COCA-CN|3|321|0.00934579,GACA-JP|1|585|0.0017094	0.5	227	82	2	225346646	.	T	C	227	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTAGTTTGGATGTGAA;RSEQ=TGATCATTAACTGTAAATAT;CSQ=C|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257197.2|protein_coding|13/15||NM_001257197.2:c.1794A>G|NP_001244126.1:p.Gln598%3D|2148|1794|598|Q|caA/caG|rs2070127&COSV52361484||-1||EntrezGene||||||2:g.225346646T>C|0.1842|0.2619|0.2458|0.1141|0.2742|0.1577|0.1341|0.1689|0.2659|0.3057|SAS|benign|0&1|1&1,C|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257198.2|protein_coding|14/16||NM_001257198.2:c.2010A>G|NP_001244127.1:p.Gln670%3D|2193|2010|670|Q|caA/caG|rs2070127&COSV52361484||-1||EntrezGene||YES||||2:g.225346646T>C|0.1842|0.2619|0.2458|0.1141|0.2742|0.1577|0.1341|0.1689|0.2659|0.3057|SAS|benign|0&1|1&1,C|synonymous_variant|LOW|CUL3|8452|Transcript|NM_003590.5|protein_coding|14/16||NM_003590.5:c.1992A>G|NP_003581.1:p.Gln664%3D|2346|1992|664|Q|caA/caG|rs2070127&COSV52361484||-1||EntrezGene||||||2:g.225346646T>C|0.1842|0.2619|0.2458|0.1141|0.2742|0.1577|0.1341|0.1689|0.2659|0.3057|SAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:82:82:49,33:0,0:0,82:1:0,2:40.8:1:35.8:1:1:0:60:26.333:1:0:1.2
    945. 

  945. 2	225346739	225346739	G	T	exonic	CUL3	.	synonymous SNV	CUL3:NM_001257197:exon13:c.C1701A:p.S567S,CUL3:NM_001257198:exon14:c.C1917A:p.S639S,CUL3:NM_003590:exon14:c.C1899A:p.S633S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	92	2	225346739	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.89905;SOR=0;LSEQ=GTTGGTTTACCACAGGCGAG;RSEQ=GACTGTAGGGCTCTAACAAG;CSQ=T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257197.2|protein_coding|13/15||NM_001257197.2:c.1701C>A|NP_001244126.1:p.Ser567%3D|2055|1701|567|S|tcC/tcA|||-1||EntrezGene||||||2:g.225346739G>T||||||||||||||,T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257198.2|protein_coding|14/16||NM_001257198.2:c.1917C>A|NP_001244127.1:p.Ser639%3D|2100|1917|639|S|tcC/tcA|||-1||EntrezGene||YES||||2:g.225346739G>T||||||||||||||,T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_003590.5|protein_coding|14/16||NM_003590.5:c.1899C>A|NP_003581.1:p.Ser633%3D|2253|1899|633|S|tcC/tcA|||-1||EntrezGene||||||2:g.225346739G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:3,2:5,0:0:2,0:44.8:1:37:0:1:0:60:10:1:0:0	0/1:92:2:1,1:42,48:90,2:0.0217:2,2:9.5:1:37:0:1:1.14:60:4:0.0217:0:1
    946. 

  946. 2	225360696	225360696	T	A	intronic	CUL3	.	.	.	0.0035	9.693e-05	0.0002	0.0012	0	0	0	0	0	rs544483610	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	149	2	225360696	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=2;MSI=7;MSILEN=1;SSF=0.88898;SOR=0;LSEQ=CCATCTTCCTGTTTCATTTT;RSEQ=AAAAAAATATAAACAAAGAC;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|CUL3|8452|Transcript|NM_001257197.2|protein_coding||11/14|NM_001257197.2:c.1510-13A>T|||||||rs544483610||-1||EntrezGene||||||2:g.225360696T>A|3.283e-05|0.0002489|6.116e-05|0|5.586e-05|0|0|0|3.439e-05|0.0008|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|CUL3|8452|Transcript|NM_001257198.2|protein_coding||12/15|NM_001257198.2:c.1726-13A>T|||||||rs544483610||-1||EntrezGene||YES||||2:g.225360696T>A|3.283e-05|0.0002489|6.116e-05|0|5.586e-05|0|0|0|3.439e-05|0.0008|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|CUL3|8452|Transcript|NM_003590.5|protein_coding||12/15|NM_003590.5:c.1708-13A>T|||||||rs544483610||-1||EntrezGene||||||2:g.225360696T>A|3.283e-05|0.0002489|6.116e-05|0|5.586e-05|0|0|0|3.439e-05|0.0008|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:4,5:9,0:0:2,0:37.3:1:37:0:1:0:60:18:1:0:0	0/1:149:2:1,1:58,89:147,2:0.0134:2,2:40:1:37:0:1:1.53:60:4:0.0134:0:1
    947. 

  947. 2	225362478	225362478	C	T	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon11:c.G1501A:p.V501I,CUL3:NM_001257198:exon12:c.G1717A:p.V573I,CUL3:NM_003590:exon12:c.G1699A:p.V567I	0.28	0.0855	0.0310	0.1902	0.0861	0.2714	0.0921	0.0872	0.1255	rs3738952	rs3738952	0.192	0.210	T	0.0	0.026	B	0.002	0.158	B	0.000	0.559	D	0.000	0.506	P	0.69	0.170	N	-0.76	0.734	T	-0.27	0.114	N	0.06	0.211	-1.111	0.029	T	0.000	0.000	T	.	.	.	3.432	0.471	23.0	0.990	0.502	0.890	0.489	D	c	-0.118	0.156	0.993	0.330	0.732	0.924	0	6.16	0.993	2.693	0.464	0.935	0.490	1.000	0.715	1.000	0.888	20.860	0.998	Cullin homology|Cullin, N-terminal	ENSG00000228446.2|ENSG00000228446.2|ENSG00000228446.2|ENSG00000228446.2|ENSG00000036257.8|ENSG00000228446.2|ENSG00000228446.2|ENSG00000228446.2	Adipose_Subcutaneous|Cells_Transformed_fibroblasts|Colon_Transverse|Esophagus_Muscularis|Muscle_Skeletal|Muscle_Skeletal|Skin_Sun_Exposed_Lower_leg|Thyroid	ID=COSV52361494;OCCURENCE=1(breast),1(lung)	250581	Autosomal_dominant_pseudohypoaldosteronism_type_1|Pseudohypoaldosteronism_type_2E|not_specified	MONDO:MONDO:0008329,MedGen:C1449842,OMIM:177735,Orphanet:ORPHA171871|MONDO:MONDO:0013782,MedGen:C3469606,OMIM:614496,Orphanet:ORPHA300530|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU80665581	LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.75	257	149	2	225362478	.	C	T	257	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=6;AF=0.4615;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCAATATTTACCTTTTTAA;RSEQ=TGGTCCATAAAATGTGGCAT;CSQ=T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|11/15||NM_001257197.2:c.1501G>A|NP_001244126.1:p.Val501Ile|1855|1501|501|V/I|Gtt/Att|rs3738952&COSV52361494||-1||EntrezGene||||||2:g.225362478C>T|0.1313|0.02554|0.2117|0.06413|0.2701|0.09713|0.09502|0.1274|0.1952|0.2701|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|12/16||NM_001257198.2:c.1717G>A|NP_001244127.1:p.Val573Ile|1900|1717|573|V/I|Gtt/Att|rs3738952&COSV52361494||-1||EntrezGene||YES||||2:g.225362478C>T|0.1313|0.02554|0.2117|0.06413|0.2701|0.09713|0.09502|0.1274|0.1952|0.2701|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|12/16||NM_003590.5:c.1699G>A|NP_003581.1:p.Val567Ile|2053|1699|567|V/I|Gtt/Att|rs3738952&COSV52361494||-1||EntrezGene||||||2:g.225362478C>T|0.1313|0.02554|0.2117|0.06413|0.2701|0.09713|0.09502|0.1274|0.1952|0.2701|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:13:6:3,3:4,3:7,6:0.4615:2,2:36:1:35:1:1:1.30401:60:12:0.5455:0:1	1/1:149:149:89,60:0,0:0,149:1:0,2:37.1:1:35.6:1:1:0:60:28.8:1:0:1.1
    948. 

  948. 2	225362536	225362536	C	T	exonic	CUL3	.	synonymous SNV	CUL3:NM_001257197:exon11:c.G1443A:p.Q481Q,CUL3:NM_001257198:exon12:c.G1659A:p.Q553Q,CUL3:NM_003590:exon12:c.G1641A:p.Q547Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	25	184	2	225362536	.	C	T	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.83761;SOR=0;LSEQ=ATATGATGCTGGAGTGTGAG;RSEQ=TGTCGACCACTGTGTTTGGC;CSQ=T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257197.2|protein_coding|11/15||NM_001257197.2:c.1443G>A|NP_001244126.1:p.Gln481%3D|1797|1443|481|Q|caG/caA|||-1||EntrezGene||||||2:g.225362536C>T||||||||||||||,T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_001257198.2|protein_coding|12/16||NM_001257198.2:c.1659G>A|NP_001244127.1:p.Gln553%3D|1842|1659|553|Q|caG/caA|||-1||EntrezGene||YES||||2:g.225362536C>T||||||||||||||,T|synonymous_variant|LOW|CUL3|8452|Transcript|NM_003590.5|protein_coding|12/16||NM_003590.5:c.1641G>A|NP_003581.1:p.Gln547%3D|1995|1641|547|Q|caG/caA|||-1||EntrezGene||||||2:g.225362536C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:17:0:0,0:9,8:17,0:0:2,0:45.4:1:34.8:1:1:0:60:16:1:0:0.8	0/1:184:2:1,1:85,97:182,2:0.0109:2,2:56:1:25:0:1:1.14:60:4:0.0109:0:1.5
    949. 

  949. 2	225365056	225365056	A	G	intronic	CUL3	.	.	.	0.31	0.1836	0.2724	0.2303	0.1325	0.2695	0.1474	0.1305	0.1684	rs3768889	rs3768889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52361608;OCCURENCE=1(breast),1(bone)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU80665600	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.75	287	237	2	225365056	.	A	G	287	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=91;VD=46;AF=0.5055;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACTTACTTGTACACAGTG;RSEQ=TACAAAGTCTGATTTTGATT;CSQ=G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||10/14|NM_001257197.2:c.1412+24T>C|||||||rs3768889&COSV52361608||-1||EntrezGene||||||2:g.225365056A>G|0.1841|0.2625|0.2402|0.1106|0.2707|0.1573|0.1333|0.1697|0.2616|0.3057|SAS||0&1|0&1,G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257198.2|protein_coding||11/15|NM_001257198.2:c.1628+24T>C|||||||rs3768889&COSV52361608||-1||EntrezGene||YES||||2:g.225365056A>G|0.1841|0.2625|0.2402|0.1106|0.2707|0.1573|0.1333|0.1697|0.2616|0.3057|SAS||0&1|0&1,G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_003590.5|protein_coding||11/15|NM_003590.5:c.1610+24T>C|||||||rs3768889&COSV52361608||-1||EntrezGene||||||2:g.225365056A>G|0.1841|0.2625|0.2402|0.1106|0.2707|0.1573|0.1333|0.1697|0.2616|0.3057|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:91:46:28,18:27,18:45,46:0.5055:2,2:26.6:1:37:0:1:1.04:60:92:0.5111:0:1	1/1:237:237:164,73:0,0:0,237:1:0,2:38:1:36.4:1:1:0:60:117.5:1:0:1.1
    950. 

  950. 2	225365083	225365083	C	T	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon10:c.G1409A:p.R470K,CUL3:NM_001257198:exon11:c.G1625A:p.R542K,CUL3:NM_003590:exon11:c.G1607A:p.R536K	.	.	.	.	.	.	.	.	.	.	.	0.731	0.043	T	0.001	0.067	B	0.003	0.104	B	0.000	0.843	D	1	0.810	D	-0.13	0.045	N	-0.64	0.721	T	0.11	0.069	N	0.6	0.649	-0.848	0.521	T	0.139	0.458	T	0.049	0.635	D	2.604	0.374	20.2	0.894	0.182	0.990	0.891	D	c	-0.214	0.098	1.000	0.747	0.732	0.924	0	6.03	0.978	7.539	0.808	0.935	0.490	1.000	0.715	1.000	0.888	20.567	0.994	Cullin homology|Cullin, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	302	2	225365083	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=150;VD=2;AF=0.0133;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.10964;SOR=inf;LSEQ=GTCTGATTTTGATTTACCTT;RSEQ=TGAATATCTCAAAAGCATGT;CSQ=T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|10/15||NM_001257197.2:c.1409G>A|NP_001244126.1:p.Arg470Lys|1763|1409|470|R/K|aGa/aAa|||-1||EntrezGene||||||2:g.225365083C>T||||||||||||||,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|11/16||NM_001257198.2:c.1625G>A|NP_001244127.1:p.Arg542Lys|1808|1625|542|R/K|aGa/aAa|||-1||EntrezGene||YES||||2:g.225365083C>T||||||||||||||,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|11/16||NM_003590.5:c.1607G>A|NP_003581.1:p.Arg536Lys|1961|1607|536|R/K|aGa/aAa|||-1||EntrezGene||||||2:g.225365083C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:150:2:1,1:83,65:148,2:0.0133:2,2:21:0:37:0:1:1.27482:60:4:0.0134:0:1	0/0:302:0:0,0:183,119:302,0:0:2,0:40:1:36:1:1:0:60:49.333:1:0:0.9
    951. 

  951. 2	225365228	225365228	T	A	intronic	CUL3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	213	2	225365228	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=87;VD=2;AF=0.023;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.08341;SOR=inf;LSEQ=TGTAAAACAGAAAGAGATAT;RSEQ=CCCCTCAAAATTAACTAGGA;CSQ=A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||9/14|NM_001257197.2:c.1288-24A>T|||||||||-1||EntrezGene||||||2:g.225365228T>A||||||||||||||,A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257198.2|protein_coding||10/15|NM_001257198.2:c.1504-24A>T|||||||||-1||EntrezGene||YES||||2:g.225365228T>A||||||||||||||,A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_003590.5|protein_coding||10/15|NM_003590.5:c.1486-24A>T|||||||||-1||EntrezGene||||||2:g.225365228T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:87:2:1,1:31,54:85,2:0.023:2,2:46.5:1:37:0:1:1.73:60:4:0.0233:0:1	0/0:213:0:0,0:63,150:213,0:0:2,0:36:1:36.3:1:1:0:60:52.25:1:0:0.2
    952. 

  952. 2	225365232	225365232	C	A	intronic	CUL3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	205	2	225365232	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=81;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.36673;SOR=0;LSEQ=AAACAGAAAGAGATATTCCC;RSEQ=TCAAAATTAACTAGGATTTG;CSQ=A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||9/14|NM_001257197.2:c.1288-28G>T|||||||||-1||EntrezGene||||||2:g.225365232C>A||||||||||||||,A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257198.2|protein_coding||10/15|NM_001257198.2:c.1504-28G>T|||||||||-1||EntrezGene||YES||||2:g.225365232C>A||||||||||||||,A|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_003590.5|protein_coding||10/15|NM_003590.5:c.1486-28G>T|||||||||-1||EntrezGene||||||2:g.225365232C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:81:0:0,0:29,52:81,0:0:2,0:26.7:1:36.7:1:1:0:60:162:1:0:0	0/1:205:3:1,2:59,143:202,3:0.0146:2,2:32.7:1:28.3:1:1:1.21:60:2:0.0099:0:1.7
    953. 

  953. 2	225367752	225367752	C	A	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon9:c.G1217T:p.G406V,CUL3:NM_001257198:exon10:c.G1433T:p.G478V,CUL3:NM_003590:exon10:c.G1415T:p.G472V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.996	0.875	D	0.000	0.843	D	1	0.810	D	3.22	0.896	M	-0.69	0.727	T	-7.14	0.955	D	0.965	0.967	0.380	0.888	D	0.645	0.876	D	0.069	0.708	D	7.175	0.944	34	0.998	0.886	0.991	0.917	D	c	1.009	0.967	1.000	0.747	0.707	0.730	0	6.03	0.978	7.568	0.814	0.935	0.490	1.000	0.715	1.000	0.888	20.557	0.993	Cullin homology|Cullin, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	129	2	225367752	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=15;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.80186;SOR=0;LSEQ=TGCTCATATCCCTAAACATT;RSEQ=CTTCCAGTTTTGACGTGAAC;CSQ=A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|9/15||NM_001257197.2:c.1217G>T|NP_001244126.1:p.Gly406Val|1571|1217|406|G/V|gGa/gTa|||-1||EntrezGene||||||2:g.225367752C>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|10/16||NM_001257198.2:c.1433G>T|NP_001244127.1:p.Gly478Val|1616|1433|478|G/V|gGa/gTa|||-1||EntrezGene||YES||||2:g.225367752C>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|10/16||NM_003590.5:c.1415G>T|NP_003581.1:p.Gly472Val|1769|1415|472|G/V|gGa/gTa|||-1||EntrezGene||||||2:g.225367752C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:7,8:15,0:0:2,0:44.3:1:37:0:1:0:60:30:1:0:0.4	0/1:129:2:1,1:58,69:127,2:0.0155:2,2:53:0:37:0:1:1.19:60:4:0.0157:0:1
    954. 

  954. 2	225371555	225371555	A	G	intronic	CUL3	.	.	.	0.	.	.	.	.	.	.	.	.	rs780192374	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	118	2	225371555	.	A	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.96681;SOR=0;LSEQ=CCTTTATCATAAACACAGAG;RSEQ=ATCTTCTGGGTTTACTTACC;CSQ=G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||6/14|NM_001257197.2:c.831+20T>C|||||||rs780192374||-1||EntrezGene||||||2:g.225371555A>G|4.04e-06|0|0|0|0|0|8.897e-06|0|0|8.897e-06|gnomAD_NFE|||,G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257198.2|protein_coding||7/15|NM_001257198.2:c.1047+20T>C|||||||rs780192374||-1||EntrezGene||YES||||2:g.225371555A>G|4.04e-06|0|0|0|0|0|8.897e-06|0|0|8.897e-06|gnomAD_NFE|||,G|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_003590.5|protein_coding||7/15|NM_003590.5:c.1029+20T>C|||||||rs780192374||-1||EntrezGene||||||2:g.225371555A>G|4.04e-06|0|0|0|0|0|8.897e-06|0|0|8.897e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:56:1:37:0:1:0:60:4:1:0:0	0/1:118:2:1,1:84,31:115,2:0.0169:2,2:29.5:1:37:0:0.47392:2.68283:60:4:0.0172:0:1
    955. 

  955. 2	225376215	225376215	G	A	exonic	CUL3	.	stopgain	CUL3:NM_001257197:exon5:c.C541T:p.R181X,CUL3:NM_001257198:exon6:c.C757T:p.R253X,CUL3:NM_003590:exon6:c.C739T:p.R247X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.370	0.974	37	0.998	0.858	0.978	0.770	D	c	0.982	0.878	1.000	0.747	0.732	0.924	0	5.64	0.864	7.536	0.808	0.998	0.613	1.000	0.715	1.000	0.888	14.855	0.698	Cullin repeat-like-containing domain|Cullin, N-terminal	.	.	.	514460	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Likely_pathogenic	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	65	2	225376215	.	G	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.91308;SOR=0;LSEQ=GTCAAGGCAGTGCATCACTC;RSEQ=TTCTATTTCTTCATTAATTC;CSQ=A|stop_gained|HIGH|CUL3|8452|Transcript|NM_001257197.2|protein_coding|5/15||NM_001257197.2:c.541C>T|NP_001244126.1:p.Arg181Ter|895|541|181|R/*|Cga/Tga|rs201496024||-1||EntrezGene||||||2:g.225376215G>A||||||||||||likely_pathogenic||1,A|stop_gained|HIGH|CUL3|8452|Transcript|NM_001257198.2|protein_coding|6/16||NM_001257198.2:c.757C>T|NP_001244127.1:p.Arg253Ter|940|757|253|R/*|Cga/Tga|rs201496024||-1||EntrezGene||YES||||2:g.225376215G>A||||||||||||likely_pathogenic||1,A|stop_gained|HIGH|CUL3|8452|Transcript|NM_003590.5|protein_coding|6/16||NM_003590.5:c.739C>T|NP_003581.1:p.Arg247Ter|1093|739|247|R/*|Cga/Tga|rs201496024||-1||EntrezGene||||||2:g.225376215G>A||||||||||||likely_pathogenic||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:37.3:1:37:0:1:0:60:6:1:0:0	0/1:65:2:1,1:29,34:63,2:0.0308:2,2:56.5:1:37:0:1:1.17:60:4:0.0328:0:1
    956. 

  956. 2	225379394	225379394	C	A	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon3:c.G276T:p.R92S,CUL3:NM_001257198:exon4:c.G492T:p.R164S,CUL3:NM_003590:exon4:c.G474T:p.R158S	.	.	.	.	.	.	.	.	.	.	.	0.051	0.393	T	0.9	0.499	P	0.487	0.496	P	0.000	0.843	D	1.000	0.548	D	1.5	0.380	L	-0.74	0.732	T	-3.77	0.714	D	0.825	0.813	-0.535	0.674	T	0.332	0.700	T	0.028	0.513	D	3.346	0.461	22.9	0.997	0.789	0.878	0.471	D	c	0.247	0.263	0.999	0.383	0.732	0.924	0	2.97	0.333	0.950	0.285	0.935	0.490	1.000	0.715	1.000	0.888	7.377	0.258	Cullin repeat-like-containing domain|Cullin, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	147	2	225379394	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.87629;SOR=0;LSEQ=AGAGTTTGCCGTAGATGATC;RSEQ=CTAATACACCCATAACGTAC;CSQ=A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|3/15||NM_001257197.2:c.276G>T|NP_001244126.1:p.Arg92Ser|630|276|92|R/S|agG/agT|||-1||EntrezGene||||||2:g.225379394C>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|4/16||NM_001257198.2:c.492G>T|NP_001244127.1:p.Arg164Ser|675|492|164|R/S|agG/agT|||-1||EntrezGene||YES||||2:g.225379394C>A||||||||||||||,A|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|4/16||NM_003590.5:c.474G>T|NP_003581.1:p.Arg158Ser|828|474|158|R/S|agG/agT|||-1||EntrezGene||||||2:g.225379394C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:6,4:10,0:0:2,0:39.6:1:35.8:1:1:0:60:20:1:0:0	0/1:147:2:1,1:72,73:145,2:0.0136:2,2:46.5:1:37:0:1:1.01:60:4:0.0136:0:1
    957. 

  957. 2	225379486	225379486	G	T	exonic	CUL3	.	nonsynonymous SNV	CUL3:NM_001257197:exon3:c.C184A:p.R62S,CUL3:NM_001257198:exon4:c.C400A:p.R134S,CUL3:NM_003590:exon4:c.C382A:p.R128S	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.95	0.671	D	0.000	0.843	D	1	0.810	D	3.695	0.947	H	1.06	0.398	T	-5.24	0.839	D	0.923	0.923	0.030	0.829	D	0.394	0.747	T	0.066	0.698	D	6.632	0.910	32	0.998	0.894	0.970	0.717	D	c	1.025	0.951	1.000	0.747	0.732	0.924	0	6.06	0.983	5.727	0.680	1.048	0.713	1.000	0.715	1.000	0.888	15.367	0.741	Cullin repeat-like-containing domain|Cullin, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	78	2	225379486	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.88246;SOR=0;LSEQ=ATTTTGTTGTACATACACAC;RSEQ=GTCCTACAGTTAAAGTCATA;CSQ=T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257197.2|protein_coding|3/15||NM_001257197.2:c.184C>A|NP_001244126.1:p.Arg62Ser|538|184|62|R/S|Cgt/Agt|COSV52372491||-1||EntrezGene||||||2:g.225379486G>T|||||||||||||1|1,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_001257198.2|protein_coding|4/16||NM_001257198.2:c.400C>A|NP_001244127.1:p.Arg134Ser|583|400|134|R/S|Cgt/Agt|COSV52372491||-1||EntrezGene||YES||||2:g.225379486G>T|||||||||||||1|1,T|missense_variant|MODERATE|CUL3|8452|Transcript|NM_003590.5|protein_coding|4/16||NM_003590.5:c.382C>A|NP_003581.1:p.Arg128Ser|736|382|128|R/S|Cgt/Agt|COSV52372491||-1||EntrezGene||||||2:g.225379486G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:2,3:5,0:0:2,0:42.4:1:37:0:1:0:60:10:1:0:0	0/1:78:2:1,1:25,51:76,2:0.0256:2,2:37.5:1:37:0:1:2.02:60:4:0.0256:0:1
    958. 

  958. 2	225422537	225422537	C	-	exonic	CUL3	.	frameshift deletion	CUL3:NM_001257198:exon2:c.121delG:p.D41Tfs*3,CUL3:NM_003590:exon2:c.103delG:p.D35Tfs*3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	42	2	225422536	.	TC	T	37	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=3;VD=2;AF=0.6667;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.00303;SOR=inf;LSEQ=GAATTGCATTTTTCAGAAGG;RSEQ=CCAAATGCTGTTTACATATT;CSQ=-|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||1/14|NM_001257197.2:c.67-22179del|||||||||-1||EntrezGene||||||2:g.225422539del||||||||||||||,-|frameshift_variant|HIGH|CUL3|8452|Transcript|NM_001257198.2|protein_coding|2/16||NM_001257198.2:c.121del|NP_001244127.1:p.Asp41ThrfsTer3|304|121|41|D/X|Gac/ac|||-1||EntrezGene||YES||||2:g.225422539del||||||||||||||,-|frameshift_variant|HIGH|CUL3|8452|Transcript|NM_003590.5|protein_coding|2/16||NM_003590.5:c.103del|NP_003581.1:p.Asp35ThrfsTer3|457|103|35|D/X|Gac/ac|||-1||EntrezGene||||||2:g.225422539del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25:1:37:0:1:0:60:4:0.6667:0:1	0/0:42:0:0,0:27,15:42,0:0:2,0:47.7:1:36.4:1:1:0:60:41:1:0:0.3
    959. 

  959. 2	225434532	225434532	T	C	UTR5	CUL3	NM_001257198:c.-43A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	11	2	225434532	.	T	C	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTTTAGTCCTCTGTGAA;RSEQ=AATTTTCTACAAGAAAAAAT;CSQ=C|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_001257197.2|protein_coding||1/14|NM_001257197.2:c.66+15129A>G|||||||||-1||EntrezGene||||||2:g.225434532T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|CUL3|8452|Transcript|NM_001257198.2|protein_coding|1/16||NM_001257198.2:c.-43A>G||141|||||||-1||EntrezGene||YES||||2:g.225434532T>C||||||||||||||,C|intron_variant|MODIFIER|CUL3|8452|Transcript|NM_003590.5|protein_coding||1/15|NM_003590.5:c.67-11959A>G|||||||||-1||EntrezGene||||||2:g.225434532T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:11:2:1,1:1,8:9,2:0.1818:2,2:55:1:37:0:0.34545:6:60:4:0.1818:0:1
    960. 

  960. 2	227662043	227662043	T	C	exonic	IRS1	.	nonsynonymous SNV	IRS1:NM_005544:exon1:c.A1412G:p.K471R	.	.	.	.	.	.	.	.	.	.	.	0.048	0.400	D	0.993	0.637	D	0.978	0.725	D	0.000	0.497	D	0.517	0.318	D	0.55	0.145	N	0.44	0.566	T	-0.46	0.150	N	0.585	0.614	-0.624	0.639	T	0.218	0.581	T	0.021	0.433	T	2.489	0.360	19.40	0.994	0.631	0.944	0.608	D	c	0.542	0.574	1.000	0.747	0.718	0.821	0	5.38	0.772	5.558	0.668	0.964	0.580	1.000	0.715	0.645	0.297	13.963	0.635	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	0	2	227662043	.	T	C	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=2;AF=0.6667;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTCAGGGTGGAGGGCCCC;RSEQ=TGCCACCCATGCAGATATAG;CSQ=C|upstream_gene_variant|MODIFIER|RHBDD1|84236|Transcript|NM_001349069.2|protein_coding||||||||||rs763246616|2832|1||EntrezGene||YES||||2:g.227662043T>C||||||||||||||,C|missense_variant|MODERATE|IRS1|3667|Transcript|NM_005544.3|protein_coding|1/2||NM_005544.3:c.1412A>G|NP_005535.1:p.Lys471Arg|2494|1412|471|K/R|aAg/aGg|rs763246616||-1||EntrezGene||YES||||2:g.227662043T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:3:2:1,1:1,0:1,2:0.6667:0,2:18:1:37:0:1:0:60:4:0.6667:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    961. 

  961. 2	227662881	227662881	T	C	exonic	IRS1	.	nonsynonymous SNV	IRS1:NM_005544:exon1:c.A574G:p.I192V	.	.	.	.	.	.	.	.	.	.	.	0.16	0.237	T	0.984	0.588	D	0.991	0.782	D	0.000	0.629	D	1.000	0.588	D	0.52	0.136	N	-0.75	0.733	T	-0.47	0.152	N	0.345	0.406	-0.346	0.737	T	0.377	0.735	T	0.012	0.304	T	3.267	0.452	22.8	0.997	0.799	0.894	0.496	D	c	0.419	0.490	1.0	0.983	0.767	0.994	0	5.79	0.917	4.113	0.574	1.061	0.807	1.000	0.715	1.000	0.888	16.119	0.811	IRS-type PTB domain|PH domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	3	2	227662881	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.95313;SOR=inf;LSEQ=GTTCAGCTTCACGAAGCTGA;RSEQ=GGTCTTGCTGGTCAGGCAAA;CSQ=C|upstream_gene_variant|MODIFIER|RHBDD1|84236|Transcript|NM_001349069.2|protein_coding|||||||||||1994|1||EntrezGene||YES||||2:g.227662881T>C||||||||||||||,C|missense_variant|MODERATE|IRS1|3667|Transcript|NM_005544.3|protein_coding|1/2||NM_005544.3:c.574A>G|NP_005535.1:p.Ile192Val|1656|574|192|I/V|Atc/Gtc|||-1||EntrezGene||YES||||2:g.227662881T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:2:1,1:30,92:122,2:0.0161:2,2:31:1:37:0:0.43902:3.03:60:4:0.0163:0:1	0/0:3:0:0,0:0,3:3,0:0:0,0:32:1:37:0:1:0:60:6:1:0:0
    962. 

  962. 2	234580454	234580454	T	-	intronic	UGT1A10;UGT1A8	.	.	.	0.69	0.6080	0.5564	0.4827	0.5604	0.4291	0.7050	0.6383	0.6767	rs3832043	rs3832043	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	227745	SN-38_response_-_Other	MedGen:CN236455	reviewed_by_expert_panel	drug_response	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	244	166	2	234580453	.	AT	A	244	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=214;VD=97;AF=0.4533;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.12497;SOR=0.77176;LSEQ=TAAATCATTGTCAGTGACTG;RSEQ=TTTTTTTTTATGAAAGGATA;CSQ=-|intron_variant|MODIFIER|UGT1A10|54575|Transcript|NM_019075.2|protein_coding||1/4|NM_019075.2:c.855+34440del|||||||rs3832043||1||EntrezGene||YES||||2:g.234580463del||||||||||0.6892|SAS|drug_response||1,-|intron_variant|MODIFIER|UGT1A8|54576|Transcript|NM_019076.5|protein_coding||1/4|NM_019076.5:c.855+53255del|||||||rs3832043||1||EntrezGene||YES||||2:g.234580463del||||||||||0.6892|SAS|drug_response||1,-|upstream_gene_variant|MODIFIER|UGT1A9|54600|Transcript|NM_021027.3|protein_coding||||||||||rs3832043|90|1||EntrezGene||YES||||2:g.234580463del||||||||||0.6892|SAS|drug_response||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:214:97:71,26:82,32:114,97:0.4533:2,2:33.9:1:37:1:0.87788:1.07:60:194:0.4575:0.0467:0.1	1/0:166:86:60,26:57,21:78,86:0.5181:2,2:42.5:1:36.8:1:0.7301:1.17503:60:172:0.5276:0.0482:0.2
    963. 

  963. 2	234668880	234668881	AT	-	intronic	UGT1A10;UGT1A3;UGT1A4;UGT1A5;UGT1A6;UGT1A7;UGT1A8;UGT1A9	.	.	.	.	0.0219	0.0711	0.0038	0	0	0.0003	0.0029	0.0042	rs57191451	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	540563	Irinotecan_response|none_provided	MedGen:CN077989|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign,_drug_response	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU6752999	PACA-AU|3|391|0.00767263	0.5	159	226	2	234668879	.	CAT	C	159	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=522;VD=20;AF=0.0383;SHIFT3=13;MSI=7;MSILEN=2;SSF=0.53285;SOR=0.96066;LSEQ=GTGTATCGATTGGTTTTTGC;RSEQ=ATATATATATATAAGTAGGA;CSQ=-|upstream_gene_variant|MODIFIER|UGT1A1|54658|Transcript|NM_000463.3|protein_coding||||||||||rs3064744|35|1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A6|54578|Transcript|NM_001072.4|protein_coding||1/4|NM_001072.4:c.862-6787_862-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A4|54657|Transcript|NM_007120.3|protein_coding||1/4|NM_007120.3:c.868-6787_868-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A10|54575|Transcript|NM_019075.2|protein_coding||1/4|NM_019075.2:c.856-6787_856-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A8|54576|Transcript|NM_019076.5|protein_coding||1/4|NM_019076.5:c.856-6787_856-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A7|54577|Transcript|NM_019077.3|protein_coding||1/4|NM_019077.3:c.856-6787_856-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A5|54579|Transcript|NM_019078.2|protein_coding||1/4|NM_019078.2:c.868-6787_868-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A3|54659|Transcript|NM_019093.4|protein_coding||1/4|NM_019093.4:c.868-6787_868-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A9|54600|Transcript|NM_021027.3|protein_coding||1/4|NM_021027.3:c.856-6787_856-6786del|||||||rs3064744||1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|intron_variant|MODIFIER|UGT1A6|54578|Transcript|NM_205862.2|protein_coding||2/5|NM_205862.2:c.61-6787_61-6786del|||||||rs3064744||1||EntrezGene||||||2:g.234668893_234668894del||||||||||||||1,-|upstream_gene_variant|MODIFIER|LOC100286922|100286922|Transcript|NR_037694.1|transcribed_pseudogene||||||||||rs3064744|4889|-1||EntrezGene||YES||||2:g.234668893_234668894del||||||||||||||1,-|upstream_gene_variant|MODIFIER|LOC100286922|100286922|Transcript|NR_037695.1|transcribed_pseudogene||||||||||rs3064744|4889|-1||EntrezGene||||||2:g.234668893_234668894del||||||||||||||1,-|upstream_gene_variant|MODIFIER|LOC100286922|100286922|Transcript|NR_037696.1|transcribed_pseudogene||||||||||rs3064744|4889|-1||EntrezGene||||||2:g.234668893_234668894del||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:522:20:13,7:317,185:502,20:0.0383:2,2:30.9:1:37:1:1:1.08:60:40:0.0391:0.0038:0.1	0/1:226:9:5,4:140,74:214,9:0.0398:2,2:43.2:1:36.9:1:0.72289:1.51062:60:18:0.0407:0.0044:0
    964. 

  964. 2	234669144	234669144	G	A	exonic	UGT1A1	.	nonsynonymous SNV	UGT1A1:NM_000463:exon1:c.G211A:p.G71R	0.15	0.0149	0.0005	0.0227	0	0.1434	0.0426	0.0023	0.0244	rs4148323	rs4148323	0.04	0.421	D	0.127	0.581	B	0.183	0.497	B	.	.	.	0.599	0.309	P	1.39	0.351	L	0.09	0.615	T	-1.77	0.486	N	0.097	0.100	-1.081	0.071	T	0.001	0.002	T	.	.	.	4.055	0.545	23.7	0.997	0.801	0.339	0.247	N	c	-0.077	-0.054	1.000	0.500	0.487	0.133	0	5.14	0.699	3.900	0.558	1.048	0.713	0.572	0.273	0.951	0.427	7.612	0.271	.	.	.	ID=COSV59383881;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),3(lung),1(large_intestine)	27319	Gilbert_syndrome|Lucey-Driscoll_syndrome|Crigler-Najjar_syndrome,_type_II|Crigler-Najjar_syndrome_type_1|Bilirubin,_serum_level_of,_quantitative_trait_locus_1|Irinotecan_response|not_specified|SN-38_response_-_Other|irinotecan_response_-_Other	MONDO:MONDO:0007745,MedGen:C0017551,OMIM:143500,SNOMED_CT:27503000|MONDO:MONDO:0009383,MedGen:C0270210,OMIM:237900,Orphanet:ORPHA2312,SNOMED_CT:47444008|MONDO:MONDO:0011725,MedGen:C2931132,OMIM:606785,Orphanet:ORPHA79235,SNOMED_CT:68067009|MONDO:MONDO:0021020,MedGen:CN029644,OMIM:218800,Orphanet:ORPHA79234|MedGen:C1866173,OMIM:601816|MedGen:CN077989|MedGen:CN169374|MedGen:CN236455|MedGen:CN236597	reviewed_by_expert_panel	drug_response	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	MU13449765	LAML-KR|1|205|0.00487805,LUSC-KR|3|170|0.0176471,COCA-CN|2|321|0.00623053	0.25	280	429	2	234669144	.	G	A	280	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3532;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCGTTGTACATCAGAGAC;RSEQ=GAGCATTTTACACCTTGAAG;CSQ=A|missense_variant|MODERATE|UGT1A1|54658|Transcript|NM_000463.3|protein_coding|1/5||NM_000463.3:c.211G>A|NP_000454.1:p.Gly71Arg|229|211|71|G/R|Gga/Aga|rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A6|54578|Transcript|NM_001072.4|protein_coding||1/4|NM_001072.4:c.862-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A4|54657|Transcript|NM_007120.3|protein_coding||1/4|NM_007120.3:c.868-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A10|54575|Transcript|NM_019075.2|protein_coding||1/4|NM_019075.2:c.856-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A8|54576|Transcript|NM_019076.5|protein_coding||1/4|NM_019076.5:c.856-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A7|54577|Transcript|NM_019077.3|protein_coding||1/4|NM_019077.3:c.856-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A5|54579|Transcript|NM_019078.2|protein_coding||1/4|NM_019078.2:c.868-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A3|54659|Transcript|NM_019093.4|protein_coding||1/4|NM_019093.4:c.868-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A9|54600|Transcript|NM_021027.3|protein_coding||1/4|NM_021027.3:c.856-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||YES||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1,A|intron_variant|MODIFIER|UGT1A6|54578|Transcript|NM_205862.2|protein_coding||2/5|NM_205862.2:c.61-6536G>A|||||||rs4148323&CM930722&COSV59383881||1||EntrezGene||||||2:g.234669144G>A|0.02235|0.0008619|0.02405|0.005258|0.1538|0.04611|0.001987|0.01091|0.0196|0.1538|gnomAD_EAS|conflicting_interpretations_of_pathogenicity&likely_pathogenic&association&benign/likely_benign&pathogenic&drug_response|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3532:0:0,0:1774,1757:3531,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:429:216:116,100:103,108:211,216:0.5035:2,2:37.6:1:36.2:1:0.33364:1.22:60:71:0.5071:0:1.1
    965. 

  965. 2	242793273	242793273	A	G	exonic	PDCD1	.	synonymous SNV	PDCD1:NM_005018:exon5:c.T804C:p.A268A	0.76	0.6047	0.5763	0.6124	0.5894	0.7311	0.7071	0.5808	0.6462	rs2227981	rs2227981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57691079;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU142527	LAML-KR|1|205|0.00487805,COCA-CN|5|321|0.0155763	0.5	400	206	2	242793273	.	A	G	400	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1953;VD=1946;AF=0.9964;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGGGCACTCCGAGGGCCGTC;RSEQ=GCTGAGCCCCTGCGGGCGGG;CSQ=G|synonymous_variant|LOW|PDCD1|5133|Transcript|NM_005018.3|protein_coding|5/5||NM_005018.3:c.804T>C|NP_005009.2:p.Ala268%3D|860|804|268|A|gcT/gcC|rs2227981&COSV57691079||-1||EntrezGene||YES||||2:g.242793273A>G|0.6317|0.579|0.6214|0.6177|0.7278|0.7093|0.5822|0.6089|0.7496|0.7587|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1953:1946:1037,909:0,0:0,1946:0.9964:0,2:36.8:1:36.7:1:1:0:60:323.333:0.9964:0:1.1	0/0:206:0:0,0:108,98:206,0:0:2,0:8:0:11:0:1:0:60:0:0:0:3
    966. 

  966. 2	242793433	242793433	G	A	exonic	PDCD1	.	nonsynonymous SNV	PDCD1:NM_005018:exon5:c.C644T:p.A215V	0.49	0.0492	0.0108	0.2053	0.0033	0.4845	0.0515	0.0160	0.0562	rs2227982	rs2227982	0.019	0.501	D	0.816	0.436	P	0.261	0.378	B	0.072	0.214	N	1	0.090	P	1.59	0.404	L	-0.1	0.643	T	-1.18	0.301	N	0.033	0.333	-0.921	0.454	T	0.000	0.000	T	.	.	.	1.737	0.270	14.62	0.989	0.474	0.037	0.088	N	c	-0.411	-0.517	0.847	0.249	0.635	0.413	0	2.9	0.327	-0.195	0.095	0.782	0.315	0.000	0.063	0.002	0.062	7.501	0.265	.	.	.	ID=COSV57690833;OCCURENCE=1(breast),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU19558515	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|6|321|0.0186916	0.5	366	121	2	242793433	.	G	A	366	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=1124;VD=1122;AF=0.9982;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CCACAGAGAACACAGGCACG;RSEQ=CTGAGGGGTCCTCCTTCTTT;CSQ=A|missense_variant|MODERATE|PDCD1|5133|Transcript|NM_005018.3|protein_coding|5/5||NM_005018.3:c.644C>T|NP_005009.2:p.Ala215Val|700|644|215|A/V|gCc/gTc|rs2227982&COSV57690833||-1||EntrezGene||YES||||2:g.242793433G>A|0.09222|0.01174|0.2633|0.01316|0.4869|0.05189|0.01177|0.06095|0.06196|0.4869|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1124:1122:440,682:0,0:0,1122:0.9982:0,2:34:1:36.2:1:1:0:60:79.143:0.9991:0:1.2	0/0:121:0:0,0:40,81:121,0:0:2,0:36.3:1:35.7:1:1:0:60:39.333:1:0:0.1
    967. 

  967. 2	242794143	242794143	G	A	intronic	PDCD1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57692383;OCCURENCE=1(skin)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	69	2	242794143	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=617;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00998;SOR=0;LSEQ=GCTCCTATTGTCCCTGCAGA;RSEQ=AAACACACTTGGGGTCACCA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PDCD1|5133|Transcript|NM_005018.3|protein_coding||3/4|NM_005018.3:c.593-8C>T|||||||COSV57692383||-1||EntrezGene||YES||||2:g.242794143G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:617:0:0,0:303,314:617,0:0:2,0:41.1:1:36.5:1:1:0:60:87.143:1:0:0.1	0/1:69:2:1,1:34,33:67,2:0.029:2,2:49:0:37:0:1:1.02986:60:4:0.0294:0:1
    968. 

  968. 2	242794848	242794848	A	G	exonic	PDCD1	.	nonsynonymous SNV	PDCD1:NM_005018:exon2:c.T361C:p.Y121H	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.486	D	0.751	0.339	D	3.82	0.957	H	-3.45	0.945	D	-4.98	0.821	D	0.806	0.795	1.088	0.992	D	0.909	0.970	D	0.076	0.724	D	4.475	0.599	24.2	0.997	0.839	0.627	0.316	D	c	0.468	0.301	0.994	0.335	0.660	0.495	0	3.55	0.396	0.527	0.225	0.825	0.337	0.049	0.212	0.752	0.322	8.776	0.337	Immunoglobulin V-set domain|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	140	2	242794848	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1356;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0087;SOR=0;LSEQ=GGAGATGGCCCCACAGAGGT;RSEQ=GGTGCCGCTGTCATTGCGCC;CSQ=G|missense_variant|MODERATE|PDCD1|5133|Transcript|NM_005018.3|protein_coding|2/5||NM_005018.3:c.361T>C|NP_005009.2:p.Tyr121His|417|361|121|Y/H|Tac/Cac|||-1||EntrezGene||YES||||2:g.242794848A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1356:0:0,0:902,452:1354,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:140:2:1,1:98,40:138,2:0.0143:2,2:50:1:37:0:0.50144:2.43227:60:4:0.0144:0:1
    969. 

  969. 2	242800900	242800900	G	A	intronic	PDCD1	.	.	.	0.6	0.0590	0.0411	0.2088	0.0033	0.5	0.0514	0.0164	0.0562	rs35933396	rs35933396	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57690636;OCCURENCE=4(liver),1(biliary_tract),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU19558701	LUSC-KR|1|170|0.00588235,COCA-CN|6|321|0.0186916	0.5	301	45	2	242800900	.	G	A	301	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=356;VD=356;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGGCTCTGGGACACCTGACC;RSEQ=CCGACCCCACCTACCTAAGA;CSQ=A|intron_variant|MODIFIER|PDCD1|5133|Transcript|NM_005018.3|protein_coding||1/4|NM_005018.3:c.76+15C>T|||||||rs35933396&COSV57690636||-1||EntrezGene||YES||||2:g.242800900G>A|0.09877|0.04576|0.2605|0.01314|0.4992|0.05186|0.012|0.06608|0.0625|0.4992|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:356:356:191,165:0,0:0,356:1:0,2:36.6:1:35.6:1:1:0:60:34.6:1:0:1.3	0/0:45:0:0,0:24,21:45,0:0:2,0:38.8:1:37:0:1:0:60:90:1:0:0.2
    970. 

  970. 2	242800921	242800921	A	G	exonic	PDCD1	.	nonsynonymous SNV	PDCD1:NM_005018:exon1:c.T70C:p.F24L	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.090	0.204	N	0.999	0.218	N	-1.545	0.005	N	0.14	0.609	T	1.0	0.014	N	0.131	0.150	-0.993	0.319	T	0.044	0.188	T	0.004	0.096	T	0.923	0.182	10.21	0.851	0.152	0.012	0.041	N	c	-1.014	-0.849	1.000	0.747	0.495	0.175	0	1.16	0.198	0.753	0.259	-0.101	0.116	0.162	0.236	0.197	0.217	3.548	0.073	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	55	2	242800921	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=400;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.01438;SOR=0;LSEQ=CCGACCCCACCTACCTAAGA;RSEQ=CCATCCTGGCCGCCAGCCCA;CSQ=G|missense_variant|MODERATE|PDCD1|5133|Transcript|NM_005018.3|protein_coding|1/5||NM_005018.3:c.70T>C|NP_005009.2:p.Phe24Leu|126|70|24|F/L|Ttc/Ctc|rs1417261485||-1||EntrezGene||YES||||2:g.242800921A>G|4.76e-06|0|0|0.000109|0|0|0|0|0|0.000109|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:400:0:0,0:204,194:398,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:55:2:1,1:28,24:52,2:0.0364:2,2:35.5:1:37:0:1:1.16333:60:4:0.0377:0:1
    971. 

  971. 3	10070336	10070336	G	C	UTR5	FANCD2	NM_033084:c.-6G>C;NM_001018115:c.-6G>C;NM_001319984:c.-6G>C	.	.	0.039	0.0021	0.0013	0.0024	0	0.0197	0	0.0011	0.0031	rs3732974	rs3732974	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV104599157;OCCURENCE=4(prostate)	291526	Fanconi_anemia,_complementation_group_D2	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	212	125	3	10070336	.	G	C	212	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTAAGTGCACAAGACATTG;RSEQ=TCAAAATGGTTTCCAAAAGA;CSQ=C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|2/44||NM_001018115.3:c.-6G>C||65|||||rs3732974&COSV104599157||1||EntrezGene||||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|2/44||NM_001319984.2:c.-6G>C||218|||||rs3732974&COSV104599157||1||EntrezGene||||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|2/43||NM_001374253.1:c.-6G>C||65|||||rs3732974&COSV104599157||1||EntrezGene||||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|2/42||NM_001374254.1:c.-6G>C||65|||||rs3732974&COSV104599157||1||EntrezGene||||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|2/10||NM_001374255.1:c.-6G>C||218|||||rs3732974&COSV104599157||1||EntrezGene||||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|5_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding|2/43||NM_033084.6:c.-6G>C||65|||||rs3732974&COSV104599157||1||EntrezGene||YES||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1,C|upstream_gene_variant|MODIFIER|CIDECP|152302|Transcript|NR_002786.1|transcribed_pseudogene||||||||||rs3732974&COSV104599157|2516|-1||EntrezGene||YES||||3:g.10070336G>C|0.006519|0.0005536|0.004337|0.0007938|0.02637|9.24e-05|0.00183|0.006197|0.02414|0.0387|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:94:0:0,0:53,41:94,0:0:2,0:38.9:1:36.2:1:1:0:60:46:1:0:0.1	0/1:125:61:36,25:38,26:64,61:0.488:2,2:40.9:1:35.8:1:1:1.01484:60:60:0.4878:0:1
    972. 

  972. 3	10070375	10070375	G	T	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon2:c.G34T:p.D12Y,FANCD2:NM_001319984:exon2:c.G34T:p.D12Y,FANCD2:NM_033084:exon2:c.G34T:p.D12Y	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	0.955	0.604	P	0.748	0.565	P	0.149	0.180	N	0.999	0.217	N	2.36	0.681	M	0.73	0.507	T	-2.18	0.522	N	0.396	0.455	-0.951	0.408	T	0.179	0.525	T	0.017	0.392	T	4.770	0.640	24.7	0.992	0.538	0.832	0.420	D	c	0.270	0.217	0.998	0.365	0.732	0.924	0	3.31	0.369	2.324	0.432	0.980	0.597	0.998	0.411	0.673	0.303	6.521	0.213	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	154	3	10070375	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=117;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.32202;SOR=0;LSEQ=GAAGACTGTCAAAATCTGAG;RSEQ=ATAAAGAGAGCCTGACAGAA;CSQ=T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|2/44||NM_001018115.3:c.34G>T|NP_001018125.1:p.Asp12Tyr|104|34|12|D/Y|Gat/Tat|||1||EntrezGene||||||3:g.10070375G>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|2/44||NM_001319984.2:c.34G>T|NP_001306913.1:p.Asp12Tyr|257|34|12|D/Y|Gat/Tat|||1||EntrezGene||||||3:g.10070375G>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|2/43||NM_001374253.1:c.34G>T|NP_001361182.1:p.Asp12Tyr|104|34|12|D/Y|Gat/Tat|||1||EntrezGene||||||3:g.10070375G>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|2/42||NM_001374254.1:c.34G>T|NP_001361183.1:p.Asp12Tyr|104|34|12|D/Y|Gat/Tat|||1||EntrezGene||||||3:g.10070375G>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|2/10||NM_001374255.1:c.34G>T|NP_001361184.1:p.Asp12Tyr|257|34|12|D/Y|Gat/Tat|||1||EntrezGene||||||3:g.10070375G>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|2/43||NM_033084.6:c.34G>T|NP_149075.2:p.Asp12Tyr|104|34|12|D/Y|Gat/Tat|||1||EntrezGene||YES||||3:g.10070375G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|CIDECP|152302|Transcript|NR_002786.1|transcribed_pseudogene|||||||||||2555|-1||EntrezGene||YES||||3:g.10070375G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:117:0:0,0:65,52:117,0:0:2,0:39.5:1:36:1:1:0:60:57.5:1:0:0.2	0/1:154:2:1,1:78,74:152,2:0.013:2,2:50.5:1:37:0:1:1.05372:60:4:0.0132:0:1
    973. 

  973. 3	10076153	10076153	C	T	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon4:c.C206T:p.A69V,FANCD2:NM_001319984:exon4:c.C206T:p.A69V,FANCD2:NM_033084:exon4:c.C206T:p.A69V	.	.	.	.	.	.	.	.	.	.	.	0.084	0.330	T	0.069	0.223	B	0.082	0.276	B	0.000	0.466	N	0.964	0.384	D	1.875	0.501	L	0.44	0.566	T	-1.72	0.527	N	0.098	0.143	-0.991	0.322	T	0.140	0.459	T	0.038	0.583	D	1.837	0.282	15.21	0.996	0.767	0.904	0.512	D	c	-0.215	-0.161	0.012	0.123	0.732	0.924	0	1.85	0.243	2.713	0.466	-0.070	0.120	1.000	0.715	0.861	0.359	5.522	0.161	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	112	3	10076153	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=2;AF=0.0136;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.32118;SOR=inf;LSEQ=CTCTTCTTTTTTCTGCATAG;RSEQ=TGTGGATCAAATAGCTTTCC;CSQ=T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|4/44||NM_001018115.3:c.206C>T|NP_001018125.1:p.Ala69Val|276|206|69|A/V|gCt/gTt|||1||EntrezGene||||||3:g.10076153C>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|4/44||NM_001319984.2:c.206C>T|NP_001306913.1:p.Ala69Val|429|206|69|A/V|gCt/gTt|||1||EntrezGene||||||3:g.10076153C>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|4/43||NM_001374253.1:c.206C>T|NP_001361182.1:p.Ala69Val|276|206|69|A/V|gCt/gTt|||1||EntrezGene||||||3:g.10076153C>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|4/42||NM_001374254.1:c.206C>T|NP_001361183.1:p.Ala69Val|276|206|69|A/V|gCt/gTt|||1||EntrezGene||||||3:g.10076153C>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|4/10||NM_001374255.1:c.206C>T|NP_001361184.1:p.Ala69Val|429|206|69|A/V|gCt/gTt|||1||EntrezGene||||||3:g.10076153C>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|4/43||NM_033084.6:c.206C>T|NP_149075.2:p.Ala69Val|276|206|69|A/V|gCt/gTt|||1||EntrezGene||YES||||3:g.10076153C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:147:2:1,1:78,67:145,2:0.0136:2,2:31:0:37:0:1:1.16297:60:4:0.0139:0:1	0/0:112:0:0,0:73,39:112,0:0:2,0:39.4:1:36.1:1:1:0:60:55:1:0:0.1
    974. 

  974. 3	10076219	10076219	A	T	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon4:c.A272T:p.K91I,FANCD2:NM_001319984:exon4:c.A272T:p.K91I,FANCD2:NM_033084:exon4:c.A272T:p.K91I	.	.	.	.	.	.	.	.	.	.	.	0.08	0.410	T	0.546	0.361	P	0.149	0.325	B	0.455	0.124	N	1	0.810	D	2.34	0.674	M	0.67	0.522	T	-2.63	0.673	D	0.382	0.453	-1.031	0.201	T	0.100	0.372	T	0.022	0.446	T	2.499	0.362	19.46	0.993	0.598	0.890	0.490	D	c	-0.236	-0.195	0.004	0.102	0.732	0.924	0	0.359	0.153	1.160	0.312	1.021	0.644	0.362	0.256	0.997	0.653	5.254	0.148	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	136	3	10076219	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=138;VD=2;AF=0.0145;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.25275;SOR=inf;LSEQ=GAGACACCCTTCCTATCCCA;RSEQ=AGTATGTATTTTTCCCCTGG;CSQ=T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|4/44||NM_001018115.3:c.272A>T|NP_001018125.1:p.Lys91Ile|342|272|91|K/I|aAa/aTa|||1||EntrezGene||||||3:g.10076219A>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|4/44||NM_001319984.2:c.272A>T|NP_001306913.1:p.Lys91Ile|495|272|91|K/I|aAa/aTa|||1||EntrezGene||||||3:g.10076219A>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|4/43||NM_001374253.1:c.272A>T|NP_001361182.1:p.Lys91Ile|342|272|91|K/I|aAa/aTa|||1||EntrezGene||||||3:g.10076219A>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|4/42||NM_001374254.1:c.272A>T|NP_001361183.1:p.Lys91Ile|342|272|91|K/I|aAa/aTa|||1||EntrezGene||||||3:g.10076219A>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|4/10||NM_001374255.1:c.272A>T|NP_001361184.1:p.Lys91Ile|495|272|91|K/I|aAa/aTa|||1||EntrezGene||||||3:g.10076219A>T||||||||||||||,T|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|4/43||NM_033084.6:c.272A>T|NP_149075.2:p.Lys91Ile|342|272|91|K/I|aAa/aTa|||1||EntrezGene||YES||||3:g.10076219A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:138:2:1,1:59,77:136,2:0.0145:2,2:19.5:1:37:0:1:1.3:60:4:0.015:0:1	0/0:136:0:0,0:69,67:136,0:0:2,0:37.2:1:34.4:1:1:0:60:21.667:1:0:0.1
    975. 

  975. 3	10076237	10076237	T	A	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	142	3	10076237	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=116;VD=2;AF=0.0172;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.20119;SOR=inf;LSEQ=CAAAGTATGTATTTTTCCCC;RSEQ=GGTATTTTTGCTTGTGCCAG;CSQ=A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||4/43|NM_001018115.3:c.273+17T>A|||||||||1||EntrezGene||||||3:g.10076237T>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||4/43|NM_001319984.2:c.273+17T>A|||||||||1||EntrezGene||||||3:g.10076237T>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||4/42|NM_001374253.1:c.273+17T>A|||||||||1||EntrezGene||||||3:g.10076237T>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||4/41|NM_001374254.1:c.273+17T>A|||||||||1||EntrezGene||||||3:g.10076237T>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding||4/9|NM_001374255.1:c.273+17T>A|||||||||1||EntrezGene||||||3:g.10076237T>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||4/42|NM_033084.6:c.273+17T>A|||||||||1||EntrezGene||YES||||3:g.10076237T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:116:2:1,1:48,66:114,2:0.0172:2,2:40.5:1:37:0:1:1.37:60:4:0.0174:0:1	0/0:142:0:0,0:71,71:142,0:0:2,0:37.9:1:34.6:1:1:0:60:19.286:1:0:0.1
    976. 

  976. 3	10076842	10076842	-	T	intronic	FANCD2	.	.	.	0.46	6.748e-05	0	0	0	0.0013	0	0	0	rs766876118	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112191638	BTCA-SG|1|71|0.0140845	0.25	39	199	3	10076842	.	C	CT	39	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=29;VD=2;AF=0.069;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.04332;SOR=14.3432;LSEQ=GCAAAGTGGAAAACAGATTT;RSEQ=TTTTTTTTTTACAGTATGGG;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||5/43|NM_001018115.3:c.378-5dup|||||||rs55973240||1||EntrezGene||||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||5/43|NM_001319984.2:c.378-5dup|||||||rs55973240||1||EntrezGene||||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||5/42|NM_001374253.1:c.378-5dup|||||||rs55973240||1||EntrezGene||||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||5/41|NM_001374254.1:c.378-5dup|||||||rs55973240||1||EntrezGene||||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374255.1|protein_coding||5/9|NM_001374255.1:c.378-5dup|||||||rs55973240||1||EntrezGene||||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding||5/42|NM_033084.6:c.378-5dup|||||||rs55973240||1||EntrezGene||YES||||3:g.10076852dup|0.0009044|0|0.0007754|0.001032|0.001357|0.004345|0.0005437|0.001162|0.0005177|0.004345|gnomAD_FIN|benign&likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:29:2:1,1:18,8:26,2:0.069:2,2:49.3:1:39.2:0:1:2.17949:63.6:4:0.0714:0:0	0/0:199:1:0,1:117,69:186,1:0.005:2,0:45.6:0:39.2:0:0.37433:0:63.6:2:0.0057:0:4.2
    977. 

  977. 3	10081397	10081397	T	C	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	150	3	10081397	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=284;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.11893;SOR=0;LSEQ=GCAGTTCTAATAGTGTCTTC;RSEQ=ACTGCAGGACCTCACCACCA;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||8/43|NM_001018115.3:c.571-8T>C|||||||||1||EntrezGene||||||3:g.10081397T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||8/43|NM_001319984.2:c.571-8T>C|||||||||1||EntrezGene||||||3:g.10081397T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||8/42|NM_001374253.1:c.571-8T>C|||||||||1||EntrezGene||||||3:g.10081397T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||8/41|NM_001374254.1:c.571-8T>C|||||||||1||EntrezGene||||||3:g.10081397T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374255.1|protein_coding||8/9|NM_001374255.1:c.571-8T>C|||||||||1||EntrezGene||||||3:g.10081397T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding||8/42|NM_033084.6:c.571-8T>C|||||||||1||EntrezGene||YES||||3:g.10081397T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:284:0:0,0:187,97:284,0:0:2,0:29.4:1:36.7:1:1:0:60:568:1:0:0	0/1:150:2:1,1:89,59:148,2:0.0133:2,2:42.5:1:37:0:1:1.50419:60:4:0.0134:0:1.5
    978. 

  978. 3	10083327	10083327	C	A	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon10:c.C716A:p.T239N,FANCD2:NM_001319984:exon10:c.C716A:p.T239N,FANCD2:NM_033084:exon10:c.C716A:p.T239N	.	.	.	.	.	.	.	.	.	.	.	0.087	0.324	T	1.0	0.899	D	0.989	0.769	D	0.000	0.629	D	0.878	0.357	D	2.745	0.805	M	0.66	0.524	T	-2.1	0.478	N	0.194	0.259	-0.617	0.641	T	0.240	0.609	T	0.021	0.436	T	3.839	0.518	23.4	0.989	0.475	0.955	0.647	D	c	0.309	0.213	0.008	0.116	0.707	0.730	0	3.23	0.360	2.458	0.444	0.847	0.346	0.980	0.350	0.995	0.604	8.775	0.337	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	152	3	10083327	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=196;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.19007;SOR=0;LSEQ=TGACCTACTGATAGAGAATA;RSEQ=TTCACTCACTGTCCCAATCC;CSQ=A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|10/44||NM_001018115.3:c.716C>A|NP_001018125.1:p.Thr239Asn|786|716|239|T/N|aCt/aAt|||1||EntrezGene||||||3:g.10083327C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|10/44||NM_001319984.2:c.716C>A|NP_001306913.1:p.Thr239Asn|939|716|239|T/N|aCt/aAt|||1||EntrezGene||||||3:g.10083327C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|10/43||NM_001374253.1:c.716C>A|NP_001361182.1:p.Thr239Asn|786|716|239|T/N|aCt/aAt|||1||EntrezGene||||||3:g.10083327C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|10/42||NM_001374254.1:c.716C>A|NP_001361183.1:p.Thr239Asn|786|716|239|T/N|aCt/aAt|||1||EntrezGene||||||3:g.10083327C>A||||||||||||||,A|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|||||||||||957|1||EntrezGene||||||3:g.10083327C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|10/43||NM_033084.6:c.716C>A|NP_149075.2:p.Thr239Asn|786|716|239|T/N|aCt/aAt|||1||EntrezGene||YES||||3:g.10083327C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:196:0:0,0:121,75:196,0:0:2,0:31.1:1:35.9:1:1:0:60:48:1:0:0.1	0/1:152:2:1,1:94,56:150,2:0.0132:2,2:52:1:37:0:1:1.67254:60:4:0.0132:0:1
    979. 

  979. 3	10084782	10084782	C	T	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon12:c.C937T:p.P313S,FANCD2:NM_001319984:exon12:c.C937T:p.P313S,FANCD2:NM_033084:exon12:c.C937T:p.P313S	.	.	.	.	.	.	.	.	.	.	.	0.02	0.496	D	1.0	0.899	D	0.966	0.697	D	0.000	0.843	D	0.994	0.423	D	2.745	0.805	M	-0.0	0.626	T	-4.42	0.774	D	0.383	0.443	-0.275	0.757	T	0.421	0.766	T	0.097	0.767	D	4.042	0.543	23.7	0.999	0.973	0.956	0.652	D	c	0.511	0.437	0.827	0.246	0.707	0.730	0	5.09	0.685	4.608	0.606	0.884	0.388	1.000	0.715	0.942	0.416	16.07	0.806	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	292	3	10084782	.	C	T	37	v3;pSTD	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=197;VD=2;AF=0.0102;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.35584;SOR=2.97788;LSEQ=ATCTGCAGCATTGTGTTTTG;RSEQ=CATCACGGTTACAGGCTTCC;CSQ=T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|12/44||NM_001018115.3:c.937C>T|NP_001018125.1:p.Pro313Ser|1007|937|313|P/S|Cca/Tca|||1||EntrezGene||||||3:g.10084782C>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|12/44||NM_001319984.2:c.937C>T|NP_001306913.1:p.Pro313Ser|1160|937|313|P/S|Cca/Tca|||1||EntrezGene||||||3:g.10084782C>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|12/43||NM_001374253.1:c.937C>T|NP_001361182.1:p.Pro313Ser|1007|937|313|P/S|Cca/Tca|||1||EntrezGene||||||3:g.10084782C>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|12/42||NM_001374254.1:c.937C>T|NP_001361183.1:p.Pro313Ser|1007|937|313|P/S|Cca/Tca|||1||EntrezGene||||||3:g.10084782C>T||||||||||||||,T|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|||||||||||2412|1||EntrezGene||||||3:g.10084782C>T||||||||||||||,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|12/43||NM_033084.6:c.937C>T|NP_149075.2:p.Pro313Ser|1007|937|313|P/S|Cca/Tca|||1||EntrezGene||YES||||3:g.10084782C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:197:2:1,1:94,100:194,2:0.0102:2,2:54:0:37:0:1:1.06:60:4:0.0103:0:1	0/0:292:1:1,0:144,147:291,1:0.0034:2,0:19:0:37:0:0.49658:0:60:2:0.0034:0:1
    980. 

  980. 3	10085493	10085493	A	G	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	82	3	10085493	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=2;AF=0.0152;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37936;SOR=inf;LSEQ=TGTGTCATAATATTTTTGTG;RSEQ=CTCTCTCCTGTTTTTTCAGG;CSQ=G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||13/43|NM_001018115.3:c.1099-20A>G|||||||||1||EntrezGene||||||3:g.10085493A>G||||||||||||||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||13/43|NM_001319984.2:c.1099-20A>G|||||||||1||EntrezGene||||||3:g.10085493A>G||||||||||||||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||13/42|NM_001374253.1:c.1099-20A>G|||||||||1||EntrezGene||||||3:g.10085493A>G||||||||||||||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||13/41|NM_001374254.1:c.1099-20A>G|||||||||1||EntrezGene||||||3:g.10085493A>G||||||||||||||,G|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding|||||||||||3123|1||EntrezGene||||||3:g.10085493A>G||||||||||||||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||13/42|NM_033084.6:c.1099-20A>G|||||||||1||EntrezGene||YES||||3:g.10085493A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:132:2:1,1:71,59:130,2:0.0152:2,2:40.5:1:37:0:1:1.20169:60:4:0.0155:0:1	0/0:82:0:0,0:35,47:82,0:0:2,0:37.6:1:36:1:1:0:59.2:164:1:0:0.2
    981. 

  981. 3	10085567	10085567	G	A	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	65	3	10085567	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=116;VD=2;AF=0.0172;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.40945;SOR=inf;LSEQ=AGGTAATGTTCATGTACTAT;RSEQ=CATTTTCAGTATTGCAGACT;CSQ=A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||14/43|NM_001018115.3:c.1134+19G>A|||||||rs1297718450||1||EntrezGene||||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||14/43|NM_001319984.2:c.1134+19G>A|||||||rs1297718450||1||EntrezGene||||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||14/42|NM_001374253.1:c.1134+19G>A|||||||rs1297718450||1||EntrezGene||||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||14/41|NM_001374254.1:c.1134+19G>A|||||||rs1297718450||1||EntrezGene||||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374255.1|protein_coding||||||||||rs1297718450|3197|1||EntrezGene||||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||14/42|NM_033084.6:c.1134+19G>A|||||||rs1297718450||1||EntrezGene||YES||||3:g.10085567G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:116:2:1,1:51,63:114,2:0.0172:2,2:17.5:1:37:0:1:1.23:60:4:0.0179:0:1	0/0:65:0:0,0:25,40:65,0:0:2,0:38.7:1:35.5:1:1:0:54.8:64:1:0:0.1
    982. 

  982. 3	10088223	10088223	T	G	intronic	FANCD2	.	.	.	0.057	0.3075	0.4089	0.2261	0.0955	0.2818	0.3344	0.2554	0.2920	rs200221245	rs200221245	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55034403;OCCURENCE=3(large_intestine),1(biliary_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29544769	LUSC-KR|3|170|0.0176471,COCA-CN|3|321|0.00934579,BTCA-JP|2|239|0.0083682	0.5	103	64	3	10088223	.	T	G	103	v3;pSTD;NM5.25	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=1;AF=0.0588;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.46595;SOR=0.51251;LSEQ=TTGTAGCAAATGTACTGATT;RSEQ=GTTAACTGTTTTTCTGTTGT;CSQ=G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||14/43|NM_001018115.3:c.1135-41T>G|||||||rs200221245&COSV55034403||1||EntrezGene||||||3:g.10088223T>G|0.002264|0.001814|0.0006437|0.0003429|0.0005451|0.005432|0.003572|0.0001884|0.000435|0.005432|gnomAD_FIN||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||14/43|NM_001319984.2:c.1135-41T>G|||||||rs200221245&COSV55034403||1||EntrezGene||||||3:g.10088223T>G|0.002264|0.001814|0.0006437|0.0003429|0.0005451|0.005432|0.003572|0.0001884|0.000435|0.005432|gnomAD_FIN||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||14/42|NM_001374253.1:c.1135-41T>G|||||||rs200221245&COSV55034403||1||EntrezGene||||||3:g.10088223T>G|0.002264|0.001814|0.0006437|0.0003429|0.0005451|0.005432|0.003572|0.0001884|0.000435|0.005432|gnomAD_FIN||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||14/41|NM_001374254.1:c.1135-41T>G|||||||rs200221245&COSV55034403||1||EntrezGene||||||3:g.10088223T>G|0.002264|0.001814|0.0006437|0.0003429|0.0005451|0.005432|0.003572|0.0001884|0.000435|0.005432|gnomAD_FIN||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||14/42|NM_033084.6:c.1135-41T>G|||||||rs200221245&COSV55034403||1||EntrezGene||YES||||3:g.10088223T>G|0.002264|0.001814|0.0006437|0.0003429|0.0005451|0.005432|0.003572|0.0001884|0.000435|0.005432|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:17:1:1,0:9,7:16,1:0.0588:2,0:39:0:37:0:1:0:60:2:0.0588:0:6	0/1:64:7:7,0:47,10:57,7:0.1094:2,0:16.4:1:37:0:0.58425:0:39.6:14:0.1094:0:6.9
    983. 

  983. 3	10088239	10088242	GTTG	ATTA	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	127	85	3	10088239	.	GTTG	ATTA	127	NM5.25	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Complex;DP=22;VD=4;AF=0.1818;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.37028;SOR=1.48886;LSEQ=GATTTGTTAACTGTTTTTCT;RSEQ=TTGCATATTTATTGACAATA;CSQ=ATTA|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||14/43|NM_001018115.3:c.1135-25_1135-22delinsATTA|||||||||1||EntrezGene||||||3:g.10088239_10088242delinsATTA||||||||||||||,ATTA|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||14/43|NM_001319984.2:c.1135-25_1135-22delinsATTA|||||||||1||EntrezGene||||||3:g.10088239_10088242delinsATTA||||||||||||||,ATTA|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||14/42|NM_001374253.1:c.1135-25_1135-22delinsATTA|||||||||1||EntrezGene||||||3:g.10088239_10088242delinsATTA||||||||||||||,ATTA|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||14/41|NM_001374254.1:c.1135-25_1135-22delinsATTA|||||||||1||EntrezGene||||||3:g.10088239_10088242delinsATTA||||||||||||||,ATTA|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||14/42|NM_033084.6:c.1135-25_1135-22delinsATTA|||||||||1||EntrezGene||YES||||3:g.10088239_10088242delinsATTA||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:22:4:2,2:11,7:18,4:0.1818:2,2:22.5:1:36.2:1:1:1.53863:51.5:8:0.1905:0:6	0/1:85:11:9,2:56,18:74,11:0.1294:2,2:26:1:37:1:1:1.44:38.4:22:0.131:0.0118:6.5
    984. 

  984. 3	10088266	10088266	G	T	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon15:c.G1137T:p.V379V,FANCD2:NM_001319984:exon15:c.G1137T:p.V379V,FANCD2:NM_033084:exon15:c.G1137T:p.V379V	0.43	0.4393	0.4755	0.3902	0.3111	0.4121	0.4545	0.4184	0.4326	rs72492997	rs72492997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55036171;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(skin),1(thyroid),1(upper_aerodigestive_tract)	288498	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia,_complementation_group_A|Fanconi_anemia	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4554264	LAML-KR|1|205|0.00487805,COCA-CN|6|321|0.0186916	0.5	159	121	3	10088266	.	G	T	159	NM5.25	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=6;AF=0.1818;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.50131;SOR=1.12135;LSEQ=CATATTTATTGACAATAGGT;RSEQ=TTTGACCTGGTGATGCTTTT;CSQ=T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|15/44||NM_001018115.3:c.1137G>T|NP_001018125.1:p.Val379%3D|1207|1137|379|V|gtG/gtT|rs72492997&COSV55036171||1||EntrezGene||||||3:g.10088266G>T|0.1378|0.1822|0.04451|0.07442|0.0694|0.2968|0.1846|0.0898|0.05383|0.2968|gnomAD_FIN|benign|0&1|1&1,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|15/44||NM_001319984.2:c.1137G>T|NP_001306913.1:p.Val379%3D|1360|1137|379|V|gtG/gtT|rs72492997&COSV55036171||1||EntrezGene||||||3:g.10088266G>T|0.1378|0.1822|0.04451|0.07442|0.0694|0.2968|0.1846|0.0898|0.05383|0.2968|gnomAD_FIN|benign|0&1|1&1,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|15/43||NM_001374253.1:c.1137G>T|NP_001361182.1:p.Val379%3D|1207|1137|379|V|gtG/gtT|rs72492997&COSV55036171||1||EntrezGene||||||3:g.10088266G>T|0.1378|0.1822|0.04451|0.07442|0.0694|0.2968|0.1846|0.0898|0.05383|0.2968|gnomAD_FIN|benign|0&1|1&1,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|15/42||NM_001374254.1:c.1137G>T|NP_001361183.1:p.Val379%3D|1207|1137|379|V|gtG/gtT|rs72492997&COSV55036171||1||EntrezGene||||||3:g.10088266G>T|0.1378|0.1822|0.04451|0.07442|0.0694|0.2968|0.1846|0.0898|0.05383|0.2968|gnomAD_FIN|benign|0&1|1&1,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|15/43||NM_033084.6:c.1137G>T|NP_149075.2:p.Val379%3D|1207|1137|379|V|gtG/gtT|rs72492997&COSV55036171||1||EntrezGene||YES||||3:g.10088266G>T|0.1378|0.1822|0.04451|0.07442|0.0694|0.2968|0.1846|0.0898|0.05383|0.2968|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:33:6:2,4:15,12:27,6:0.1818:2,2:33.8:1:35:1:0.39832:2.4317:51:12:0.1818:0:5.7	0/1:121:20:11,9:72,29:101,20:0.1653:2,2:34.4:1:37:0:0.18868:2.01851:35.1:40:0.1681:0:5.5
    985. 

  985. 3	10088299	10088299	C	T	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon15:c.C1170T:p.S390S,FANCD2:NM_001319984:exon15:c.C1170T:p.S390S,FANCD2:NM_033084:exon15:c.C1170T:p.S390S	0.47	0.4501	0.4796	0.4059	0.3421	0.4245	0.4638	0.4337	0.4401	rs112887807	rs112887807	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55040833;OCCURENCE=3(large_intestine),1(kidney),1(lung),1(upper_aerodigestive_tract)	291535	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia|not_specified	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU23560209	LUSC-KR|6|170|0.0352941,COCA-CN|8|321|0.0249221,RECA-EU|1|422|0.00236967	0.5	162	145	3	10088299	.	C	T	162	NM5.25	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=39;VD=6;AF=0.1538;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.57319;SOR=1.01644;LSEQ=ATGCTTTTCATCATCTATAG;RSEQ=ACCAATACTCAGACAAAGAA;CSQ=T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|15/44||NM_001018115.3:c.1170C>T|NP_001018125.1:p.Ser390%3D|1240|1170|390|S|agC/agT|rs112887807&COSV55040833||1||EntrezGene||||||3:g.10088299C>T|0.2231|0.2723|0.09291|0.1653|0.13|0.3726|0.2824|0.1658|0.1138|0.3726|gnomAD_FIN|benign&likely_benign|0&1|1&1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|15/44||NM_001319984.2:c.1170C>T|NP_001306913.1:p.Ser390%3D|1393|1170|390|S|agC/agT|rs112887807&COSV55040833||1||EntrezGene||||||3:g.10088299C>T|0.2231|0.2723|0.09291|0.1653|0.13|0.3726|0.2824|0.1658|0.1138|0.3726|gnomAD_FIN|benign&likely_benign|0&1|1&1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|15/43||NM_001374253.1:c.1170C>T|NP_001361182.1:p.Ser390%3D|1240|1170|390|S|agC/agT|rs112887807&COSV55040833||1||EntrezGene||||||3:g.10088299C>T|0.2231|0.2723|0.09291|0.1653|0.13|0.3726|0.2824|0.1658|0.1138|0.3726|gnomAD_FIN|benign&likely_benign|0&1|1&1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|15/42||NM_001374254.1:c.1170C>T|NP_001361183.1:p.Ser390%3D|1240|1170|390|S|agC/agT|rs112887807&COSV55040833||1||EntrezGene||||||3:g.10088299C>T|0.2231|0.2723|0.09291|0.1653|0.13|0.3726|0.2824|0.1658|0.1138|0.3726|gnomAD_FIN|benign&likely_benign|0&1|1&1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|15/43||NM_033084.6:c.1170C>T|NP_149075.2:p.Ser390%3D|1240|1170|390|S|agC/agT|rs112887807&COSV55040833||1||EntrezGene||YES||||3:g.10088299C>T|0.2231|0.2723|0.09291|0.1653|0.13|0.3726|0.2824|0.1658|0.1138|0.3726|gnomAD_FIN|benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:39:6:2,4:17,16:33,6:0.1538:2,2:55.8:1:32.7:1:0.66142:2.08513:51:5:0.1351:0:5.7	0/1:145:22:11,11:78,45:123,22:0.1517:2,2:51.7:1:36.5:1:0.24463:1.72644:32.5:44:0.1583:0:5.3
    986. 

  986. 3	10088308	10088308	T	C	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon15:c.T1179C:p.T393T,FANCD2:NM_001319984:exon15:c.T1179C:p.T393T,FANCD2:NM_033084:exon15:c.T1179C:p.T393T	0.47	0.4504	0.4799	0.4082	0.3480	0.4244	0.4642	0.4338	0.4410	rs72492998	rs72492998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55032659;OCCURENCE=4(large_intestine),1(kidney),1(lung),1(upper_aerodigestive_tract)	291537	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia,_complementation_group_A|Fanconi_anemia|not_specified	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4081966	LUSC-KR|7|170|0.0411765,COCA-CN|9|321|0.0280374,RECA-EU|1|422|0.00236967	0.5	162	159	3	10088308	.	T	C	162	NM5.25	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=6;AF=0.1429;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.55566;SOR=1.03769;LSEQ=ATCATCTATAGCACCAATAC;RSEQ=CAGACAAAGAAGTACATTGA;CSQ=C|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|15/44||NM_001018115.3:c.1179T>C|NP_001018125.1:p.Thr393%3D|1249|1179|393|T|acT/acC|rs72492998&COSV55032659||1||EntrezGene||||||3:g.10088308T>C|0.2362|0.2802|0.1056|0.1841|0.1398|0.3802|0.2953|0.1799|0.1287|0.3802|gnomAD_FIN|benign&likely_benign|0&1|1&1,C|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|15/44||NM_001319984.2:c.1179T>C|NP_001306913.1:p.Thr393%3D|1402|1179|393|T|acT/acC|rs72492998&COSV55032659||1||EntrezGene||||||3:g.10088308T>C|0.2362|0.2802|0.1056|0.1841|0.1398|0.3802|0.2953|0.1799|0.1287|0.3802|gnomAD_FIN|benign&likely_benign|0&1|1&1,C|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|15/43||NM_001374253.1:c.1179T>C|NP_001361182.1:p.Thr393%3D|1249|1179|393|T|acT/acC|rs72492998&COSV55032659||1||EntrezGene||||||3:g.10088308T>C|0.2362|0.2802|0.1056|0.1841|0.1398|0.3802|0.2953|0.1799|0.1287|0.3802|gnomAD_FIN|benign&likely_benign|0&1|1&1,C|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|15/42||NM_001374254.1:c.1179T>C|NP_001361183.1:p.Thr393%3D|1249|1179|393|T|acT/acC|rs72492998&COSV55032659||1||EntrezGene||||||3:g.10088308T>C|0.2362|0.2802|0.1056|0.1841|0.1398|0.3802|0.2953|0.1799|0.1287|0.3802|gnomAD_FIN|benign&likely_benign|0&1|1&1,C|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|15/43||NM_033084.6:c.1179T>C|NP_149075.2:p.Thr393%3D|1249|1179|393|T|acT/acC|rs72492998&COSV55032659||1||EntrezGene||YES||||3:g.10088308T>C|0.2362|0.2802|0.1056|0.1841|0.1398|0.3802|0.2953|0.1799|0.1287|0.3802|gnomAD_FIN|benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:42:6:2,4:18,18:36,6:0.1429:2,2:58:1:37:0:0.66533:1.96804:51:12:0.1429:0:5.7	0/1:159:22:11,11:81,56:137,22:0.1384:2,2:53.6:1:36.5:1:0.48826:1.44298:32.5:44:0.1384:0:5.3
    987. 

  987. 3	10088343	10088343	A	G	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon15:c.A1214G:p.N405S,FANCD2:NM_001319984:exon15:c.A1214G:p.N405S,FANCD2:NM_033084:exon15:c.A1214G:p.N405S	0.46	0.4320	0.4779	0.4005	0.2822	0.4248	0.4642	0.3959	0.4321	rs73126218	rs73126218	0.314	0.138	T	0.022	0.174	B	0.023	0.188	B	0.011	0.298	N	0.999	0.220	N	1.465	0.370	L	0.89	0.456	T	-0.98	0.260	N	0.031	0.012	-0.975	0.361	T	0.000	0.000	T	.	.	.	0.077	0.101	3.368	0.878	0.169	0.229	0.217	N	c	-0.651	-0.546	0.002	0.090	0.707	0.730	0	0.307	0.150	0.211	0.171	1.110	0.879	0.265	0.248	0.999	0.750	5.115	0.141	.	ENSG00000254999.2	Muscle_Skeletal	ID=COSV55032016;OCCURENCE=5(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),1(kidney),2(lung),3(thyroid),20(upper_aerodigestive_tract)	291427	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	MU4081957	LAML-KR|1|205|0.00487805,LUSC-KR|5|170|0.0294118,COCA-CN|9|321|0.0280374,THCA-CN|1|50|0.02	0.5	151	172	3	10088343	.	A	G	151	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=33;VD=5;AF=0.1515;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37371;SOR=1.35496;LSEQ=CATTGACAGGGTGCTAAGAA;RSEQ=TAAGATTCGATCAGGCTGCA;CSQ=G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|15/44||NM_001018115.3:c.1214A>G|NP_001018125.1:p.Asn405Ser|1284|1214|405|N/S|aAt/aGt|rs73126218&COSV55032016||1||EntrezGene||||||3:g.10088343A>G|0.2277|0.2814|0.1106|0.171|0.1449|0.3458|0.2842|0.1738|0.1252|0.3458|gnomAD_FIN|benign|0&1|1&1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|15/44||NM_001319984.2:c.1214A>G|NP_001306913.1:p.Asn405Ser|1437|1214|405|N/S|aAt/aGt|rs73126218&COSV55032016||1||EntrezGene||||||3:g.10088343A>G|0.2277|0.2814|0.1106|0.171|0.1449|0.3458|0.2842|0.1738|0.1252|0.3458|gnomAD_FIN|benign|0&1|1&1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|15/43||NM_001374253.1:c.1214A>G|NP_001361182.1:p.Asn405Ser|1284|1214|405|N/S|aAt/aGt|rs73126218&COSV55032016||1||EntrezGene||||||3:g.10088343A>G|0.2277|0.2814|0.1106|0.171|0.1449|0.3458|0.2842|0.1738|0.1252|0.3458|gnomAD_FIN|benign|0&1|1&1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|15/42||NM_001374254.1:c.1214A>G|NP_001361183.1:p.Asn405Ser|1284|1214|405|N/S|aAt/aGt|rs73126218&COSV55032016||1||EntrezGene||||||3:g.10088343A>G|0.2277|0.2814|0.1106|0.171|0.1449|0.3458|0.2842|0.1738|0.1252|0.3458|gnomAD_FIN|benign|0&1|1&1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|15/43||NM_033084.6:c.1214A>G|NP_149075.2:p.Asn405Ser|1284|1214|405|N/S|aAt/aGt|rs73126218&COSV55032016||1||EntrezGene||YES||||3:g.10088343A>G|0.2277|0.2814|0.1106|0.171|0.1449|0.3458|0.2842|0.1738|0.1252|0.3458|gnomAD_FIN|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:33:5:1,4:12,16:28,5:0.1515:2,2:40.4:1:32.2:1:0.62534:2.9122:49.2:10:0.1562:0:5.6	0/1:172:20:9,11:76,76:152,20:0.1163:2,2:40:1:35.1:1:0.81289:1.2208:32.2:19:0.1124:0:5.2
    988. 

  988. 3	10089553	10089553	A	G	intronic	FANCD2	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs760895492	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	75	3	10089553	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=25;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.56061;SOR=0;LSEQ=CAACTCTTAGGTTGTGTACT;RSEQ=ACTGTTTCCTACAGCTTCTT;CSQ=G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||15/43|NM_001018115.3:c.1279-48A>G|||||||rs760895492||1||EntrezGene||||||3:g.10089553A>G|1.421e-05|0|3.867e-05|0|0|0|1.746e-05|0|0|3.867e-05|gnomAD_AMR|||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||15/43|NM_001319984.2:c.1279-48A>G|||||||rs760895492||1||EntrezGene||||||3:g.10089553A>G|1.421e-05|0|3.867e-05|0|0|0|1.746e-05|0|0|3.867e-05|gnomAD_AMR|||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||15/42|NM_001374253.1:c.1279-48A>G|||||||rs760895492||1||EntrezGene||||||3:g.10089553A>G|1.421e-05|0|3.867e-05|0|0|0|1.746e-05|0|0|3.867e-05|gnomAD_AMR|||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||15/41|NM_001374254.1:c.1279-48A>G|||||||rs760895492||1||EntrezGene||||||3:g.10089553A>G|1.421e-05|0|3.867e-05|0|0|0|1.746e-05|0|0|3.867e-05|gnomAD_AMR|||,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||15/42|NM_033084.6:c.1279-48A>G|||||||rs760895492||1||EntrezGene||YES||||3:g.10089553A>G|1.421e-05|0|3.867e-05|0|0|0|1.746e-05|0|0|3.867e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:25:0:0,0:18,7:25,0:0:2,0:30.4:1:36.5:1:1:0:55.3:50:1:0:0.2	0/1:75:2:1,1:57,16:73,2:0.0267:2,2:9:0:37:0:0.40432:3.48615:45:4:0.0278:0:1
    989. 

  989. 3	10089683	10089683	G	C	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon16:c.G1361C:p.G454A,FANCD2:NM_001319984:exon16:c.G1361C:p.G454A,FANCD2:NM_033084:exon16:c.G1361C:p.G454A	.	.	.	.	.	.	.	.	.	.	.	0.038	0.427	D	0.886	0.468	P	0.449	0.443	P	0.000	0.843	N	0.999	0.462	D	2.025	0.556	M	-0.1	0.643	T	-2.35	0.519	N	0.595	0.630	-0.673	0.617	T	0.230	0.596	T	0.032	0.544	D	2.362	0.345	18.57	0.996	0.763	0.878	0.472	D	c	0.382	0.393	0.424	0.203	0.707	0.730	0	3.56	0.397	5.540	0.667	0.897	0.411	1.000	0.715	0.998	0.697	9.878	0.402	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	187	3	10089683	.	G	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=163;VD=2;AF=0.0123;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.21618;SOR=inf;LSEQ=CCAGAGTATAATTTCATTTG;RSEQ=CAGTCTCCTATACAAATATG;CSQ=C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|16/44||NM_001018115.3:c.1361G>C|NP_001018125.1:p.Gly454Ala|1431|1361|454|G/A|gGc/gCc|||1||EntrezGene||||||3:g.10089683G>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|16/44||NM_001319984.2:c.1361G>C|NP_001306913.1:p.Gly454Ala|1584|1361|454|G/A|gGc/gCc|||1||EntrezGene||||||3:g.10089683G>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|16/43||NM_001374253.1:c.1361G>C|NP_001361182.1:p.Gly454Ala|1431|1361|454|G/A|gGc/gCc|||1||EntrezGene||||||3:g.10089683G>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|16/42||NM_001374254.1:c.1361G>C|NP_001361183.1:p.Gly454Ala|1431|1361|454|G/A|gGc/gCc|||1||EntrezGene||||||3:g.10089683G>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|16/43||NM_033084.6:c.1361G>C|NP_149075.2:p.Gly454Ala|1431|1361|454|G/A|gGc/gCc|||1||EntrezGene||YES||||3:g.10089683G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:163:2:1,1:90,70:160,2:0.0123:2,2:33.5:1:37:0:1:1.28369:60:4:0.0126:0:1	0/0:187:0:0,0:89,97:186,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    990. 

  990. 3	10089722	10089722	C	T	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon16:c.C1400T:p.T467M,FANCD2:NM_001319984:exon16:c.C1400T:p.T467M,FANCD2:NM_033084:exon16:c.C1400T:p.T467M	0.	.	.	.	.	.	.	.	.	rs760246372	.	0.086	0.326	T	0.521	0.357	P	0.115	0.303	B	0.000	0.559	D	0.939	0.268	N	2.43	0.707	M	0.65	0.527	T	-2.95	0.615	D	0.197	0.299	-0.867	0.508	T	0.202	0.559	T	0.028	0.510	D	3.287	0.454	22.8	0.983	0.396	0.895	0.497	D	c	-0.161	-0.077	0.615	0.218	0.707	0.730	0	3.83	0.431	2.549	0.452	-0.017	0.130	0.991	0.370	0.777	0.329	8.988	0.350	.	.	.	.	291542	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia|not_provided	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	173	3	10089722	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=168;VD=2;AF=0.0119;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.24199;SOR=inf;LSEQ=TGCATTTAAGTTTTTTGACA;RSEQ=GTACTGCCAGCAGGTATGTT;CSQ=T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|16/44||NM_001018115.3:c.1400C>T|NP_001018125.1:p.Thr467Met|1470|1400|467|T/M|aCg/aTg|rs760246372||1||EntrezGene||||||3:g.10089722C>T|1.988e-05|0|2.891e-05|0|0|0|3.516e-05|0|0|3.516e-05|gnomAD_NFE|uncertain_significance||1,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|16/44||NM_001319984.2:c.1400C>T|NP_001306913.1:p.Thr467Met|1623|1400|467|T/M|aCg/aTg|rs760246372||1||EntrezGene||||||3:g.10089722C>T|1.988e-05|0|2.891e-05|0|0|0|3.516e-05|0|0|3.516e-05|gnomAD_NFE|uncertain_significance||1,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|16/43||NM_001374253.1:c.1400C>T|NP_001361182.1:p.Thr467Met|1470|1400|467|T/M|aCg/aTg|rs760246372||1||EntrezGene||||||3:g.10089722C>T|1.988e-05|0|2.891e-05|0|0|0|3.516e-05|0|0|3.516e-05|gnomAD_NFE|uncertain_significance||1,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|16/42||NM_001374254.1:c.1400C>T|NP_001361183.1:p.Thr467Met|1470|1400|467|T/M|aCg/aTg|rs760246372||1||EntrezGene||||||3:g.10089722C>T|1.988e-05|0|2.891e-05|0|0|0|3.516e-05|0|0|3.516e-05|gnomAD_NFE|uncertain_significance||1,T|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|16/43||NM_033084.6:c.1400C>T|NP_149075.2:p.Thr467Met|1470|1400|467|T/M|aCg/aTg|rs760246372||1||EntrezGene||YES||||3:g.10089722C>T|1.988e-05|0|2.891e-05|0|0|0|3.516e-05|0|0|3.516e-05|gnomAD_NFE|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:168:2:1,1:90,76:166,2:0.0119:2,2:38.5:1:37:0:1:1.18301:60:4:0.012:0:1	0/0:173:0:0,0:85,88:173,0:0:2,0:40.8:1:36.2:1:1:0:58.5:42.25:1:0:0.1
    991. 

  991. 3	10089733	10089733	C	A	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon16:c.C1411A:p.Q471K,FANCD2:NM_001319984:exon16:c.C1411A:p.Q471K,FANCD2:NM_033084:exon16:c.C1411A:p.Q471K	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.998	0.875	D	0.000	0.843	D	1.000	0.511	D	2.79	0.817	M	0.45	0.565	T	-3.04	0.628	D	0.617	0.720	-0.438	0.708	T	0.350	0.714	T	0.041	0.596	D	6.778	0.923	32	0.995	0.697	0.974	0.741	D	c	0.803	0.785	1.000	0.747	0.707	0.730	0	5.65	0.868	6.846	0.750	0.803	0.325	1.000	0.715	0.996	0.625	17.222	0.868	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	3	10089733	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=162;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.25993;SOR=0;LSEQ=TTTTTGACACGTACTGCCAG;RSEQ=AGGTATGTTGAAACATTTAT;CSQ=A|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|16/44||NM_001018115.3:c.1411C>A|NP_001018125.1:p.Gln471Lys|1481|1411|471|Q/K|Cag/Aag|||1||EntrezGene||||||3:g.10089733C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|16/44||NM_001319984.2:c.1411C>A|NP_001306913.1:p.Gln471Lys|1634|1411|471|Q/K|Cag/Aag|||1||EntrezGene||||||3:g.10089733C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|16/43||NM_001374253.1:c.1411C>A|NP_001361182.1:p.Gln471Lys|1481|1411|471|Q/K|Cag/Aag|||1||EntrezGene||||||3:g.10089733C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|16/42||NM_001374254.1:c.1411C>A|NP_001361183.1:p.Gln471Lys|1481|1411|471|Q/K|Cag/Aag|||1||EntrezGene||||||3:g.10089733C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|16/43||NM_033084.6:c.1411C>A|NP_149075.2:p.Gln471Lys|1481|1411|471|Q/K|Cag/Aag|||1||EntrezGene||YES||||3:g.10089733C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:162:0:0,0:88,74:162,0:0:2,0:38.7:1:36.8:1:1:0:59.8:324:1:0:0.2	0/1:169:2:1,1:83,84:167,2:0.0118:2,2:29.5:1:37:0:1:1.01:60:4:0.0119:0:1
    992. 

  992. 3	10089759	10089759	C	T	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	146	3	10089759	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=160;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.22683;SOR=0;LSEQ=TGTTGAAACATTTATTTTGG;RSEQ=AAGGAGGGAACACAGAAAGG;CSQ=T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||16/43|NM_001018115.3:c.1413+24C>T|||||||||1||EntrezGene||||||3:g.10089759C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||16/43|NM_001319984.2:c.1413+24C>T|||||||||1||EntrezGene||||||3:g.10089759C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||16/42|NM_001374253.1:c.1413+24C>T|||||||||1||EntrezGene||||||3:g.10089759C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||16/41|NM_001374254.1:c.1413+24C>T|||||||||1||EntrezGene||||||3:g.10089759C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||16/42|NM_033084.6:c.1413+24C>T|||||||||1||EntrezGene||YES||||3:g.10089759C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:160:0:0,0:82,78:160,0:0:2,0:34.3:1:35.8:1:1:0:60:39:1:0:0.2	0/1:146:2:1,1:64,80:144,2:0.0137:2,2:9.5:1:37:0:1:1.25:60:4:0.0138:0:1
    993. 

  993. 3	10091124	10091124	G	A	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon17:c.G1480A:p.D494N,FANCD2:NM_001319984:exon17:c.G1480A:p.D494N,FANCD2:NM_033084:exon17:c.G1480A:p.D494N	.	.	.	.	.	.	.	.	.	.	.	0.147	0.249	T	0.992	0.629	D	0.888	0.612	P	0.000	0.463	D	0.992	0.415	D	2.535	0.741	M	0.54	0.549	T	-2.46	0.537	N	0.131	0.150	-0.621	0.640	T	0.262	0.634	T	0.039	0.586	D	4.164	0.558	23.8	0.998	0.922	0.917	0.539	D	c	0.458	0.416	0.100	0.164	0.732	0.924	0	4.7	0.586	5.246	0.650	0.879	0.385	1.000	0.715	0.473	0.266	13.582	0.612	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	296	3	10091124	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08667;SOR=inf;LSEQ=CTGAAGTTGATACTGCCTTA;RSEQ=ATGTCCTTCTAGAGTTGGTA;CSQ=A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|17/44||NM_001018115.3:c.1480G>A|NP_001018125.1:p.Asp494Asn|1550|1480|494|D/N|Gat/Aat|||1||EntrezGene||||||3:g.10091124G>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|17/44||NM_001319984.2:c.1480G>A|NP_001306913.1:p.Asp494Asn|1703|1480|494|D/N|Gat/Aat|||1||EntrezGene||||||3:g.10091124G>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|17/43||NM_001374253.1:c.1480G>A|NP_001361182.1:p.Asp494Asn|1550|1480|494|D/N|Gat/Aat|||1||EntrezGene||||||3:g.10091124G>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|17/42||NM_001374254.1:c.1480G>A|NP_001361183.1:p.Asp494Asn|1550|1480|494|D/N|Gat/Aat|||1||EntrezGene||||||3:g.10091124G>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|17/43||NM_033084.6:c.1480G>A|NP_149075.2:p.Asp494Asn|1550|1480|494|D/N|Gat/Aat|||1||EntrezGene||YES||||3:g.10091124G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:124:2:1,1:46,76:122,2:0.0161:2,2:21:0:37:0:1:1.65:60:4:0.0165:0:1	0/0:296:0:0,0:135,161:296,0:0:2,0:41.4:1:36.4:1:1:0:51.9:147:1:0:0.2
    994. 

  994. 3	10091131	10091131	T	C	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon17:c.T1487C:p.L496P,FANCD2:NM_001319984:exon17:c.T1487C:p.L496P,FANCD2:NM_033084:exon17:c.T1487C:p.L496P	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.992	0.790	D	0.000	0.537	D	1	0.810	D	2.79	0.817	M	0.05	0.619	T	-5.51	0.859	D	0.985	0.988	0.563	0.914	D	0.713	0.901	D	0.282	0.903	D	4.842	0.650	24.8	0.999	0.940	0.924	0.553	D	c	0.627	0.538	0.915	0.264	0.732	0.924	0	5.59	0.846	6.556	0.736	0.890	0.394	1.000	0.715	0.145	0.203	13.867	0.629	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	291	3	10091131	.	T	C	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=99;VD=2;AF=0.0202;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.06395;SOR=inf;LSEQ=TGATACTGCCTTAGATGTCC;RSEQ=TCTAGAGTTGGTAGTGTTAA;CSQ=C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|17/44||NM_001018115.3:c.1487T>C|NP_001018125.1:p.Leu496Pro|1557|1487|496|L/P|cTt/cCt|||1||EntrezGene||||||3:g.10091131T>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|17/44||NM_001319984.2:c.1487T>C|NP_001306913.1:p.Leu496Pro|1710|1487|496|L/P|cTt/cCt|||1||EntrezGene||||||3:g.10091131T>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|17/43||NM_001374253.1:c.1487T>C|NP_001361182.1:p.Leu496Pro|1557|1487|496|L/P|cTt/cCt|||1||EntrezGene||||||3:g.10091131T>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|17/42||NM_001374254.1:c.1487T>C|NP_001361183.1:p.Leu496Pro|1557|1487|496|L/P|cTt/cCt|||1||EntrezGene||||||3:g.10091131T>C||||||||||||||,C|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|17/43||NM_033084.6:c.1487T>C|NP_149075.2:p.Leu496Pro|1557|1487|496|L/P|cTt/cCt|||1||EntrezGene||YES||||3:g.10091131T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:99:2:1,1:33,64:97,2:0.0202:2,2:62:1:31:1:1:1.93:60:4:0.0204:0:1	0/0:291:0:0,0:128,163:291,0:0:2,0:41.2:1:36.3:1:1:0:51.5:96:1:0:0.2
    995. 

  995. 3	10106366	10106366	T	C	intronic	FANCD2	.	.	.	0.0001	0.0003	0.0005	0	0	0.0022	0	7.167e-05	0	rs4019782	rs4019782	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55035994;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11401077	LUSC-KR|2|170|0.0117647,PRAD-UK|1|140|0.00714286	0.5	235	110	3	10106366	.	T	C	235	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1036;VD=86;AF=0.083;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.57101;SOR=1.01589;LSEQ=TAGTGGTTTTCCCTGTAGCC;RSEQ=TGCGTATTCCTGAGCTGCAA;CSQ=C|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||22/43|NM_001018115.3:c.2022-47T>C|||||||rs4019782&COSV55035994||1||EntrezGene||||||3:g.10106366T>C|3.984e-06|0|0|0|0|4.684e-05|0|0|0|4.684e-05|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||22/43|NM_001319984.2:c.2022-47T>C|||||||rs4019782&COSV55035994||1||EntrezGene||||||3:g.10106366T>C|3.984e-06|0|0|0|0|4.684e-05|0|0|0|4.684e-05|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||21/42|NM_001374253.1:c.1911-47T>C|||||||rs4019782&COSV55035994||1||EntrezGene||||||3:g.10106366T>C|3.984e-06|0|0|0|0|4.684e-05|0|0|0|4.684e-05|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||22/41|NM_001374254.1:c.2022-47T>C|||||||rs4019782&COSV55035994||1||EntrezGene||||||3:g.10106366T>C|3.984e-06|0|0|0|0|4.684e-05|0|0|0|4.684e-05|gnomAD_FIN||0&1|0&1,C|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||22/42|NM_033084.6:c.2022-47T>C|||||||rs4019782&COSV55035994||1||EntrezGene||YES||||3:g.10106366T>C|3.984e-06|0|0|0|0|4.684e-05|0|0|0|4.684e-05|gnomAD_FIN||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1036:86:78,8:613,337:950,86:0.083:2,2:15.7:1:36.7:1:0:5.35:19:172:0.0846:0:3.8	0/1:110:9:7,2:71,30:101,9:0.0818:2,2:15.1:1:37:0:1:1.47:22.7:18:0.0818:0:3.9
    996. 

  996. 3	10106386	10106386	A	G	intronic	FANCD2	.	.	.	0.0004	0.0004	0.0006	0	0	0.0007	0.0006	0.0003	0	rs4019783	rs4019783	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55034741;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),1(prostate)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29395696	LAML-KR|2|205|0.0097561,LUSC-KR|3|170|0.0176471	0.5	264	153	3	10106386	.	A	G	264	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1301;VD=143;AF=0.1099;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.42883;SOR=0.9262;LSEQ=TTGCGTATTCCTGAGCTGCA;RSEQ=CATCAGATTCTGGTTTTTCT;CSQ=G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||22/43|NM_001018115.3:c.2022-27A>G|||||||rs4019783&COSV55034741||1||EntrezGene||||||3:g.10106386A>G|0.0001436|0|0.0003181|0|0|0.0002857|0.0001496|0.0001631|3.267e-05|0.0003181|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||22/43|NM_001319984.2:c.2022-27A>G|||||||rs4019783&COSV55034741||1||EntrezGene||||||3:g.10106386A>G|0.0001436|0|0.0003181|0|0|0.0002857|0.0001496|0.0001631|3.267e-05|0.0003181|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||21/42|NM_001374253.1:c.1911-27A>G|||||||rs4019783&COSV55034741||1||EntrezGene||||||3:g.10106386A>G|0.0001436|0|0.0003181|0|0|0.0002857|0.0001496|0.0001631|3.267e-05|0.0003181|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||22/41|NM_001374254.1:c.2022-27A>G|||||||rs4019783&COSV55034741||1||EntrezGene||||||3:g.10106386A>G|0.0001436|0|0.0003181|0|0|0.0002857|0.0001496|0.0001631|3.267e-05|0.0003181|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||22/42|NM_033084.6:c.2022-27A>G|||||||rs4019783&COSV55034741||1||EntrezGene||YES||||3:g.10106386A>G|0.0001436|0|0.0003181|0|0|0.0002857|0.0001496|0.0001631|3.267e-05|0.0003181|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1301:143:137,6:727,429:1156,143:0.1099:2,1:23.6:1:36.9:1:0:13.46:23:286:0.1116:0:3	0/1:153:18:15,3:96,39:135,18:0.1176:2,2:20.6:1:37:0:0.40102:2.02:27.3:36:0.1184:0:2.9
    997. 

  997. 3	10106408	10106408	C	T	intronic	FANCD2	.	.	.	0.0063	0.0025	0.0035	0.0042	0	0.0073	0.0016	0.0017	0.0023	rs4019784	rs4019784	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55031929;OCCURENCE=1(large_intestine),1(biliary_tract)	215265	Fanconi_anemia,_complementation_group_D2|Fanconi_anemia,_complementation_group_A|not_specified|not_provided	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646|MONDO:MONDO:0009215,MedGen:C3469521,OMIM:227650|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU29395713	LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.5	288	208	3	10106408	.	C	T	288	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1743;VD=247;AF=0.1417;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.35026;SOR=0.90812;LSEQ=ATCAGATTCTGGTTTTTCTC;RSEQ=GCAGTGACTTTCCATTTCCT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||22/43|NM_001018115.3:c.2022-5C>T|||||||rs4019784&COSV55031929||1||EntrezGene||||||3:g.10106408C>T|0.0002771|0.0001895|5.846e-05|0|0.0003375|0.001642|0.0001341|0.0003315|0.0002646|0.001642|gnomAD_FIN|likely_benign&benign/likely_benign|0&1|1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||22/43|NM_001319984.2:c.2022-5C>T|||||||rs4019784&COSV55031929||1||EntrezGene||||||3:g.10106408C>T|0.0002771|0.0001895|5.846e-05|0|0.0003375|0.001642|0.0001341|0.0003315|0.0002646|0.001642|gnomAD_FIN|likely_benign&benign/likely_benign|0&1|1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||21/42|NM_001374253.1:c.1911-5C>T|||||||rs4019784&COSV55031929||1||EntrezGene||||||3:g.10106408C>T|0.0002771|0.0001895|5.846e-05|0|0.0003375|0.001642|0.0001341|0.0003315|0.0002646|0.001642|gnomAD_FIN|likely_benign&benign/likely_benign|0&1|1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||22/41|NM_001374254.1:c.2022-5C>T|||||||rs4019784&COSV55031929||1||EntrezGene||||||3:g.10106408C>T|0.0002771|0.0001895|5.846e-05|0|0.0003375|0.001642|0.0001341|0.0003315|0.0002646|0.001642|gnomAD_FIN|likely_benign&benign/likely_benign|0&1|1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding||22/42|NM_033084.6:c.2022-5C>T|||||||rs4019784&COSV55031929||1||EntrezGene||YES||||3:g.10106408C>T|0.0002771|0.0001895|5.846e-05|0|0.0003375|0.001642|0.0001341|0.0003315|0.0002646|0.001642|gnomAD_FIN|likely_benign&benign/likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1743:247:202,45:887,607:1494,247:0.1417:2,2:31.2:1:36.3:1:0:3.07:27.6:81.333:0.1417:0:2.2	0/1:208:32:25,7:122,54:176,32:0.1538:2,2:27.4:1:36.6:1:0.40042:1.58:32.7:64:0.1576:0:1.9
    998. 

  998. 3	10107587	10107587	A	G	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon25:c.A2309G:p.K770R,FANCD2:NM_001319984:exon25:c.A2309G:p.K770R,FANCD2:NM_033084:exon25:c.A2309G:p.K770R	0.001	3.228e-05	0	0	0	0	0.0003	0	0	rs533245636	.	0.432	0.095	T	0.171	0.271	B	0.117	0.304	B	0.000	0.439	N	0.971	0.257	N	0.03	0.081	N	0.32	0.585	T	-1.37	0.340	N	0.129	0.147	-1.019	0.240	T	0.085	0.332	T	0.017	0.390	T	0.988	0.189	10.59	0.976	0.343	0.532	0.291	D	c	-0.775	-0.696	0.001	0.080	0.707	0.730	0	-2.5	0.060	1.474	0.348	-0.745	0.035	0.995	0.385	0.894	0.377	7.457	0.263	.	.	.	ID=COSV105156017;OCCURENCE=1(pancreas)	931656	Fanconi_anemia	MONDO:MONDO:0019391,MedGen:C0015625,OMIM:PS227650,Orphanet:ORPHA84,SNOMED_CT:30575002	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	226	207	3	10107587	.	A	G	226	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=309;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TGACCTGGAGCCTGGAGAGA;RSEQ=GTTGGAGTCCATGTCTGCTA;CSQ=G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|25/44||NM_001018115.3:c.2309A>G|NP_001018125.1:p.Lys770Arg|2379|2309|770|K/R|aAg/aGg|rs533245636||1||EntrezGene||||||3:g.10107587A>G|4.38e-05|0|0.0001446|0|5.437e-05|0|4.407e-05|0|0|0.001|EUR|uncertain_significance||1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|25/44||NM_001319984.2:c.2309A>G|NP_001306913.1:p.Lys770Arg|2532|2309|770|K/R|aAg/aGg|rs533245636||1||EntrezGene||||||3:g.10107587A>G|4.38e-05|0|0.0001446|0|5.437e-05|0|4.407e-05|0|0|0.001|EUR|uncertain_significance||1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|24/43||NM_001374253.1:c.2198A>G|NP_001361182.1:p.Lys733Arg|2268|2198|733|K/R|aAg/aGg|rs533245636||1||EntrezGene||||||3:g.10107587A>G|4.38e-05|0|0.0001446|0|5.437e-05|0|4.407e-05|0|0|0.001|EUR|uncertain_significance||1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|25/42||NM_001374254.1:c.2309A>G|NP_001361183.1:p.Lys770Arg|2379|2309|770|K/R|aAg/aGg|rs533245636||1||EntrezGene||||||3:g.10107587A>G|4.38e-05|0|0.0001446|0|5.437e-05|0|4.407e-05|0|0|0.001|EUR|uncertain_significance||1,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|25/43||NM_033084.6:c.2309A>G|NP_149075.2:p.Lys770Arg|2379|2309|770|K/R|aAg/aGg|rs533245636||1||EntrezGene||YES||||3:g.10107587A>G|4.38e-05|0|0.0001446|0|5.437e-05|0|4.407e-05|0|0|0.001|EUR|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:309:0:0,0:157,152:309,0:0:2,0:36.4:1:34.8:1:1:0:58.4:19.6:1:0:0.1	0/1:207:76:30,46:58,73:131,76:0.3671:2,2:39.5:1:36.2:1:0.56053:1.2171:47.2:75:0.3641:0:1
    999. 

  999. 3	10116209	10116209	C	A	intronic	FANCD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	114	3	10116209	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.84461;SOR=0;LSEQ=CTTTGTTGCTGTGACTTCCC;RSEQ=ATAGGAGTTCACAGGGAAGG;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||28/43|NM_001018115.3:c.2716-5C>A|||||||||1||EntrezGene||||||3:g.10116209C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||28/43|NM_001319984.2:c.2716-5C>A|||||||||1||EntrezGene||||||3:g.10116209C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||27/42|NM_001374253.1:c.2605-5C>A|||||||||1||EntrezGene||||||3:g.10116209C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||28/41|NM_001374254.1:c.2716-5C>A|||||||||1||EntrezGene||||||3:g.10116209C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding||28/42|NM_033084.6:c.2716-5C>A|||||||||1||EntrezGene||YES||||3:g.10116209C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:7,3:10,0:0:2,0:32.4:1:37:0:1:0:60:20:1:0:0	0/1:114:2:1,1:70,42:112,2:0.0175:2,2:26.5:1:37:0:1:1.65883:60:4:0.0182:0:1
    1000. 

  1000. 3	10128793	10128793	G	A	intronic	FANCD2;FANCD2OS	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	75	3	10128793	.	G	A	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=170;VD=2;AF=0.0118;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.4806;SOR=inf;LSEQ=CATAGGATACTATTGCATTT;RSEQ=TTTGTTTTTCTTGTCTCCTT;CSQ=A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||33/43|NM_001018115.3:c.3336-25G>A|||||||||1||EntrezGene||||||3:g.10128793G>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||33/43|NM_001319984.2:c.3336-25G>A|||||||||1||EntrezGene||||||3:g.10128793G>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||32/42|NM_001374253.1:c.3225-25G>A|||||||||1||EntrezGene||||||3:g.10128793G>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||33/41|NM_001374254.1:c.3336-25G>A|||||||||1||EntrezGene||||||3:g.10128793G>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||33/42|NM_033084.6:c.3336-25G>A|||||||||1||EntrezGene||YES||||3:g.10128793G>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-5578C>T|||||||||-1||EntrezGene||||||3:g.10128793G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:170:2:1,1:91,77:168,2:0.0118:2,2:13:0:31:1:1:1.18065:60:4:0.0118:0:1	0/0:75:0:0,0:48,27:75,0:0:2,0:39.1:1:36.7:1:1:0:60:150:1:0:0.1
    1001. 

  1001. 3	10128818	10128818	C	T	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon34:c.C3336T:p.S1112S,FANCD2:NM_001319984:exon34:c.C3336T:p.S1112S,FANCD2:NM_033084:exon34:c.C3336T:p.S1112S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	MU129774400	UCEC-US|1|531|0.00188324	0.25	31	96	3	10128818	.	C	T	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=212;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.09645;SOR=0;LSEQ=TTTTTCTTGTCTCCTTACAG;RSEQ=CAGAGCGTCCATTACTTGCA;CSQ=T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|34/44||NM_001018115.3:c.3336C>T|NP_001018125.1:p.Ser1112%3D|3406|3336|1112|S|agC/agT|||1||EntrezGene||||||3:g.10128818C>T||||||||||||||,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|34/44||NM_001319984.2:c.3336C>T|NP_001306913.1:p.Ser1112%3D|3559|3336|1112|S|agC/agT|||1||EntrezGene||||||3:g.10128818C>T||||||||||||||,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|33/43||NM_001374253.1:c.3225C>T|NP_001361182.1:p.Ser1075%3D|3295|3225|1075|S|agC/agT|||1||EntrezGene||||||3:g.10128818C>T||||||||||||||,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|34/42||NM_001374254.1:c.3336C>T|NP_001361183.1:p.Ser1112%3D|3406|3336|1112|S|agC/agT|||1||EntrezGene||||||3:g.10128818C>T||||||||||||||,T|splice_region_variant&synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|34/43||NM_033084.6:c.3336C>T|NP_149075.2:p.Ser1112%3D|3406|3336|1112|S|agC/agT|||1||EntrezGene||YES||||3:g.10128818C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-5603G>A|||||||||-1||EntrezGene||||||3:g.10128818C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:212:0:0,0:107,104:211,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:96:2:1,1:53,41:94,2:0.0208:2,2:5:0:31:1:1:1.28918:60:4:0.0213:0:1.5
    1002. 

  1002. 3	10128935	10128935	C	T	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon34:c.C3453T:p.N1151N,FANCD2:NM_001319984:exon34:c.C3453T:p.N1151N,FANCD2:NM_033084:exon34:c.C3453T:p.N1151N	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	85	73	3	10128935	.	C	T	85	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=5;AF=0.0532;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.05387;SOR=inf;LSEQ=TCAACAGCTTCTGCTCAGAA;RSEQ=AAAGAAAAAATTGGTGATGG;CSQ=T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|34/44||NM_001018115.3:c.3453C>T|NP_001018125.1:p.Asn1151%3D|3523|3453|1151|N|aaC/aaT|CD072415||1||EntrezGene||||||3:g.10128935C>T||||||||||||||1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|34/44||NM_001319984.2:c.3453C>T|NP_001306913.1:p.Asn1151%3D|3676|3453|1151|N|aaC/aaT|CD072415||1||EntrezGene||||||3:g.10128935C>T||||||||||||||1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|33/43||NM_001374253.1:c.3342C>T|NP_001361182.1:p.Asn1114%3D|3412|3342|1114|N|aaC/aaT|CD072415||1||EntrezGene||||||3:g.10128935C>T||||||||||||||1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|34/42||NM_001374254.1:c.3453C>T|NP_001361183.1:p.Asn1151%3D|3523|3453|1151|N|aaC/aaT|CD072415||1||EntrezGene||||||3:g.10128935C>T||||||||||||||1,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|34/43||NM_033084.6:c.3453C>T|NP_149075.2:p.Asn1151%3D|3523|3453|1151|N|aaC/aaT|CD072415||1||EntrezGene||YES||||3:g.10128935C>T||||||||||||||1,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-5720G>A|||||||CD072415||-1||EntrezGene||||||3:g.10128935C>T||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:94:5:3,2:41,48:89,5:0.0532:2,2:43.8:1:37:0:0.66221:1.75:60:10:0.0667:0:1	0/0:73:0:0,0:31,41:72,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1003. 

  1003. 3	10130153	10130153	C	A	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon35:c.C3487A:p.L1163I,FANCD2:NM_001319984:exon35:c.C3487A:p.L1163I,FANCD2:NM_033084:exon35:c.C3487A:p.L1163I	.	.	.	.	.	.	.	.	.	.	.	0.014	0.531	D	1.0	0.899	D	0.992	0.790	D	0.000	0.843	D	1	0.810	D	2.79	0.817	M	0.17	0.605	T	-1.61	0.387	N	0.362	0.594	-0.117	0.797	T	0.430	0.772	T	0.116	0.795	D	7.163	0.944	34	0.996	0.756	0.992	0.929	D	c	0.859	0.826	1.000	0.747	0.707	0.730	0	5.7	0.886	6.345	0.728	0.932	0.445	1.000	0.715	0.424	0.258	17.387	0.873	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	269	3	10130153	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=441;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.05401;SOR=0;LSEQ=CTTCCCTTGCCAGACAATTC;RSEQ=TCTGTCGGGTGTGGCCAAGT;CSQ=A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|35/44||NM_001018115.3:c.3487C>A|NP_001018125.1:p.Leu1163Ile|3557|3487|1163|L/I|Ctc/Atc|||1||EntrezGene||||||3:g.10130153C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|35/44||NM_001319984.2:c.3487C>A|NP_001306913.1:p.Leu1163Ile|3710|3487|1163|L/I|Ctc/Atc|||1||EntrezGene||||||3:g.10130153C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|34/43||NM_001374253.1:c.3376C>A|NP_001361182.1:p.Leu1126Ile|3446|3376|1126|L/I|Ctc/Atc|||1||EntrezGene||||||3:g.10130153C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|35/42||NM_001374254.1:c.3487C>A|NP_001361183.1:p.Leu1163Ile|3557|3487|1163|L/I|Ctc/Atc|||1||EntrezGene||||||3:g.10130153C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|35/43||NM_033084.6:c.3487C>A|NP_149075.2:p.Leu1163Ile|3557|3487|1163|L/I|Ctc/Atc|||1||EntrezGene||YES||||3:g.10130153C>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-6938G>T|||||||||-1||EntrezGene||||||3:g.10130153C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:441:0:0,0:240,201:441,0:0:2,0:37.7:1:36.1:1:1:0:60:48:1:0:0.1	0/1:269:3:2,1:141,125:266,3:0.0112:2,2:13.3:1:28.3:1:1:1.77:60:2:0.0077:0:1.3
    1004. 

  1004. 3	10130485	10130485	G	-	intronic	FANCD2;FANCD2OS	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	189	3	10130484	.	TG	T	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=103;VD=3;AF=0.0291;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.04306;SOR=inf;LSEQ=TATTCTACTTTGTTAATTAG;RSEQ=GGTCAAATATTTGACTCTCA;CSQ=-|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||35/43|NM_001018115.3:c.3561-25del|||||||||1||EntrezGene||||||3:g.10130487del||||||||||||||,-|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||35/43|NM_001319984.2:c.3561-25del|||||||||1||EntrezGene||||||3:g.10130487del||||||||||||||,-|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||34/42|NM_001374253.1:c.3450-25del|||||||||1||EntrezGene||||||3:g.10130487del||||||||||||||,-|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||35/41|NM_001374254.1:c.3561-25del|||||||||1||EntrezGene||||||3:g.10130487del||||||||||||||,-|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||35/42|NM_033084.6:c.3561-25del|||||||||1||EntrezGene||YES||||3:g.10130487del||||||||||||||,-|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-7270del|||||||||-1||EntrezGene||||||3:g.10130487del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:103:3:2,1:77,23:100,3:0.0291:2,2:49:1:37:0:0.55285:1.66452:60:6:0.0291:0:0	0/0:189:0:0,0:119,69:188,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1005. 

  1005. 3	10131970	10131970	T	C	intronic	FANCD2;FANCD2OS	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	176	3	10131970	.	T	C	25	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1237;VD=2;AF=0.0016;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.0781;SOR=0.14124;LSEQ=GCACGCATGCTTTTCCCGTC;RSEQ=TCTAGGCATACTTTTGTTGT;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||36/43|NM_001018115.3:c.3684-6T>C|||||||||1||EntrezGene||||||3:g.10131970T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||36/43|NM_001319984.2:c.3684-6T>C|||||||||1||EntrezGene||||||3:g.10131970T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||35/42|NM_001374253.1:c.3573-6T>C|||||||||1||EntrezGene||||||3:g.10131970T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||36/41|NM_001374254.1:c.3684-6T>C|||||||||1||EntrezGene||||||3:g.10131970T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding||36/42|NM_033084.6:c.3684-6T>C|||||||||1||EntrezGene||YES||||3:g.10131970T>C||||||||||||||,C|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-8755A>G|||||||||-1||EntrezGene||||||3:g.10131970T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1237:2:1,1:634,601:1235,2:0.0016:2,2:57.5:1:37:0:1:1.05489:60:4:0.0016:0:1	0/1:176:2:1,1:105,69:174,2:0.0114:2,2:44:1:25:0:1:1.51797:60:4:0.0117:0:1
    1006. 

  1006. 3	10133868	10133868	C	A	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon38:c.C3781A:p.H1261N,FANCD2:NM_001319984:exon38:c.C3781A:p.H1261N,FANCD2:NM_033084:exon38:c.C3781A:p.H1261N	.	.	.	.	.	.	.	.	.	.	.	0.32	0.135	T	0.981	0.577	D	0.7	0.523	P	0.000	0.843	D	1	0.810	D	2.52	0.738	M	0.82	0.481	T	-1.29	0.324	N	0.233	0.285	-0.834	0.531	T	0.193	0.546	T	0.020	0.423	T	3.428	0.470	23.0	0.989	0.470	0.995	0.964	D	c	0.625	0.666	1.000	0.747	0.707	0.730	0	5.57	0.840	7.155	0.769	0.932	0.445	1.000	0.715	0.975	0.474	17.110	0.865	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	170	3	10133868	.	C	A	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=511;VD=1;AF=0.002;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.15542;SOR=0.16525;LSEQ=ATATTTGGCTGCCCCAGATT;RSEQ=ATGAAGAGAAACTCCTCTAC;CSQ=A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|38/44||NM_001018115.3:c.3781C>A|NP_001018125.1:p.His1261Asn|3851|3781|1261|H/N|Cat/Aat|||1||EntrezGene||||||3:g.10133868C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|38/44||NM_001319984.2:c.3781C>A|NP_001306913.1:p.His1261Asn|4004|3781|1261|H/N|Cat/Aat|||1||EntrezGene||||||3:g.10133868C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|37/43||NM_001374253.1:c.3670C>A|NP_001361182.1:p.His1224Asn|3740|3670|1224|H/N|Cat/Aat|||1||EntrezGene||||||3:g.10133868C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|38/42||NM_001374254.1:c.3781C>A|NP_001361183.1:p.His1261Asn|3851|3781|1261|H/N|Cat/Aat|||1||EntrezGene||||||3:g.10133868C>A||||||||||||||,A|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_033084.6|protein_coding|38/43||NM_033084.6:c.3781C>A|NP_149075.2:p.His1261Asn|3851|3781|1261|H/N|Cat/Aat|||1||EntrezGene||YES||||3:g.10133868C>A||||||||||||||,A|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*44-10653G>T|||||||||-1||EntrezGene||||||3:g.10133868C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:511:1:1,0:320,190:510,1:0.002:2,0:62:0:11:0:1:0:60:0:0:0:3	0/1:170:2:1,1:78,90:168,2:0.0118:2,2:47.5:1:37:0:1:1.15:60:4:0.0118:0:1
    1007. 

  1007. 3	10136913	10136913	C	T	exonic	FANCD2	.	synonymous SNV	FANCD2:NM_001018115:exon41:c.C3993T:p.F1331F,FANCD2:NM_001319984:exon41:c.C3993T:p.F1331F,FANCD2:NM_033084:exon41:c.C3993T:p.F1331F	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	254	3	10136913	.	C	T	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=198;VD=2;AF=0.0101;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.19134;SOR=inf;LSEQ=CTGAGCTTACTGGAAACCTT;RSEQ=CAGTTGGACACAAGGCTGCT;CSQ=T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|41/44||NM_001018115.3:c.3993C>T|NP_001018125.1:p.Phe1331%3D|4063|3993|1331|F|ttC/ttT|||1||EntrezGene||||||3:g.10136913C>T||||||||||||||,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|41/44||NM_001319984.2:c.3993C>T|NP_001306913.1:p.Phe1331%3D|4216|3993|1331|F|ttC/ttT|||1||EntrezGene||||||3:g.10136913C>T||||||||||||||,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|40/43||NM_001374253.1:c.3882C>T|NP_001361182.1:p.Phe1294%3D|3952|3882|1294|F|ttC/ttT|||1||EntrezGene||||||3:g.10136913C>T||||||||||||||,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|40/42||NM_001374254.1:c.3954C>T|NP_001361183.1:p.Phe1318%3D|4024|3954|1318|F|ttC/ttT|||1||EntrezGene||||||3:g.10136913C>T||||||||||||||,T|synonymous_variant|LOW|FANCD2|2177|Transcript|NM_033084.6|protein_coding|41/43||NM_033084.6:c.3993C>T|NP_149075.2:p.Phe1331%3D|4063|3993|1331|F|ttC/ttT|||1||EntrezGene||YES||||3:g.10136913C>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*43+8969G>A|||||||||-1||EntrezGene||||||3:g.10136913C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:198:2:1,1:129,67:196,2:0.0101:2,2:5:0:37:0:1:1.91862:60:4:0.0102:0:1	0/0:254:0:0,0:137,117:254,0:0:2,0:41:1:36.7:1:1:0:60:253:1:0:0
    1008. 

  1008. 3	10140678	10140678	C	T	UTR3	FANCD2	NM_033084:c.*44C>T	.	.	0.0001	.	.	.	.	.	.	.	.	rs370459744	rs370459744	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	288509	Fanconi_anemia,_complementation_group_D2	MONDO:MONDO:0009214,MedGen:C3160738,OMIM:227646	criteria_provided,_single_submitter	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	84	3	10140678	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=103;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20045;SOR=0;LSEQ=TTGGGACCCAGAAGAAACAA;RSEQ=GACACAATCTTAGAATCACT;CSQ=T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding||43/43|NM_001018115.3:c.4281+179C>T|||||||rs370459744||1||EntrezGene||||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|downstream_gene_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_001164839.2|protein_coding||||||||||rs370459744|4943|-1||EntrezGene||YES||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding||43/43|NM_001319984.2:c.4281+179C>T|||||||rs370459744||1||EntrezGene||||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|intron_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding||42/42|NM_001374253.1:c.4170+179C>T|||||||rs370459744||1||EntrezGene||||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|42/42||NM_001374254.1:c.*44C>T||4491|||||rs370459744||1||EntrezGene||||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding|43/43||NM_033084.6:c.*44C>T||4530|||||rs370459744||1||EntrezGene||YES||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*43+5204G>A|||||||rs370459744||-1||EntrezGene||||||3:g.10140678C>T|1.994e-05|0|0|0|0|0|1.765e-05|0.0001636|6.533e-05|0.0001636|gnomAD_OTH|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:103:0:0,0:29,74:103,0:0:2,0:34.6:1:36.3:1:1:0:60:102:1:0:0.5	0/1:84:2:1,1:20,62:82,2:0.0238:2,2:14:1:37:0:0.43976:3.05:60:4:0.0241:0:1
    1009. 

  1009. 3	10142879	10142879	A	G	exonic	FANCD2	.	nonsynonymous SNV	FANCD2:NM_001018115:exon44:c.A4289G:p.E1430G,FANCD2:NM_001319984:exon44:c.A4289G:p.E1430G	0.	.	.	.	.	.	.	.	.	rs767416501	.	0.036	0.433	D	0.004	0.112	B	0.004	0.093	B	.	.	.	1.000	0.090	N	.	.	.	0.69	0.517	T	-2.33	0.516	N	0.046	0.040	-1.014	0.258	T	0.069	0.284	T	0.003	0.063	T	0.938	0.184	10.30	0.988	0.462	0.525	0.289	D	c	-0.622	-0.633	0.947	0.277	0.732	0.924	0	-0.796	0.103	1.651	0.367	1.001	0.622	0.973	0.343	0.579	0.285	0.554	0.006	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	158	3	10142879	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=428;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.07236;SOR=0;LSEQ=CTTTGCCCCTTAGGATGGTG;RSEQ=AGAAGACGAAGTAAGTGCTG;CSQ=G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|44/44||NM_001018115.3:c.4289A>G|NP_001018125.1:p.Glu1430Gly|4359|4289|1430|E/G|gAa/gGa|rs767416501||1||EntrezGene||||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|downstream_gene_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_001164839.2|protein_coding||||||||||rs767416501|2742|-1||EntrezGene||YES||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|44/44||NM_001319984.2:c.4289A>G|NP_001306913.1:p.Glu1430Gly|4512|4289|1430|E/G|gAa/gGa|rs767416501||1||EntrezGene||||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|missense_variant|MODERATE|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|43/43||NM_001374253.1:c.4178A>G|NP_001361182.1:p.Glu1393Gly|4248|4178|1393|E/G|gAa/gGa|rs767416501||1||EntrezGene||||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||||||||||rs767416501|1852|1||EntrezGene||||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||||||||||rs767416501|1852|1||EntrezGene||YES||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||,G|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*43+3003T>C|||||||rs767416501||-1||EntrezGene||||||3:g.10142879A>G|7.954e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:428:0:0,0:261,167:428,0:0:2,0:32.7:1:36.3:1:1:0:60:84.6:1:0:0.2	0/1:158:2:1,1:93,63:156,2:0.0127:2,2:37:0:37:0:1:1.47243:60:4:0.0129:0:2
    1010. 

  1010. 3	10142949	10142949	C	T	UTR3	FANCD2	NM_001018115:c.*3C>T;NM_001319984:c.*3C>T	.	.	0.47	0.3122	0.0833	0.2512	0.4834	0.1103	0.4501	0.4301	0.3905	rs3172417	rs3172417	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55031865;OCCURENCE=1(stomach),17(soft_tissue)	250849	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	228	173	3	10142949	.	C	T	228	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=608;VD=38;AF=0.0625;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=0.07791;LSEQ=TATGATGACTCTGATTAGAC;RSEQ=CCAGATAAATTGTTGCCTGC;CSQ=T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|44/44||NM_001018115.3:c.*3C>T||4429|||||rs3172417&COSV55031865||1||EntrezGene||||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_001164839.2|protein_coding||||||||||rs3172417&COSV55031865|2672|-1||EntrezGene||YES||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|44/44||NM_001319984.2:c.*3C>T||4582|||||rs3172417&COSV55031865||1||EntrezGene||||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|43/43||NM_001374253.1:c.*3C>T||4318|||||rs3172417&COSV55031865||1||EntrezGene||||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding||||||||||rs3172417&COSV55031865|1922|1||EntrezGene||||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding||||||||||rs3172417&COSV55031865|1922|1||EntrezGene||YES||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*43+2933G>A|||||||rs3172417&COSV55031865||-1||EntrezGene||||||3:g.10142949C>T|0.3303|0.0692|0.2087|0.4715|0.1234|0.4677|0.4223|0.3872|0.2349|0.4715|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:608:38:18,20:284,283:567,38:0.0625:2,2:44.1:1:36.4:1:0.86719:1.11484:60:76:0.064:0:1.3	0/1:173:80:36,44:40,53:93,80:0.4624:2,2:40.4:1:36.1:1:0.87808:1.08:60:79:0.4647:0:1.1
    1011. 

  1011. 3	10142961	10142961	G	T	UTR3	FANCD2	NM_001018115:c.*15G>T;NM_001319984:c.*15G>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	162	3	10142961	.	G	T	44	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=609;VD=1;AF=0.0016;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.03089;SOR=0.08757;LSEQ=GATTAGACCCCAGATAAATT;RSEQ=TTGCCTGCTTCTGTGTCTCT;CSQ=T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001018115.3|protein_coding|44/44||NM_001018115.3:c.*15G>T||4441|||||||1||EntrezGene||||||3:g.10142961G>T||||||||||||||,T|downstream_gene_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_001164839.2|protein_coding|||||||||||2660|-1||EntrezGene||YES||||3:g.10142961G>T||||||||||||||,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001319984.2|protein_coding|44/44||NM_001319984.2:c.*15G>T||4594|||||||1||EntrezGene||||||3:g.10142961G>T||||||||||||||,T|3_prime_UTR_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374253.1|protein_coding|43/43||NM_001374253.1:c.*15G>T||4330|||||||1||EntrezGene||||||3:g.10142961G>T||||||||||||||,T|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_001374254.1|protein_coding|||||||||||1934|1||EntrezGene||||||3:g.10142961G>T||||||||||||||,T|downstream_gene_variant|MODIFIER|FANCD2|2177|Transcript|NM_033084.6|protein_coding|||||||||||1934|1||EntrezGene||YES||||3:g.10142961G>T||||||||||||||,T|intron_variant|MODIFIER|FANCD2OS|115795|Transcript|NM_173472.2|protein_coding||2/2|NM_173472.2:c.*43+2921C>A|||||||||-1||EntrezGene||||||3:g.10142961G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:609:1:1,0:303,305:608,1:0.0016:2,0:53:0:11:0:0.49918:0:60:0:0:0:1	0/1:162:3:1,2:71,88:159,3:0.0185:2,2:53.3:1:28.3:1:1:1.60907:60:2:0.0127:0:1.3
    1012. 

  1012. 3	10183551	10183551	A	C	exonic	VHL	.	nonsynonymous SNV	VHL:NM_000551:exon1:c.A20C:p.N7T,VHL:NM_198156:exon1:c.A20C:p.N7T	.	.	.	.	.	.	.	.	.	.	.	0.015	0.524	D	0.013	0.154	B	0.025	0.193	B	0.345	0.042	N	1	0.090	N	0.345	0.112	N	-1.87	0.844	D	-0.81	0.223	N	0.114	0.124	-0.696	0.606	T	0.343	0.709	T	0.072	0.715	D	-1.839	0.010	0.002	0.232	0.010	0.151	0.186	N	c	-1.771	-1.871	1.000	0.747	0.442	0.072	0	-5.05	0.027	-1.528	0.023	-1.870	0.006	0.000	0.063	0.000	0.016	11.953	0.521	.	.	.	ID=COSV56571931;OCCURENCE=1(soft_tissue)	630696	Von_Hippel-Lindau_syndrome|Erythrocytosis,_familial,_2	MONDO:MONDO:0008667,MedGen:C0019562,OMIM:193300,Orphanet:ORPHA892,SNOMED_CT:46659004|MONDO:MONDO:0009892,MedGen:C1837915,OMIM:263400,Orphanet:ORPHA238557	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	17	123	3	10183551	.	A	C	17	f0.01;p8;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=355;VD=3;AF=0.0085;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.38269;SOR=0.51641;LSEQ=AATGCCCCGGAGGGCGGAGA;RSEQ=CTGGGACGAGGCCGAGGTAG;CSQ=C|missense_variant|MODERATE|VHL|7428|Transcript|NM_000551.4|protein_coding|1/3||NM_000551.4:c.20A>C|NP_000542.1:p.Asn7Thr|90|20|7|N/T|aAc/aCc|rs1575920892&COSV56571931||1||EntrezGene||YES||||3:g.10183551A>C||||||||||||uncertain_significance|0&1|1&1,C|missense_variant|MODERATE|VHL|7428|Transcript|NM_001354723.2|protein_coding|1/3||NM_001354723.2:c.20A>C|NP_001341652.1:p.Asn7Thr|90|20|7|N/T|aAc/aCc|rs1575920892&COSV56571931||1||EntrezGene||||||3:g.10183551A>C||||||||||||uncertain_significance|0&1|1&1,C|missense_variant|MODERATE|VHL|7428|Transcript|NM_198156.3|protein_coding|1/2||NM_198156.3:c.20A>C|NP_937799.1:p.Asn7Thr|90|20|7|N/T|aAc/aCc|rs1575920892&COSV56571931||1||EntrezGene||||||3:g.10183551A>C||||||||||||uncertain_significance|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:355:3:2,1:168,184:352,3:0.0085:2,2:7.3:1:11:0:0.60866:2.19:60:0:0:0:1	0/1:123:2:2,0:58,61:119,2:0.0163:2,0:52:1:31:1:0.2438:0:60:4:0.0177:0:2.5
    1013. 

  1013. 3	10183659	10183659	C	A	exonic	VHL	.	nonsynonymous SNV	VHL:NM_000551:exon1:c.C128A:p.S43Y,VHL:NM_198156:exon1:c.C128A:p.S43Y	.	.	.	.	.	.	.	.	.	rs202164771	rs202164771	0.781	0.033	T	0.688	0.396	P	0.178	0.341	B	0.692	0.061	N	1	0.090	N	0.695	0.181	N	-1.91	0.847	D	-0.24	0.236	N	0.314	0.375	-0.695	0.607	T	0.370	0.730	T	0.031	0.534	D	1.050	0.195	10.94	0.805	0.128	0.297	0.237	N	c	-0.882	-0.981	1.000	0.747	0.442	0.072	0	0.996	0.189	0.325	0.192	0.784	0.316	0.066	0.217	0.012	0.117	10.712	0.450	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	44	87	3	10183659	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=226;VD=3;AF=0.0133;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.37504;SOR=inf;LSEQ=GGAGTCCGGCCCGGAAGAGT;RSEQ=CGGCCCGGAGGAACTGGGCG;CSQ=A|missense_variant|MODERATE|VHL|7428|Transcript|NM_000551.4|protein_coding|1/3||NM_000551.4:c.128C>A|NP_000542.1:p.Ser43Tyr|198|128|43|S/Y|tCc/tAc|rs202164771&COSV56544115||1||EntrezGene||YES||||3:g.10183659C>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|VHL|7428|Transcript|NM_001354723.2|protein_coding|1/3||NM_001354723.2:c.128C>A|NP_001341652.1:p.Ser43Tyr|198|128|43|S/Y|tCc/tAc|rs202164771&COSV56544115||1||EntrezGene||||||3:g.10183659C>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|VHL|7428|Transcript|NM_198156.3|protein_coding|1/2||NM_198156.3:c.128C>A|NP_937799.1:p.Ser43Tyr|198|128|43|S/Y|tCc/tAc|rs202164771&COSV56544115||1||EntrezGene||||||3:g.10183659C>A|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:226:3:2,1:116,107:223,3:0.0133:2,2:32.3:1:28.3:1:1:1.84:60:2:0.0097:0:3	0/0:87:0:0,0:46,41:87,0:0:2,0:37.1:1:30.8:1:1:0:60:4.438:1:0:0.4
    1014. 

  1014. 3	10183786	10183786	G	T	exonic	VHL	.	synonymous SNV	VHL:NM_000551:exon1:c.G255T:p.L85L,VHL:NM_198156:exon1:c.G255T:p.L85L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	473451	Von_Hippel-Lindau_syndrome|Erythrocytosis,_familial,_2|Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0008667,MedGen:C0019562,OMIM:193300,Orphanet:ORPHA892,SNOMED_CT:46659004|MONDO:MONDO:0009892,MedGen:C1837915,OMIM:263400,Orphanet:ORPHA238557|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_multiple_submitters,_no_conflicts	Likely_benign	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	79	3	10183786	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=450;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.02206;SOR=0;LSEQ=CGCAGTCCGCGCGTCGTGCT;RSEQ=CCCGTATGGCTCAACTTCGA;CSQ=T|synonymous_variant|LOW|VHL|7428|Transcript|NM_000551.4|protein_coding|1/3||NM_000551.4:c.255G>T|NP_000542.1:p.Leu85%3D|325|255|85|L|ctG/ctT|rs876658508||1||EntrezGene||YES||||3:g.10183786G>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|VHL|7428|Transcript|NM_001354723.2|protein_coding|1/3||NM_001354723.2:c.255G>T|NP_001341652.1:p.Leu85%3D|325|255|85|L|ctG/ctT|rs876658508||1||EntrezGene||||||3:g.10183786G>T||||||||||||likely_benign||1,T|synonymous_variant|LOW|VHL|7428|Transcript|NM_198156.3|protein_coding|1/2||NM_198156.3:c.255G>T|NP_937799.1:p.Leu85%3D|325|255|85|L|ctG/ctT|rs876658508||1||EntrezGene||||||3:g.10183786G>T||||||||||||likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:450:0:0,0:241,209:450,0:0:2,0:35.4:1:36.6:1:1:0:60:149:1:0:0.1	0/1:79:2:1,1:27,50:77,2:0.0253:2,2:23:1:37:0:1:1.84:60:4:0.0256:0:1
    1015. 

  1015. 3	10191719	10191719	C	T	UTR3	VHL	NM_000551:c.*70C>T;NM_198156:c.*70C>T	.	.	0.003	0.0003	0	0	0	0.0056	0	0	0	rs552290225	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	887655	Von_Hippel-Lindau_syndrome	MONDO:MONDO:0008667,MedGen:C0019562,OMIM:193300,Orphanet:ORPHA892,SNOMED_CT:46659004	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	218	143	3	10191719	.	C	T	218	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=279;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GATGAGTCTTGATCTAGATA;RSEQ=AGGACTGGTTCCTTCCTTAG;CSQ=T|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_000551.4|protein_coding|3/3||NM_000551.4:c.*70C>T||782|||||rs552290225&CR175786&CR175787||1||EntrezGene||YES||||3:g.10191719C>T||||||||||0.003|EAS|benign||1&1&1,T|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_001354723.2|protein_coding|3/3||NM_001354723.2:c.*266C>T||918|||||rs552290225&CR175786&CR175787||1||EntrezGene||||||3:g.10191719C>T||||||||||0.003|EAS|benign||1&1&1,T|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_198156.3|protein_coding|2/2||NM_198156.3:c.*70C>T||659|||||rs552290225&CR175786&CR175787||1||EntrezGene||||||3:g.10191719C>T||||||||||0.003|EAS|benign||1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:279:0:0,0:81,198:279,0:0:2,0:30:1:36.3:1:1:0:60:54.8:1:0:0.1	0/1:143:69:14,55:18,56:74,69:0.4825:2,2:30.5:1:35.7:1:0.68856:1.2607:60:33.5:0.4752:0:1.1
    1016. 

  1016. 3	10191943	10191943	G	A	UTR3	VHL	NM_000551:c.*294G>A;NM_198156:c.*294G>A	.	.	0.82	0.5912	0.2929	0.6169	0.7333	0.8109	0.7376	0.6964	0.6864	rs1642742	rs1642742	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	287967	Von_Hippel-Lindau_syndrome	MONDO:MONDO:0008667,MedGen:C0019562,OMIM:193300,Orphanet:ORPHA892,SNOMED_CT:46659004	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	95	6	3	10191943	.	G	A	95	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGTATGTAAGGAGGTTT;RSEQ=TATAAGTAATTCAGTGGGAA;CSQ=A|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_000551.4|protein_coding|3/3||NM_000551.4:c.*294G>A||1006|||||rs1642742||1||EntrezGene||YES||||3:g.10191943G>A||||||||||0.8165|EAS|benign||1,A|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_001354723.2|protein_coding|3/3||NM_001354723.2:c.*490G>A||1142|||||rs1642742||1||EntrezGene||||||3:g.10191943G>A||||||||||0.8165|EAS|benign||1,A|3_prime_UTR_variant|MODIFIER|VHL|7428|Transcript|NM_198156.3|protein_coding|2/2||NM_198156.3:c.*294G>A||883|||||rs1642742||1||EntrezGene||||||3:g.10191943G>A||||||||||0.8165|EAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:6:6:1,5:0,0:0,6:1:0,2:42.2:1:37:0:1:0:60:12:1:0:1
    1017. 

  1017. 3	12393082	12393082	C	A	UTR5	PPARG	NM_015869:c.-10C>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	216	3	12393082	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=78;VD=3;AF=0.0385;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01815;SOR=inf;LSEQ=AATTACAGCAAACCCCTATT;RSEQ=CATGCTGTTATGGGTGAAAC;CSQ=A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001330615.4|protein_coding||2/6|NM_001330615.4:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354666.3|protein_coding||2/7|NM_001354666.3:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354667.3|protein_coding||1/6|NM_001354667.3:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001354668.2|protein_coding|1/5||NM_001354668.2:c.-10C>A||167|||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354669.2|protein_coding||2/6|NM_001354669.2:c.-435-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354670.2|protein_coding||2/5|NM_001354670.2:c.-2-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374261.3|protein_coding||2/6|NM_001374261.3:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374262.3|protein_coding||3/7|NM_001374262.3:c.-9+6689C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374263.2|protein_coding||2/7|NM_001374263.2:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374264.2|protein_coding||2/7|NM_001374264.2:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001374265.1|protein_coding|1/6||NM_001374265.1:c.-10C>A||167|||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374266.1|protein_coding||2/6|NM_001374266.1:c.-2-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_005037.7|protein_coding||1/6|NM_005037.7:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_015869.5|protein_coding|1/7||NM_015869.5:c.-10C>A||167|||||||1||EntrezGene||YES||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138711.6|protein_coding||2/7|NM_138711.6:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138712.5|protein_coding||2/7|NM_138712.5:c.-8-28121C>A|||||||||1||EntrezGene||||||3:g.12393082C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:78:3:2,1:53,22:75,3:0.0385:2,2:23:1:28.3:1:1:1.20155:60:2:0.026:0:2.3	0/0:216:0:0,0:154,62:216,0:0:2,0:36.9:1:36.2:1:1:0:60:42.2:1:0:0.1
    1018. 

  1018. 3	12393108	12393108	G	A	exonic	PPARG	.	nonsynonymous SNV	PPARG:NM_015869:exon1:c.G17A:p.G6E	.	.	.	.	.	.	.	.	.	.	.	0.051	0.393	T	0.244	0.293	B	0.093	0.286	B	0.027	0.259	N	1	0.810	D	0.695	0.181	N	-3.27	0.936	D	-0.1	0.085	N	0.275	0.336	-0.184	0.781	T	0.563	0.841	D	0.264	0.897	D	5.235	0.707	25.6	0.997	0.821	0.731	0.355	D	c	-0.156	-0.007	1.000	0.500	0.447	0.083	0	3.08	0.344	2.020	0.404	1.048	0.713	1.000	0.715	0.998	0.697	4.324	0.104	.	.	.	ID=COSV55144276;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	283	3	12393108	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=118;VD=2;AF=0.0169;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.08607;SOR=inf;LSEQ=TGTTATGGGTGAAACTCTGG;RSEQ=AGATTCTCCTATTGACCCAG;CSQ=A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001330615.4|protein_coding||2/6|NM_001330615.4:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354666.3|protein_coding||2/7|NM_001354666.3:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354667.3|protein_coding||1/6|NM_001354667.3:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354668.2|protein_coding|1/5||NM_001354668.2:c.17G>A|NP_001341597.1:p.Gly6Glu|193|17|6|G/E|gGa/gAa|COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354669.2|protein_coding||2/6|NM_001354669.2:c.-435-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354670.2|protein_coding||2/5|NM_001354670.2:c.-2-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374261.3|protein_coding||2/6|NM_001374261.3:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374262.3|protein_coding||3/7|NM_001374262.3:c.-9+6715G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374263.2|protein_coding||2/7|NM_001374263.2:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374264.2|protein_coding||2/7|NM_001374264.2:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374265.1|protein_coding|1/6||NM_001374265.1:c.17G>A|NP_001361194.1:p.Gly6Glu|193|17|6|G/E|gGa/gAa|COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374266.1|protein_coding||2/6|NM_001374266.1:c.-2-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_005037.7|protein_coding||1/6|NM_005037.7:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_015869.5|protein_coding|1/7||NM_015869.5:c.17G>A|NP_056953.2:p.Gly6Glu|193|17|6|G/E|gGa/gAa|COSV55144276||1||EntrezGene||YES||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138711.6|protein_coding||2/7|NM_138711.6:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1,A|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138712.5|protein_coding||2/7|NM_138712.5:c.-8-28095G>A|||||||COSV55144276||1||EntrezGene||||||3:g.12393108G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:118:2:1,1:67,49:116,2:0.0169:2,2:14:1:37:0:1:1.36365:60:4:0.0169:0:1	0/0:283:0:0,0:180,102:282,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1019. 

  1019. 3	12393112	12393112	T	C	exonic	PPARG	.	synonymous SNV	PPARG:NM_015869:exon1:c.T21C:p.D7D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	285	3	12393112	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=125;VD=2;AF=0.016;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.09243;SOR=inf;LSEQ=ATGGGTGAAACTCTGGGAGA;RSEQ=TCTCCTATTGACCCAGAAAG;CSQ=C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001330615.4|protein_coding||2/6|NM_001330615.4:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354666.3|protein_coding||2/7|NM_001354666.3:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354667.3|protein_coding||1/6|NM_001354667.3:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354668.2|protein_coding|1/5||NM_001354668.2:c.21T>C|NP_001341597.1:p.Asp7%3D|197|21|7|D|gaT/gaC|COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354669.2|protein_coding||2/6|NM_001354669.2:c.-435-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001354670.2|protein_coding||2/5|NM_001354670.2:c.-2-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374261.3|protein_coding||2/6|NM_001374261.3:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374262.3|protein_coding||3/7|NM_001374262.3:c.-9+6719T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374263.2|protein_coding||2/7|NM_001374263.2:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374264.2|protein_coding||2/7|NM_001374264.2:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374265.1|protein_coding|1/6||NM_001374265.1:c.21T>C|NP_001361194.1:p.Asp7%3D|197|21|7|D|gaT/gaC|COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_001374266.1|protein_coding||2/6|NM_001374266.1:c.-2-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_005037.7|protein_coding||1/6|NM_005037.7:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|synonymous_variant|LOW|PPARG|5468|Transcript|NM_015869.5|protein_coding|1/7||NM_015869.5:c.21T>C|NP_056953.2:p.Asp7%3D|197|21|7|D|gaT/gaC|COSV99826870||1||EntrezGene||YES||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138711.6|protein_coding||2/7|NM_138711.6:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1,C|intron_variant|MODIFIER|PPARG|5468|Transcript|NM_138712.5|protein_coding||2/7|NM_138712.5:c.-8-28091T>C|||||||COSV99826870||1||EntrezGene||||||3:g.12393112T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:125:2:1,1:69,54:123,2:0.016:2,2:52.5:1:37:0:1:1.27524:60:4:0.0172:0:1	0/0:285:0:0,0:179,106:285,0:0:2,0:38:1:35.2:1:1:0:60:27.5:1:0:0.1
    1020. 

  1020. 3	12421196	12421196	C	A	intronic	PPARG	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	56	304	3	12421196	.	C	A	56	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=422;VD=5;AF=0.0118;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.0657;SOR=inf;LSEQ=TCACAGCTAGTCTATTTTTC;RSEQ=TTTCAGAAATGACCATGGTT;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001330615.4|protein_coding||2/6|NM_001330615.4:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001354666.3|protein_coding||2/7|NM_001354666.3:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001354667.3|protein_coding||1/6|NM_001354667.3:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001354668.2|protein_coding||1/4|NM_001354668.2:c.83-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001354669.2|protein_coding||2/6|NM_001354669.2:c.-435-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001354670.2|protein_coding||2/5|NM_001354670.2:c.-2-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374261.3|protein_coding||2/6|NM_001374261.3:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374262.3|protein_coding||3/7|NM_001374262.3:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374263.2|protein_coding||2/7|NM_001374263.2:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374264.2|protein_coding||2/7|NM_001374264.2:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374265.1|protein_coding||1/5|NM_001374265.1:c.83-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_001374266.1|protein_coding||2/6|NM_001374266.1:c.-2-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_005037.7|protein_coding||1/6|NM_005037.7:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_015869.5|protein_coding||1/6|NM_015869.5:c.83-7C>A|||||||||1||EntrezGene||YES||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_138711.6|protein_coding||2/7|NM_138711.6:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PPARG|5468|Transcript|NM_138712.5|protein_coding||2/7|NM_138712.5:c.-8-7C>A|||||||||1||EntrezGene||||||3:g.12421196C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:422:5:4,1:187,230:417,5:0.0118:2,2:45.8:1:24.2:1:0.1806:4.9:60:1.5:0.0074:0:1.4	0/0:304:0:0,0:136,168:304,0:0:2,0:35.5:1:36:1:1:0:60:42.429:1:0:0.1
    1021. 

  1021. 3	12421374	12421374	G	A	exonic	PPARG	.	nonsynonymous SNV	PPARG:NM_001330615:exon2:c.G170A:p.R57K,PPARG:NM_005037:exon2:c.G170A:p.R57K,PPARG:NM_015869:exon2:c.G254A:p.R85K,PPARG:NM_138711:exon3:c.G170A:p.R57K,PPARG:NM_138712:exon3:c.G170A:p.R57K	.	3.23e-05	0.0001	0	0	0	0	0	0	.	.	0.634	0.496	T	0.679	0.400	P	0.281	0.391	B	0.000	0.449	D	0.985	0.403	D	1.245	0.315	L	0.96	0.429	T	-0.2	0.287	N	0.367	0.451	-1.063	0.111	T	0.084	0.328	T	0.020	0.425	T	0.923	0.182	10.21	0.991	0.518	0.960	0.668	D	c	-0.048	0.047	1.000	0.439	0.487	0.133	0	5.8	0.921	5.900	0.694	0.998	0.613	1.000	0.715	0.669	0.302	13.288	0.595	Peroxisome proliferator-activated receptor gamma, N-terminal	.	.	ID=COSV55145095;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU4349670	SKCM-US|1|466|0.00214592	0.25	37	215	3	12421374	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=98;VD=2;AF=0.0204;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.09734;SOR=inf;LSEQ=CGAAGACATTCCATTCACAA;RSEQ=AACAGATCCAGTGGTTGCAG;CSQ=A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001330615.4|protein_coding|3/7||NM_001330615.4:c.164G>A|NP_001317544.2:p.Arg55Lys|311|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354666.3|protein_coding|3/8||NM_001354666.3:c.164G>A|NP_001341595.2:p.Arg55Lys|554|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354667.3|protein_coding|2/7||NM_001354667.3:c.164G>A|NP_001341596.2:p.Arg55Lys|247|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354668.2|protein_coding|2/5||NM_001354668.2:c.254G>A|NP_001341597.1:p.Arg85Lys|430|254|85|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|5_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001354669.2|protein_coding|3/7||NM_001354669.2:c.-264G>A||383|||||rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354670.2|protein_coding|3/6||NM_001354670.2:c.170G>A|NP_001341599.1:p.Arg57Lys|311|170|57|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374261.3|protein_coding|3/7||NM_001374261.3:c.164G>A|NP_001361190.2:p.Arg55Lys|383|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374262.3|protein_coding|4/8||NM_001374262.3:c.164G>A|NP_001361191.2:p.Arg55Lys|399|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374263.2|protein_coding|3/8||NM_001374263.2:c.164G>A|NP_001361192.2:p.Arg55Lys|329|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374264.2|protein_coding|3/8||NM_001374264.2:c.164G>A|NP_001361193.2:p.Arg55Lys|308|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374265.1|protein_coding|2/6||NM_001374265.1:c.254G>A|NP_001361194.1:p.Arg85Lys|430|254|85|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374266.1|protein_coding|3/7||NM_001374266.1:c.170G>A|NP_001361195.1:p.Arg57Lys|311|170|57|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_005037.7|protein_coding|2/7||NM_005037.7:c.164G>A|NP_005028.5:p.Arg55Lys|319|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_015869.5|protein_coding|2/7||NM_015869.5:c.254G>A|NP_056953.2:p.Arg85Lys|430|254|85|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||YES||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138711.6|protein_coding|3/8||NM_138711.6:c.164G>A|NP_619725.3:p.Arg55Lys|311|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138712.5|protein_coding|3/8||NM_138712.5:c.164G>A|NP_619726.3:p.Arg55Lys|393|164|55|R/K|aGa/aAa|rs1196196054&COSV55145095||1||EntrezGene||||||3:g.12421374G>A|||||||||||||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:98:2:1,1:26,70:96,2:0.0204:2,2:21:0:37:0:0.47717:2.66:60:4:0.0208:0:1	0/0:215:0:0,0:85,130:215,0:0:2,0:39.1:1:36.2:1:1:0:60:106.5:1:0:0
    1022. 

  1022. 3	12421392	12421392	C	T	exonic	PPARG	.	nonsynonymous SNV	PPARG:NM_001330615:exon2:c.C188T:p.A63V,PPARG:NM_005037:exon2:c.C188T:p.A63V,PPARG:NM_015869:exon2:c.C272T:p.A91V,PPARG:NM_138711:exon3:c.C188T:p.A63V,PPARG:NM_138712:exon3:c.C188T:p.A63V	.	.	.	.	.	.	.	.	.	.	.	0.428	0.143	T	0.001	0.090	B	0.002	0.104	B	0.464	0.124	N	1	0.090	N	0	0.065	N	0.94	0.437	T	-0.53	0.255	N	0.101	0.127	-1.049	0.147	T	0.054	0.230	T	0.022	0.445	T	0.755	0.166	9.182	0.961	0.280	0.054	0.111	N	c	-0.696	-0.593	0.971	0.292	0.554	0.283	0	4.83	0.617	2.208	0.422	0.892	0.403	0.050	0.212	0.852	0.355	6.933	0.235	Peroxisome proliferator-activated receptor gamma, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	204	3	12421392	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=61;VD=2;AF=0.0328;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05232;SOR=inf;LSEQ=AAGAACAGATCCAGTGGTTG;RSEQ=AGATTACAAGTATGACCTGA;CSQ=T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001330615.4|protein_coding|3/7||NM_001330615.4:c.182C>T|NP_001317544.2:p.Ala61Val|329|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354666.3|protein_coding|3/8||NM_001354666.3:c.182C>T|NP_001341595.2:p.Ala61Val|572|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354667.3|protein_coding|2/7||NM_001354667.3:c.182C>T|NP_001341596.2:p.Ala61Val|265|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354668.2|protein_coding|2/5||NM_001354668.2:c.272C>T|NP_001341597.1:p.Ala91Val|448|272|91|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001354669.2|protein_coding|3/7||NM_001354669.2:c.-246C>T||401|||||||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354670.2|protein_coding|3/6||NM_001354670.2:c.188C>T|NP_001341599.1:p.Ala63Val|329|188|63|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374261.3|protein_coding|3/7||NM_001374261.3:c.182C>T|NP_001361190.2:p.Ala61Val|401|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374262.3|protein_coding|4/8||NM_001374262.3:c.182C>T|NP_001361191.2:p.Ala61Val|417|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374263.2|protein_coding|3/8||NM_001374263.2:c.182C>T|NP_001361192.2:p.Ala61Val|347|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374264.2|protein_coding|3/8||NM_001374264.2:c.182C>T|NP_001361193.2:p.Ala61Val|326|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374265.1|protein_coding|2/6||NM_001374265.1:c.272C>T|NP_001361194.1:p.Ala91Val|448|272|91|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374266.1|protein_coding|3/7||NM_001374266.1:c.188C>T|NP_001361195.1:p.Ala63Val|329|188|63|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_005037.7|protein_coding|2/7||NM_005037.7:c.182C>T|NP_005028.5:p.Ala61Val|337|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_015869.5|protein_coding|2/7||NM_015869.5:c.272C>T|NP_056953.2:p.Ala91Val|448|272|91|A/V|gCa/gTa|||1||EntrezGene||YES||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138711.6|protein_coding|3/8||NM_138711.6:c.182C>T|NP_619725.3:p.Ala61Val|329|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||,T|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138712.5|protein_coding|3/8||NM_138712.5:c.182C>T|NP_619726.3:p.Ala61Val|411|182|61|A/V|gCa/gTa|||1||EntrezGene||||||3:g.12421392C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:61:2:1,1:13,46:59,2:0.0328:2,2:23.5:1:37:0:0.40929:3.45:60:4:0.0339:0:1	0/0:204:0:0,0:70,134:204,0:0:2,0:37.4:1:36.4:1:1:0:60:50:1:0:0
    1023. 

  1023. 3	12434115	12434115	T	C	exonic	PPARG	.	synonymous SNV	PPARG:NM_001330615:exon4:c.T399C:p.G133G,PPARG:NM_005037:exon4:c.T399C:p.G133G,PPARG:NM_015869:exon4:c.T483C:p.G161G,PPARG:NM_138711:exon5:c.T399C:p.G133G,PPARG:NM_138712:exon5:c.T399C:p.G133G	0.011	3.229e-05	0	0	0	0.0006	0	0	0	rs201126401	rs201126401	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	887767	Obesity|Familial_partial_lipodystrophy_3|Diabetes_Mellitus,_Noninsulin-Dependent,_with_Acanthosis_Nigricans_and_Hypertension	Human_Phenotype_Ontology:HP:0001513,MeSH:D009765,MedGen:C0028754,OMIM:601665,SNOMED_CT:414916001|MONDO:MONDO:0011448,MedGen:C1720861,OMIM:604367,Orphanet:ORPHA79083|MedGen:C4016738	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	.	.	0.25	37	118	3	12434115	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=61;VD=2;AF=0.0328;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.11487;SOR=inf;LSEQ=TTTTTTATCCCTTTGCAGGG;RSEQ=TTCTTCCGGAGAACAATCAG;CSQ=C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001330615.4|protein_coding|5/7||NM_001330615.4:c.393T>C|NP_001317544.2:p.Gly131%3D|540|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354666.3|protein_coding|5/8||NM_001354666.3:c.393T>C|NP_001341595.2:p.Gly131%3D|783|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354667.3|protein_coding|4/7||NM_001354667.3:c.393T>C|NP_001341596.2:p.Gly131%3D|476|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354668.2|protein_coding|4/5||NM_001354668.2:c.483T>C|NP_001341597.1:p.Gly161%3D|659|483|161|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&5_prime_UTR_variant|LOW|PPARG|5468|Transcript|NM_001354669.2|protein_coding|5/7||NM_001354669.2:c.-35T>C||612|||||rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354670.2|protein_coding|5/6||NM_001354670.2:c.399T>C|NP_001341599.1:p.Gly133%3D|540|399|133|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374261.3|protein_coding|5/7||NM_001374261.3:c.393T>C|NP_001361190.2:p.Gly131%3D|612|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374262.3|protein_coding|6/8||NM_001374262.3:c.393T>C|NP_001361191.2:p.Gly131%3D|628|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374263.2|protein_coding|5/8||NM_001374263.2:c.393T>C|NP_001361192.2:p.Gly131%3D|558|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374264.2|protein_coding|5/8||NM_001374264.2:c.393T>C|NP_001361193.2:p.Gly131%3D|537|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374265.1|protein_coding|4/6||NM_001374265.1:c.483T>C|NP_001361194.1:p.Gly161%3D|659|483|161|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374266.1|protein_coding|5/7||NM_001374266.1:c.399T>C|NP_001361195.1:p.Gly133%3D|540|399|133|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_005037.7|protein_coding|4/7||NM_005037.7:c.393T>C|NP_005028.5:p.Gly131%3D|548|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_015869.5|protein_coding|4/7||NM_015869.5:c.483T>C|NP_056953.2:p.Gly161%3D|659|483|161|G|ggT/ggC|rs201126401||1||EntrezGene||YES||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_138711.6|protein_coding|5/8||NM_138711.6:c.393T>C|NP_619725.3:p.Gly131%3D|540|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1,C|splice_region_variant&synonymous_variant|LOW|PPARG|5468|Transcript|NM_138712.5|protein_coding|5/8||NM_138712.5:c.393T>C|NP_619726.3:p.Gly131%3D|622|393|131|G|ggT/ggC|rs201126401||1||EntrezGene||||||3:g.12434115T>C|8.766e-05|0|0.0001448|0|0.0008174|0|1.763e-05|0|0|0.001|EAS|uncertain_significance&benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:61:2:1,1:28,31:59,2:0.0328:2,2:41.5:1:37:0:1:1.11:60:4:0.0339:0:1	0/0:118:0:0,0:77,41:118,0:0:2,0:33.2:1:36.2:1:1:0:60:38.333:1:0:0.2
    1024. 

  1024. 3	12434225	12434225	G	A	exonic	PPARG	.	nonsynonymous SNV	PPARG:NM_001330615:exon4:c.G509A:p.C170Y,PPARG:NM_005037:exon4:c.G509A:p.C170Y,PPARG:NM_015869:exon4:c.G593A:p.C198Y,PPARG:NM_138711:exon5:c.G509A:p.C170Y,PPARG:NM_138712:exon5:c.G509A:p.C170Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.52	0.991	H	-5.86	0.994	D	-8.78	0.989	D	0.911	0.930	0.944	0.963	D	0.992	0.998	D	0.922	0.994	D	6.117	0.843	28.3	0.998	0.888	0.989	0.881	D	c	1.151	1.045	1.0	0.983	0.487	0.133	0	5.57	0.840	9.990	0.992	0.996	0.606	1.000	0.715	1.000	0.888	19.540	0.952	Nuclear hormone receptor, ligand-binding domain|Zinc finger, nuclear hormone receptor-type;Zinc finger, NHR/GATA-type|Zinc finger, nuclear hormone receptor-type	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	191	3	12434225	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.71367;SOR=0;LSEQ=GTACTGTCGGTTTCAGAAAT;RSEQ=CCTTGCAGTGGGGATGTCTC;CSQ=A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001330615.4|protein_coding|5/7||NM_001330615.4:c.503G>A|NP_001317544.2:p.Cys168Tyr|650|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354666.3|protein_coding|5/8||NM_001354666.3:c.503G>A|NP_001341595.2:p.Cys168Tyr|893|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354667.3|protein_coding|4/7||NM_001354667.3:c.503G>A|NP_001341596.2:p.Cys168Tyr|586|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354668.2|protein_coding|4/5||NM_001354668.2:c.593G>A|NP_001341597.1:p.Cys198Tyr|769|593|198|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354669.2|protein_coding|5/7||NM_001354669.2:c.76G>A|NP_001341598.1:p.Ala26Thr|722|76|26|A/T|Gcc/Acc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001354670.2|protein_coding|5/6||NM_001354670.2:c.509G>A|NP_001341599.1:p.Cys170Tyr|650|509|170|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374261.3|protein_coding|5/7||NM_001374261.3:c.503G>A|NP_001361190.2:p.Cys168Tyr|722|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374262.3|protein_coding|6/8||NM_001374262.3:c.503G>A|NP_001361191.2:p.Cys168Tyr|738|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374263.2|protein_coding|5/8||NM_001374263.2:c.503G>A|NP_001361192.2:p.Cys168Tyr|668|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374264.2|protein_coding|5/8||NM_001374264.2:c.503G>A|NP_001361193.2:p.Cys168Tyr|647|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374265.1|protein_coding|4/6||NM_001374265.1:c.593G>A|NP_001361194.1:p.Cys198Tyr|769|593|198|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_001374266.1|protein_coding|5/7||NM_001374266.1:c.509G>A|NP_001361195.1:p.Cys170Tyr|650|509|170|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_005037.7|protein_coding|4/7||NM_005037.7:c.503G>A|NP_005028.5:p.Cys168Tyr|658|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_015869.5|protein_coding|4/7||NM_015869.5:c.593G>A|NP_056953.2:p.Cys198Tyr|769|593|198|C/Y|tGc/tAc|||1||EntrezGene||YES||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138711.6|protein_coding|5/8||NM_138711.6:c.503G>A|NP_619725.3:p.Cys168Tyr|650|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||,A|missense_variant|MODERATE|PPARG|5468|Transcript|NM_138712.5|protein_coding|5/8||NM_138712.5:c.503G>A|NP_619726.3:p.Cys168Tyr|732|503|168|C/Y|tGc/tAc|||1||EntrezGene||||||3:g.12434225G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:35:0:0,0:14,21:35,0:0:2,0:30.9:1:34.9:1:1:0:60:34:1:0:0	0/1:191:2:1,1:86,103:189,2:0.0105:2,2:33:1:31:1:1:1.2:60:4:0.0113:0:1
    1025. 

  1025. 3	12434252	12434252	G	T	splicing	PPARG	NM_138712:exon5:c.535+1G>T;NM_005037:exon4:c.535+1G>T;NM_138711:exon5:c.535+1G>T;NM_001330615:exon4:c.535+1G>T;NM_015869:exon4:c.619+1G>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.273	0.572	24.0	0.995	0.665	0.990	0.899	D	c	1.148	0.983	1.0	0.983	0.061	0.009	0	5.57	0.840	9.990	0.992	0.996	0.606	1.000	0.715	0.984	0.507	19.540	0.952	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	156	3	12434252	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.73402;SOR=0;LSEQ=AGTGGGGATGTCTCATAATG;RSEQ=TAAGTAAACAGTCATCACCA;CSQ=T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001330615.4|protein_coding||5/6|NM_001330615.4:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001354666.3|protein_coding||5/7|NM_001354666.3:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001354667.3|protein_coding||4/6|NM_001354667.3:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001354668.2|protein_coding||4/4|NM_001354668.2:c.619+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001354669.2|protein_coding||5/6|NM_001354669.2:c.102+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001354670.2|protein_coding||5/5|NM_001354670.2:c.535+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374261.3|protein_coding||5/6|NM_001374261.3:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374262.3|protein_coding||6/7|NM_001374262.3:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374263.2|protein_coding||5/7|NM_001374263.2:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374264.2|protein_coding||5/7|NM_001374264.2:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374265.1|protein_coding||4/5|NM_001374265.1:c.619+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_001374266.1|protein_coding||5/6|NM_001374266.1:c.535+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_005037.7|protein_coding||4/6|NM_005037.7:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_015869.5|protein_coding||4/6|NM_015869.5:c.619+1G>T|||||||||1||EntrezGene||YES||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_138711.6|protein_coding||5/7|NM_138711.6:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||,T|splice_donor_variant|HIGH|PPARG|5468|Transcript|NM_138712.5|protein_coding||5/7|NM_138712.5:c.529+1G>T|||||||||1||EntrezGene||||||3:g.12434252G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:26:0:0,0:10,16:26,0:0:2,0:29.2:1:36.5:1:1:0:60:52:1:0:0	0/1:156:2:1,1:60,94:154,2:0.0128:2,2:48.5:1:37:0:1:1.56:60:4:0.0132:0:1
    1026. 

  1026. 3	12475557	12475557	C	T	exonic	PPARG	.	synonymous SNV	PPARG:NM_005037:exon7:c.C1347T:p.H449H,PPARG:NM_015869:exon7:c.C1431T:p.H477H,PPARG:NM_138711:exon8:c.C1347T:p.H449H,PPARG:NM_138712:exon8:c.C1347T:p.H449H	0.24	0.1316	0.0677	0.0883	0.0762	0.2519	0.1952	0.1422	0.1673	rs3856806	rs3856806	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55140736;OCCURENCE=1(stomach),3(haematopoietic_and_lymphoid_tissue),5(soft_tissue)	23178	Obesity|Familial_partial_lipodystrophy_3|Glioma_susceptibility_1|Diabetes_Mellitus,_Noninsulin-Dependent,_with_Acanthosis_Nigricans_and_Hypertension|not_specified	Human_Phenotype_Ontology:HP:0001513,MeSH:D009765,MedGen:C0028754,OMIM:601665,SNOMED_CT:414916001|MONDO:MONDO:0011448,MedGen:C1720861,OMIM:604367,Orphanet:ORPHA79083|MONDO:MONDO:0024498,MedGen:C2750850,OMIM:137800|MedGen:C4016738|MedGen:CN169374	criteria_provided,_single_submitter	Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU744844	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,COCA-CN|1|321|0.00311526	0.5	392	349	3	12475557	.	C	T	392	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2221;VD=2214;AF=0.9968;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=AGACAGATTGTCACGGAACA;RSEQ=GTGCAGCTACTGCAGGTGAT;CSQ=T|3_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001330615.4|protein_coding|7/7||NM_001330615.4:c.*143C>T||1037|||||rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354666.3|protein_coding|8/8||NM_001354666.3:c.1341C>T|NP_001341595.2:p.His447%3D|1731|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354667.3|protein_coding|7/7||NM_001354667.3:c.1341C>T|NP_001341596.2:p.His447%3D|1424|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001354669.2|protein_coding|7/7||NM_001354669.2:c.714C>T|NP_001341598.1:p.His238%3D|1360|714|238|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|3_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001374261.3|protein_coding|7/7||NM_001374261.3:c.*143C>T||1109|||||rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|3_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001374262.3|protein_coding|8/8||NM_001374262.3:c.*143C>T||1125|||||rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374263.2|protein_coding|8/8||NM_001374263.2:c.1341C>T|NP_001361192.2:p.His447%3D|1506|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_001374264.2|protein_coding|8/8||NM_001374264.2:c.1341C>T|NP_001361193.2:p.His447%3D|1485|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|3_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001374265.1|protein_coding|6/6||NM_001374265.1:c.*143C>T||1156|||||rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|3_prime_UTR_variant|MODIFIER|PPARG|5468|Transcript|NM_001374266.1|protein_coding|7/7||NM_001374266.1:c.*127C>T||955|||||rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_005037.7|protein_coding|7/7||NM_005037.7:c.1341C>T|NP_005028.5:p.His447%3D|1496|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_015869.5|protein_coding|7/7||NM_015869.5:c.1431C>T|NP_056953.2:p.His477%3D|1607|1431|477|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||YES||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_138711.6|protein_coding|8/8||NM_138711.6:c.1341C>T|NP_619725.3:p.His447%3D|1488|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1,T|synonymous_variant|LOW|PPARG|5468|Transcript|NM_138712.5|protein_coding|8/8||NM_138712.5:c.1341C>T|NP_619726.3:p.His447%3D|1570|1341|447|H|caC/caT|rs3856806&CM994587&COSV55140736||1||EntrezGene||||||3:g.12475557C>T|0.1341|0.06287|0.1089|0.07344|0.2412|0.1989|0.1261|0.1191|0.1432|0.2412|gnomAD_EAS|benign&likely_benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2221:2214:956,1258:0,0:0,2214:0.9968:0,2:37:1:35.3:1:1:0:60:29.329:0.9991:0:1.1	0/0:349:0:0,0:153,196:349,0:0:2,0:35.7:1:36.4:1:1:0:60:173.5:1:0:0.1
    1027. 

  1027. 3	12641385	12641385	C	T	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	234	3	12641385	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=39;VD=2;AF=0.0513;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.01996;SOR=inf;LSEQ=TGAGGGCATCAAAGGATCAA;RSEQ=CCATGTCATCTGTTTCCATA;CSQ=T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||10/17|NM_001354689.3:c.1051-78G>A|||||||||-1||EntrezGene||YES||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||9/16|NM_001354690.3:c.991-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||9/16|NM_001354691.3:c.748-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||8/15|NM_001354692.3:c.748-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||8/15|NM_001354693.3:c.892-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||9/16|NM_001354694.3:c.808-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||7/14|NM_001354695.3:c.649-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||9/16|NM_002880.4:c.991-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||9/17|NR_148940.3:n.1322-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||9/16|NR_148941.3:n.1322-78G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||9/16|NR_148942.3:n.1322-80G>A|||||||||-1||EntrezGene||||||3:g.12641385C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:39:2:1,1:12,25:37,2:0.0513:2,2:62:0:37:0:1:2.04:60:4:0.0556:0:1	0/0:234:0:0,0:91,142:233,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1028. 

  1028. 3	12641550	12641550	T	C	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV52574226;OCCURENCE=1(liver)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	150	3	12641550	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.75111;SOR=0;LSEQ=CTCCTTCATTGAATGTATTT;RSEQ=ATTAGAATCTTCTCCCAAAA;CSQ=C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||10/17|NM_001354689.3:c.1050+101A>G|||||||COSV52574226||-1||EntrezGene||YES||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||9/16|NM_001354690.3:c.990+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||9/16|NM_001354691.3:c.747+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||8/15|NM_001354692.3:c.747+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||8/15|NM_001354693.3:c.891+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||9/16|NM_001354694.3:c.807+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||7/14|NM_001354695.3:c.648+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||9/16|NM_002880.4:c.990+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||9/17|NR_148940.3:n.1321+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||9/16|NR_148941.3:n.1321+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||9/16|NR_148942.3:n.1321+101A>G|||||||COSV52574226||-1||EntrezGene||||||3:g.12641550T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:19,4:23,0:0:2,0:25.6:1:37:0:1:0:60:46:1:0:0.2	0/1:150:2:1,1:87,60:147,2:0.0133:2,2:60:1:37:0:1:1.44628:60:4:0.0133:0:1
    1029. 

  1029. 3	12642603	12642603	G	T	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	306	3	12642603	.	G	T	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=233;VD=3;AF=0.0129;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.08019;SOR=inf;LSEQ=TTAGGCTAAATTGACTAGAA;RSEQ=TTGGATTTGAAAAAGGTAAG;CSQ=T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.895-689C>A|||||||||-1||EntrezGene||YES||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.835-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.592-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.592-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.736-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.652-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.493-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.835-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1166-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1166-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1166-689C>A|||||||||-1||EntrezGene||||||3:g.12642603G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:233:3:1,2:83,147:230,3:0.0129:2,2:16:1:28.3:1:1:1.12869:60:2:0.0087:0:1.3	0/0:306:0:0,0:126,180:306,0:0:2,0:2:0:11:0:1:0:60:0:0:0:7
    1030. 

  1030. 3	12642846	12642846	T	C	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	279	3	12642846	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=125;VD=2;AF=0.016;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.0952;SOR=inf;LSEQ=ACAAAACACTGCCTTATGGG;RSEQ=AAATTTGGAAATCGGTTACA;CSQ=C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.895-932A>G|||||||||-1||EntrezGene||YES||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.835-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.592-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.592-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.736-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.652-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.493-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.835-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1166-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1166-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1166-932A>G|||||||||-1||EntrezGene||||||3:g.12642846T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:125:2:1,1:47,76:123,2:0.016:2,2:32.5:1:37:0:1:1.61:60:4:0.0161:0:1	0/0:279:0:0,0:132,147:279,0:0:2,0:37:1:36.6:1:1:0:60:558:1:0:0.1
    1031. 

  1031. 3	12643018	12643018	C	A	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	102	3	12643018	.	C	A	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATAGAATAATATAAAAC;RSEQ=ACTTGGCCCCCATATCCTAA;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.895-1104G>T|||||||||-1||EntrezGene||YES||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.835-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.592-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.592-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.736-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.652-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.493-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.835-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1166-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1166-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1166-1104G>T|||||||||-1||EntrezGene||||||3:g.12643018C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:102:2:1,1:43,57:100,2:0.0196:2,2:21.5:1:37:0:1:1.32:60:4:0.02:0:1
    1032. 

  1032. 3	12644004	12644004	C	T	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	80	3	12644004	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=86;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.23074;SOR=0;LSEQ=AGGACTGCAGGTGCACACCA;RSEQ=CAAGCCCAGCTAATTTTTAC;CSQ=T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+973G>A|||||||||-1||EntrezGene||YES||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+973G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+1631G>A|||||||||-1||EntrezGene||||||3:g.12644004C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:86:0:0,0:43,42:85,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:80:2:1,1:32,46:78,2:0.025:2,2:42.5:1:37:0:1:1.43:60:4:0.025:0:1
    1033. 

  1033. 3	12644026	12644026	T	-	intronic	RAF1	.	.	.	.	6.579e-05	0.0001	0	0	0	0	6.759e-05	0	rs1028940862	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	58	70	3	12644025	.	AT	A	58	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=81;VD=3;AF=0.037;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.36692;SOR=2.63819;LSEQ=CAAGCCCAGCTAATTTTTAC;RSEQ=TTTTTTTTGTAGAGGTGGGG;CSQ=-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+951del|||||||rs879562318||-1||EntrezGene||YES||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+951del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+1609del|||||||rs879562318||-1||EntrezGene||||||3:g.12644034del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:81:3:2,1:36,42:78,3:0.037:2,2:15:1:37:1:0.59782:2.31:60:6:0.0375:0.0247:0	0/1:70:1:1,0:29,40:69,1:0.0143:2,0:52:0:37:0:0.42857:0:60:2:0.0143:0:0
    1034. 

  1034. 3	12644434	12644434	G	A	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	182	3	12644434	.	G	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.95734;SOR=0;LSEQ=TATCAACCAAAAACACATTT;RSEQ=GTTACTAATGTATAAACAGA;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+543C>T|||||||rs1299302857||-1||EntrezGene||YES||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+543C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+1201C>T|||||||rs1299302857||-1||EntrezGene||||||3:g.12644434G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:36:1:37:0:1:0:60:8:1:0:0	0/1:182:2:1,1:69,111:180,2:0.011:2,2:10.5:1:37:0:1:1.6:60:4:0.0114:0:1.5
    1035. 

  1035. 3	12644516	12644516	-	A	intronic	RAF1	.	.	.	.	0.0051	0.0172	0.0013	0	0.0006	0	0	0	rs201273382	rs201273382	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	39	160	3	12644516	.	T	TA	39	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=9;VD=0;AF=0;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.89603;SOR=0;LSEQ=GCCTTTGGTTGGAATTGATT;RSEQ=AAAAAAAAAACTTTTTAATG;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+460dup|||||||rs201273382||-1||EntrezGene||YES||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+460dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+1118dup|||||||rs201273382||-1||EntrezGene||||||3:g.12644526dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:8,1:9,0:0:2,0:25.7:1:35.7:1:1:0:60:18:1:0:0	0/1:160:2:1,1:79,70:149,2:0.0125:2,2:15.9:1:39.2:0:1:1.12766:63.6:4:0.0134:0:0
    1036. 

  1036. 3	12644568	12644568	T	A	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	185	3	12644568	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=0;AF=0;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.61902;SOR=0;LSEQ=AAAATCTAACTTAACATTTT;RSEQ=TGTTTGTTTTTAAGGTGGAT;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+409A>T|||||||||-1||EntrezGene||YES||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+409A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+1067A>T|||||||||-1||EntrezGene||||||3:g.12644568T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:50:0:0,0:35,15:50,0:0:2,0:26.3:1:35.3:1:1:0:60:49:1:0:0	0/1:185:2:1,1:111,72:183,2:0.0108:2,2:38:0:37:0:1:1.53791:60:4:0.011:0:1
    1037. 

  1037. 3	12644882	12644882	C	A	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	172	3	12644882	.	C	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.97708;SOR=0;LSEQ=GACAAGAAATATAAATTTAA;RSEQ=TTAGCAACTATTTCATTTTT;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||8/17|NM_001354689.3:c.894+95G>T|||||||||-1||EntrezGene||YES||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||7/16|NM_001354694.3:c.651+95G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+753G>T|||||||||-1||EntrezGene||||||3:g.12644882C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2:0:0,0:1,1:2,0:0:2,0:15:1:37:0:1:0:60:4:1:0:0	0/1:172:2:1,1:119,51:170,2:0.0116:2,2:23.5:1:37:0:0.51448:2.3205:60:4:0.0121:0:3
    1038. 

  1038. 3	12645078	12645078	A	G	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	194	3	12645078	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.86961;SOR=0;LSEQ=TAAAGAAGAATAAAGAACAA;RSEQ=GGAAGTATTTAAGTGTATTC;CSQ=G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||7/17|NM_001354689.3:c.835-42T>C|||||||||-1||EntrezGene||YES||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||6/16|NM_001354694.3:c.592-42T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+557T>C|||||||||-1||EntrezGene||||||3:g.12645078A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:14:0:0,0:7,7:14,0:0:2,0:30.1:1:37:0:1:0:60:28:1:0:0	0/1:194:2:1,1:76,116:192,2:0.0103:2,2:6:0:31:1:1:1.52:60:4:0.0104:0:1
    1039. 

  1039. 3	12645155	12645155	A	G	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	180	3	12645155	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.92634;SOR=0;LSEQ=CCAATAGGACATAACCAAAA;RSEQ=GCCAAGAGAAGAAAAAGCAG;CSQ=G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||7/17|NM_001354689.3:c.835-119T>C|||||||||-1||EntrezGene||YES||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||7/16|NM_001354690.3:c.834+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||7/16|NM_001354691.3:c.591+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||6/15|NM_001354692.3:c.591+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||6/15|NM_001354693.3:c.735+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||6/16|NM_001354694.3:c.592-119T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||5/14|NM_001354695.3:c.492+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||7/16|NM_002880.4:c.834+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||7/17|NR_148940.3:n.1165+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||7/16|NR_148941.3:n.1165+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||7/16|NR_148942.3:n.1165+480T>C|||||||||-1||EntrezGene||||||3:g.12645155A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:4,3:7,0:0:2,0:31.1:1:33.6:1:1:0:60:14:1:0:0.3	0/1:180:2:1,1:90,88:178,2:0.0111:2,2:57.5:1:37:0:1:1.0226:60:4:0.0116:0:1
    1040. 

  1040. 3	12645752	12645752	G	A	exonic	RAF1	.	synonymous SNV	RAF1:NM_002880:exon7:c.C717T:p.T239T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	337	3	12645752	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=195;VD=2;AF=0.0103;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13392;SOR=inf;LSEQ=GAGGGACTGGAGGTGTTAAA;RSEQ=GTGAAGGCGTGAGGTGTAGA;CSQ=A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354689.3|protein_coding|7/18||NM_001354689.3:c.717C>T|NP_001341618.1:p.Thr239%3D|1048|717|239|T|acC/acT|||-1||EntrezGene||YES||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354690.3|protein_coding|7/17||NM_001354690.3:c.717C>T|NP_001341619.1:p.Thr239%3D|883|717|239|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354691.3|protein_coding|7/17||NM_001354691.3:c.474C>T|NP_001341620.1:p.Thr158%3D|1028|474|158|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354692.3|protein_coding|6/16||NM_001354692.3:c.474C>T|NP_001341621.1:p.Thr158%3D|935|474|158|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354693.3|protein_coding|6/16||NM_001354693.3:c.618C>T|NP_001341622.1:p.Thr206%3D|949|618|206|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354694.3|protein_coding|6/17||NM_001354694.3:c.474C>T|NP_001341623.1:p.Thr158%3D|935|474|158|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354695.3|protein_coding|5/15||NM_001354695.3:c.375C>T|NP_001341624.1:p.Thr125%3D|836|375|125|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|synonymous_variant|LOW|RAF1|5894|Transcript|NM_002880.4|protein_coding|7/17||NM_002880.4:c.717C>T|NP_002871.1:p.Thr239%3D|1048|717|239|T|acC/acT|||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA|7/18||NR_148940.3:n.1048C>T||1048|||||||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA|7/17||NR_148941.3:n.1048C>T||1048|||||||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA|7/17||NR_148942.3:n.1048C>T||1048|||||||-1||EntrezGene||||||3:g.12645752G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:195:2:1,1:73,120:193,2:0.0103:2,2:6:0:37:0:1:1.64:60:4:0.0105:0:1	0/0:337:0:0,0:119,217:336,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1041. 

  1041. 3	12645837	12645837	G	T	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	131	3	12645837	.	G	T	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.68653;SOR=0;LSEQ=GGCACTTAGGCTTTCATACT;RSEQ=GTGAAGTCTTTCAAGTACAT;CSQ=T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||6/17|NM_001354689.3:c.681-49C>A|||||||||-1||EntrezGene||YES||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||6/16|NM_001354690.3:c.681-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||6/16|NM_001354691.3:c.438-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||5/15|NM_001354692.3:c.438-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.582-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||5/16|NM_001354694.3:c.438-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.339-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||6/16|NM_002880.4:c.681-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||6/17|NR_148940.3:n.1012-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||6/16|NR_148941.3:n.1012-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||6/16|NR_148942.3:n.1012-49C>A|||||||||-1||EntrezGene||||||3:g.12645837G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:27:0:0,0:5,22:27,0:0:2,0:30.3:1:37:0:1:0:60:54:1:0:0.1	0/1:131:2:0,2:29,100:129,2:0.0153:2,0:30:1:25:0:1:0:60:4:0.0157:0:4
    1042. 

  1042. 3	12648049	12648049	T	-	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU79012877	LIRI-JP|1|258|0.00387597	0.25	37	70	3	12648048	.	CT	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=26;VD=2;AF=0.0769;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.07127;SOR=inf;LSEQ=CCTGTGTGCTTTTTCTTTTT;RSEQ=TTTTTTTTAAGATGGAGTCT;CSQ=-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.582-251del|||||||rs888518743||-1||EntrezGene||YES||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.582-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.339-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.339-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+2216del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.339-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+2216del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.582-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.913-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.913-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.913-251del|||||||rs888518743||-1||EntrezGene||||||3:g.12648057del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:26:2:1,1:12,12:24,2:0.0769:2,2:46:1:37:0:1:1:60:4:0.08:0:0	0/0:70:0:0,0:19,51:70,0:0:2,0:31.6:1:35.8:1:1:0:60:69:1:0:0.1
    1043. 

  1043. 3	12648902	12648902	T	C	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	141	3	12648902	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=425;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.06173;SOR=0;LSEQ=CACACCTGTAACCACAACAC;RSEQ=TTGGAAGGCCAAGGCGGACA;CSQ=C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.582-1104A>G|||||||||-1||EntrezGene||YES||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.582-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.339-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.339-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+1363A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.339-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+1363A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.582-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.913-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.913-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.913-1104A>G|||||||||-1||EntrezGene||||||3:g.12648902T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:425:0:0,0:205,220:425,0:0:2,0:37:1:36.1:1:1:0:60:84:1:0:0.1	0/1:141:2:1,1:46,93:139,2:0.0142:2,2:46:1:37:0:1:2.01:60:4:0.0142:0:1
    1044. 

  1044. 3	12649094	12649098	CTGTG	TTATC	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	35	48	3	12649094	.	CTGTG	TTATC	35	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Complex;DP=215;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03274;SOR=0;LSEQ=GAGGTCGAGGCTACAGTGAG;RSEQ=ATCATGCCACTGCACTCCAC;CSQ=TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.581+1167_581+1171delinsGATAA|||||||||-1||EntrezGene||YES||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.581+1167_581+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.338+1167_338+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.338+1167_338+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+1167_581+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.338+1167_338+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+1167_338+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.581+1167_581+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.912+1167_912+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.912+1167_912+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||,TTATC|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.912+1167_912+1171delinsGATAA|||||||||-1||EntrezGene||||||3:g.12649094_12649098delinsTTATC||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:215:0:0,0:79,136:215,0:0:2,0:36.9:1:36.2:1:1:0:60:52.75:1:0:0.1	0/1:48:2:1,1:19,27:46,2:0.0417:2,2:20:0:35.8:1:1:1.41:60:4:0.0417:0:3
    1045. 

  1045. 3	12649504	12649504	A	G	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	101	3	12649504	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=36;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.54208;SOR=0;LSEQ=AAAAATAAGATAAATTTTAA;RSEQ=AGCTTGTGCCATTTGTGCTA;CSQ=G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.581+761T>C|||||||||-1||EntrezGene||YES||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.581+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.338+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.338+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.338+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.581+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.912+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.912+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.912+761T>C|||||||||-1||EntrezGene||||||3:g.12649504A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:36:0:0,0:18,18:36,0:0:2,0:31.6:1:36.3:1:1:0:60:35:1:0:1.2	0/1:101:2:1,1:59,40:99,2:0.0198:2,2:34:0:37:0:1:1.46916:60:4:0.02:0:1
    1046. 

  1046. 3	12649510	12649510	G	T	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	101	3	12649510	.	G	T	38	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.40642;SOR=0;LSEQ=AAGATAAATTTTAAAAGCTT;RSEQ=TGCCATTTGTGCTACTCAAG;CSQ=T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.581+755C>A|||||||||-1||EntrezGene||YES||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.581+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.338+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.338+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.338+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.581+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.912+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.912+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.912+755C>A|||||||||-1||EntrezGene||||||3:g.12649510G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:35:0:0,0:16,19:35,0:0:2,0:33.4:1:31.1:1:1:0:60:4:1:0:1.1	0/1:101:3:3,0:56,42:98,3:0.0297:2,0:14.7:1:24.3:1:0.26396:0:53.3:2:0.0235:0:5
    1047. 

  1047. 3	12649702	12649702	T	C	intronic	RAF1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	84	3	12649702	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.74871;SOR=0;LSEQ=CAGTTTGGACCATGTACTTT;RSEQ=AATGTAAACTTTAAATTCTT;CSQ=C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||5/17|NM_001354689.3:c.581+563A>G|||||||||-1||EntrezGene||YES||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||5/16|NM_001354690.3:c.581+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||5/16|NM_001354691.3:c.338+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||4/15|NM_001354692.3:c.338+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||5/15|NM_001354693.3:c.581+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||4/16|NM_001354694.3:c.338+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||4/14|NM_001354695.3:c.338+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||5/16|NM_002880.4:c.581+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||5/17|NR_148940.3:n.912+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||5/16|NR_148941.3:n.912+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||5/16|NR_148942.3:n.912+563A>G|||||||||-1||EntrezGene||||||3:g.12649702T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:13:0:0,0:5,8:13,0:0:2,0:28.4:1:35:1:1:0:60:12:1:0:0.2	0/1:84:2:1,1:41,41:82,2:0.0238:2,2:19:1:31:1:1:1:60:4:0.0238:0:1
    1048. 

  1048. 3	12650324	12650324	C	T	exonic	RAF1	.	synonymous SNV	RAF1:NM_002880:exon5:c.G522A:p.E174E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	291	3	12650324	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=176;VD=2;AF=0.0114;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14153;SOR=inf;LSEQ=GGTACTTTGGTGCTACAGTG;RSEQ=TCATGAAATTTGTAGCCACA;CSQ=T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354689.3|protein_coding|5/18||NM_001354689.3:c.522G>A|NP_001341618.1:p.Glu174%3D|853|522|174|E|gaG/gaA|||-1||EntrezGene||YES||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354690.3|protein_coding|5/17||NM_001354690.3:c.522G>A|NP_001341619.1:p.Glu174%3D|688|522|174|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354691.3|protein_coding|5/17||NM_001354691.3:c.279G>A|NP_001341620.1:p.Glu93%3D|833|279|93|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354692.3|protein_coding|4/16||NM_001354692.3:c.279G>A|NP_001341621.1:p.Glu93%3D|740|279|93|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354693.3|protein_coding|5/16||NM_001354693.3:c.522G>A|NP_001341622.1:p.Glu174%3D|853|522|174|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354694.3|protein_coding|4/17||NM_001354694.3:c.279G>A|NP_001341623.1:p.Glu93%3D|740|279|93|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_001354695.3|protein_coding|4/15||NM_001354695.3:c.279G>A|NP_001341624.1:p.Glu93%3D|740|279|93|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|synonymous_variant|LOW|RAF1|5894|Transcript|NM_002880.4|protein_coding|5/17||NM_002880.4:c.522G>A|NP_002871.1:p.Glu174%3D|853|522|174|E|gaG/gaA|||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA|5/18||NR_148940.3:n.853G>A||853|||||||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA|5/17||NR_148941.3:n.853G>A||853|||||||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA|5/17||NR_148942.3:n.853G>A||853|||||||-1||EntrezGene||||||3:g.12650324C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:176:2:1,1:96,78:174,2:0.0114:2,2:54.5:1:37:0:1:1.2293:60:4:0.0116:0:1	0/0:291:0:0,0:140,151:291,0:0:2,0:39.1:1:35.6:1:1:0:60:23.25:1:0:0.1
    1049. 

  1049. 3	12650482	12650482	T	A	intronic	RAF1	.	.	.	1.	1	1	1	1	1	1	1	1	rs2454440	rs2454440	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	245	112	3	12650482	.	T	A	245	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=13;AF=1;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGATGACAAAAGACAAC;RSEQ=TCATTTCTTGGCCTCCAAAA;CSQ=A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||4/17|NM_001354689.3:c.424-60A>T|||||||rs2454440||-1||EntrezGene||YES||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||4/16|NM_001354690.3:c.424-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||4/16|NM_001354691.3:c.181-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||3/15|NM_001354692.3:c.181-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||4/15|NM_001354693.3:c.424-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||3/16|NM_001354694.3:c.181-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||3/14|NM_001354695.3:c.181-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||4/16|NM_002880.4:c.424-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||4/17|NR_148940.3:n.755-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||4/16|NR_148941.3:n.755-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||4/16|NR_148942.3:n.755-60A>T|||||||rs2454440||-1||EntrezGene||||||3:g.12650482T>A||||||||||1|AFR&AMR&EAS&EUR&SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:13:13:2,11:0,0:0,13:1:0,2:29.8:1:37:0:1:0:60:26:1:0:1.1	1/1:112:112:29,83:0,0:0,112:1:0,2:29.9:1:36:1:1:0:60:36.333:1:0:1.1
    1050. 

  1050. 3	12650636	12650637	TA	-	intronic	RAF1	.	.	.	.	3.319e-05	0	0	0	0	0	0	0.0011	rs151300313	rs151300313	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU7915957	ESAD-UK|1|409|0.00244499,PACA-AU|1|391|0.00255754,COCA-CN|1|321|0.00311526,PBCA-DE|1|499|0.00200401	0.25	74	59	3	12650635	.	CTA	C	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=6;VD=0;AF=0;SHIFT3=12;MSI=7;MSILEN=2;SSF=0.67223;SOR=0;LSEQ=AAGAACTTTAAACAATCCAA;RSEQ=TATATATATATACATACGCA;CSQ=-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354689.3|protein_coding||4/17|NM_001354689.3:c.423+95_423+96del|||||||rs151300313||-1||EntrezGene||YES||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354690.3|protein_coding||4/16|NM_001354690.3:c.423+95_423+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding||4/16|NM_001354691.3:c.180+95_180+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding||3/15|NM_001354692.3:c.180+95_180+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354693.3|protein_coding||4/15|NM_001354693.3:c.423+95_423+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding||3/16|NM_001354694.3:c.180+95_180+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding||3/14|NM_001354695.3:c.180+95_180+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant|MODIFIER|RAF1|5894|Transcript|NM_002880.4|protein_coding||4/16|NM_002880.4:c.423+95_423+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA||4/17|NR_148940.3:n.754+95_754+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA||4/16|NR_148941.3:n.754+95_754+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA||4/16|NR_148942.3:n.754+95_754+96del|||||||rs151300313||-1||EntrezGene||||||3:g.12650648_12650649del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:5,1:6,0:0:2,0:20:1:37:0:1:0:60:12:1:0:0	0/1:59:4:3,1:38,17:55,4:0.0678:2,2:44.5:1:37:0:1:1.34:60:8:0.0678:0:0
    1051. 

  1051. 3	12660189	12660189	A	T	exonic	RAF1	.	nonsynonymous SNV	RAF1:NM_002880:exon2:c.T32A:p.I11N	.	.	.	.	.	.	.	.	.	.	.	0.003	0.721	D	0.828	0.441	P	0.235	0.367	B	0.000	0.629	D	1.000	0.810	D	0.345	0.112	N	-1.02	0.764	T	-0.92	0.247	N	0.664	0.675	-0.429	0.711	T	0.271	0.643	T	0.094	0.763	D	4.522	0.605	24.3	0.989	0.473	0.990	0.894	D	c	0.413	0.554	1.000	0.747	0.707	0.730	0	6.03	0.978	8.633	0.907	1.199	0.960	1.000	0.715	1.000	0.888	16.558	0.843	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	182	3	12660189	.	A	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=760;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03716;SOR=0;LSEQ=TGAATCCAAAACCATTGCTG;RSEQ=TCGTCTTCCAAGCTCCCTGT;CSQ=T|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354689.3|protein_coding|2/18||NM_001354689.3:c.32T>A|NP_001341618.1:p.Ile11Asn|363|32|11|I/N|aTc/aAc|||-1||EntrezGene||YES||||3:g.12660189A>T||||||||||||||,T|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354690.3|protein_coding|2/17||NM_001354690.3:c.32T>A|NP_001341619.1:p.Ile11Asn|198|32|11|I/N|aTc/aAc|||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding|3/17||NM_001354691.3:c.-99T>A||456|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding|2/16||NM_001354692.3:c.-99T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354693.3|protein_coding|2/16||NM_001354693.3:c.32T>A|NP_001341622.1:p.Ile11Asn|363|32|11|I/N|aTc/aAc|||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding|2/17||NM_001354694.3:c.-99T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding|2/15||NM_001354695.3:c.-99T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|missense_variant|MODERATE|RAF1|5894|Transcript|NM_002880.4|protein_coding|2/17||NM_002880.4:c.32T>A|NP_002871.1:p.Ile11Asn|363|32|11|I/N|aTc/aAc|||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA|2/18||NR_148940.3:n.363T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA|2/17||NR_148941.3:n.363T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA|2/17||NR_148942.3:n.363T>A||363|||||||-1||EntrezGene||||||3:g.12660189A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:760:0:0,0:258,502:760,0:0:2,0:34.8:1:36.2:1:1:0:60:107.571:1:0:0.1	0/1:182:2:1,1:60,120:180,2:0.011:2,2:36:1:37:0:1:1.99:60:4:0.0112:0:1
    1052. 

  1052. 3	12660199	12660199	A	G	exonic	RAF1	.	nonsynonymous SNV	RAF1:NM_002880:exon2:c.T22C:p.W8R	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.996	0.670	D	0.823	0.574	P	0.000	0.843	D	1	0.810	D	1.75	0.456	L	-1.12	0.782	T	-0.51	0.160	N	0.91	0.907	-0.032	0.816	T	0.463	0.792	T	0.183	0.857	D	5.984	0.823	27.8	0.997	0.792	0.971	0.725	D	c	0.639	0.696	1.000	0.747	0.707	0.730	0	6.03	0.978	7.146	0.768	1.199	0.960	1.000	0.715	0.998	0.697	16.558	0.843	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	163	3	12660199	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=661;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03894;SOR=0;LSEQ=ACCATTGCTGATCGTCTTCC;RSEQ=AGCTCCCTGTATGTGCTCCA;CSQ=G|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354689.3|protein_coding|2/18||NM_001354689.3:c.22T>C|NP_001341618.1:p.Trp8Arg|353|22|8|W/R|Tgg/Cgg|||-1||EntrezGene||YES||||3:g.12660199A>G||||||||||||||,G|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354690.3|protein_coding|2/17||NM_001354690.3:c.22T>C|NP_001341619.1:p.Trp8Arg|188|22|8|W/R|Tgg/Cgg|||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354691.3|protein_coding|3/17||NM_001354691.3:c.-109T>C||446|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354692.3|protein_coding|2/16||NM_001354692.3:c.-109T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|missense_variant|MODERATE|RAF1|5894|Transcript|NM_001354693.3|protein_coding|2/16||NM_001354693.3:c.22T>C|NP_001341622.1:p.Trp8Arg|353|22|8|W/R|Tgg/Cgg|||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354694.3|protein_coding|2/17||NM_001354694.3:c.-109T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|RAF1|5894|Transcript|NM_001354695.3|protein_coding|2/15||NM_001354695.3:c.-109T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|missense_variant|MODERATE|RAF1|5894|Transcript|NM_002880.4|protein_coding|2/17||NM_002880.4:c.22T>C|NP_002871.1:p.Trp8Arg|353|22|8|W/R|Tgg/Cgg|||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148940.3|misc_RNA|2/18||NR_148940.3:n.353T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148941.3|misc_RNA|2/17||NR_148941.3:n.353T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|RAF1|5894|Transcript|NR_148942.3|misc_RNA|2/17||NR_148942.3:n.353T>C||353|||||||-1||EntrezGene||||||3:g.12660199A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:661:0:0,0:204,457:661,0:0:2,0:32.3:1:36.2:1:1:0:60:65.1:1:0:0.2	0/1:163:2:1,1:53,108:161,2:0.0123:2,2:33:0:31:1:1:2.03:60:4:0.0123:0:1
    1053. 

  1053. 3	14187430	14187430	G	A	UTR3	XPC	NM_004628:c.*11C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	31	3	14187430	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=331;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.00712;SOR=0;LSEQ=CTGGTGGGTGCCCCTCTAGT;RSEQ=GGCGCTCAGCTCACAGCTGC;CSQ=A|3_prime_UTR_variant|MODIFIER|XPC|7508|Transcript|NM_001354726.2|protein_coding|15/15||NM_001354726.2:c.*11C>T||2743|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1,A|3_prime_UTR_variant|MODIFIER|XPC|7508|Transcript|NM_001354727.2|protein_coding|16/16||NM_001354727.2:c.*11C>T||2861|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1,A|3_prime_UTR_variant|MODIFIER|XPC|7508|Transcript|NM_001354729.2|protein_coding|16/16||NM_001354729.2:c.*11C>T||2849|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1,A|3_prime_UTR_variant|MODIFIER|XPC|7508|Transcript|NM_001354730.2|protein_coding|16/16||NM_001354730.2:c.*11C>T||2621|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1,A|3_prime_UTR_variant|MODIFIER|XPC|7508|Transcript|NM_004628.5|protein_coding|16/16||NM_004628.5:c.*11C>T||2867|||||COSV99542417||-1||EntrezGene||YES||||3:g.14187430G>A|||||||||||||1|1,A|downstream_gene_variant|MODIFIER|TMEM43|79188|Transcript|NM_024334.3|protein_coding||||||||||COSV99542417|2250|1||EntrezGene||YES||||3:g.14187430G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|XPC|7508|Transcript|NR_148950.2|misc_RNA|15/15||NR_148950.2:n.2706C>T||2706|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|XPC|7508|Transcript|NR_148951.2|misc_RNA|14/14||NR_148951.2:n.2582C>T||2582|||||COSV99542417||-1||EntrezGene||||||3:g.14187430G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:331:0:0,0:200,131:331,0:0:2,0:39:1:36.7:1:1:0:60:164.5:1:0:1.1	0/1:31:2:1,1:17,12:29,2:0.0645:2,2:43.5:1:37:0:1:1.40053:60:4:0.0645:0:2
    1054. 

  1054. 3	14187449	14187449	G	T	exonic	XPC	.	nonsynonymous SNV	XPC:NM_004628:exon16:c.C2815A:p.Q939K	0.75	0.6556	0.7228	0.7057	0.5629	0.6382	0.6985	0.6087	0.6337	rs2228001	rs2228001	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.000	0.629	N	1.000	0.090	P	-2.455	0.001	N	1.93	0.229	T	1.67	0.006	N	0.033	0.153	-0.955	0.400	T	0.000	0.000	T	.	.	.	1.250	0.215	12.01	0.902	0.189	0.059	0.117	N	c	-0.971	-0.646	1.000	0.747	0.722	0.854	0	4.24	0.493	2.828	0.476	0.115	0.208	1.000	0.715	0.998	0.697	7.925	0.289	.	ENSG00000233121.1|ENSG00000163528.8|ENSG00000170860.3	Artery_Tibial|Muscle_Skeletal|Muscle_Skeletal	ID=COSV53207797;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),5(prostate)	187973	Xeroderma_pigmentosum,_group_C|Arrhythmogenic_right_ventricular_cardiomyopathy|Xeroderma_pigmentosum|not_specified|cisplatin_response_-_Toxicity/ADR	MONDO:MONDO:0010211,MedGen:C2752147,OMIM:278720,SNOMED_CT:25784009|MONDO:MONDO:0016587,MedGen:C0349788,OMIM:PS107970,Orphanet:ORPHA247,SNOMED_CT:253528005,SNOMED_CT:281170005|MONDO:MONDO:0019600,MedGen:C0043346,Orphanet:ORPHA910,SNOMED_CT:44600005|MedGen:CN169374|MedGen:CN236502	reviewed_by_expert_panel	drug_response	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	MU11483739	COCA-CN|5|321|0.0155763	1	310	38	3	14187449	.	G	T	310	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=418;VD=357;AF=0.8541;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00331;SOR=0;LSEQ=TGGGCGCTCAGCTCACAGCT;RSEQ=CTCAAATGGGAACAGGTGGG;CSQ=T|missense_variant|MODERATE|XPC|7508|Transcript|NM_001354726.2|protein_coding|15/15||NM_001354726.2:c.2236C>A|NP_001341655.1:p.Gln746Lys|2724|2236|746|Q/K|Cag/Aag|rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|missense_variant|MODERATE|XPC|7508|Transcript|NM_001354727.2|protein_coding|16/16||NM_001354727.2:c.2809C>A|NP_001341656.1:p.Gln937Lys|2842|2809|937|Q/K|Cag/Aag|rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|missense_variant|MODERATE|XPC|7508|Transcript|NM_001354729.2|protein_coding|16/16||NM_001354729.2:c.2797C>A|NP_001341658.1:p.Gln933Lys|2830|2797|933|Q/K|Cag/Aag|rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|missense_variant|MODERATE|XPC|7508|Transcript|NM_001354730.2|protein_coding|16/16||NM_001354730.2:c.2569C>A|NP_001341659.1:p.Gln857Lys|2602|2569|857|Q/K|Cag/Aag|rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|missense_variant|MODERATE|XPC|7508|Transcript|NM_004628.5|protein_coding|16/16||NM_004628.5:c.2815C>A|NP_004619.3:p.Gln939Lys|2848|2815|939|Q/K|Cag/Aag|rs2228001&CM070359&COSV53207797||-1||EntrezGene||YES||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|downstream_gene_variant|MODIFIER|TMEM43|79188|Transcript|NM_024334.3|protein_coding||||||||||rs2228001&CM070359&COSV53207797|2269|1||EntrezGene||YES||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|non_coding_transcript_exon_variant|MODIFIER|XPC|7508|Transcript|NR_148950.2|misc_RNA|15/15||NR_148950.2:n.2687C>A||2687|||||rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1,T|non_coding_transcript_exon_variant|MODIFIER|XPC|7508|Transcript|NR_148951.2|misc_RNA|14/14||NR_148951.2:n.2563C>A||2563|||||rs2228001&CM070359&COSV53207797||-1||EntrezGene||||||3:g.14187449G>T|0.6335|0.7303|0.7064|0.5279|0.6395|0.698|0.5917|0.604|0.6472|0.7511|AFR|likely_benign&drug_response&benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:418:357:208,149:33,28:61,357:0.8541:2,2:36.6:1:36.6:1:0.57637:1.18:60:118:0.853:0:1.3	1/1:38:38:19,19:0,0:0,38:1:0,2:31.3:1:36:1:1:0:60:37:1:0:1.2
    1055. 

  1055. 3	30664755	30664755	A	G	exonic	TGFBR2	.	synonymous SNV	TGFBR2:NM_001024847:exon2:c.A159G:p.P53P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	91	3	30664755	.	A	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.91713;SOR=0;LSEQ=TGTAATAGGACTGCCCATCC;RSEQ=CTGAGACATAGTAAAGTATC;CSQ=G|synonymous_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding|2/8||NM_001024847.2:c.159A>G|NP_001020018.1:p.Pro53%3D|541|159|53|P|ccA/ccG|||1||EntrezGene||YES||||3:g.30664755A>G||||||||||||||,G|intron_variant|MODIFIER|TGFBR2|7048|Transcript|NM_003242.6|protein_coding||1/6|NM_003242.6:c.94+16286A>G|||||||||1||EntrezGene||||||3:g.30664755A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:54.2:1:37:0:1:0:60:8:1:0:0.8	0/1:91:2:1,1:36,53:89,2:0.022:2,2:49:1:37:0:1:1.47:60:4:0.0222:0:1
    1056. 

  1056. 3	30686235	30686235	T	C	intronic	TGFBR2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	94	3	30686235	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=120;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.19179;SOR=0;LSEQ=TAATATATCTTTCTCTCTCC;RSEQ=CAGTTAATAACGACATGATA;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding||2/7|NM_001024847.2:c.170-4T>C|||||||||1||EntrezGene||YES||||3:g.30686235T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_003242.6|protein_coding||1/6|NM_003242.6:c.95-4T>C|||||||||1||EntrezGene||||||3:g.30686235T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:120:0:0,0:97,23:120,0:0:2,0:24.1:1:36:1:1:0:60:39:1:0:0	0/1:94:2:1,1:72,20:92,2:0.0213:2,2:15.5:1:37:0:0.39876:3.53732:60:4:0.0217:0:1
    1057. 

  1057. 3	30686414	30686414	A	G	intronic	TGFBR2	.	.	.	0.71	0.3733	0.3381	0.3005	0.2616	0.6901	0.3946	0.3618	0.3615	rs1155705	rs1155705	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55442809;OCCURENCE=22(large_intestine),1(haematopoietic_and_lymphoid_tissue),11(soft_tissue),2(lung)	45528	Marfan_syndrome|Loeys-Dietz_syndrome_2|Loeys-Dietz_syndrome|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|not_specified|none_provided	MONDO:MONDO:0007947,MedGen:C0024796,OMIM:154700,Orphanet:ORPHA284963,Orphanet:ORPHA558,SNOMED_CT:19346006|MONDO:MONDO:0012427,MedGen:C2674574,OMIM:610168|MONDO:MONDO:0018954,MedGen:C2697932,OMIM:PS609192,Orphanet:ORPHA60030,SNOMED_CT:446263001|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15034252	ESAD-UK|1|409|0.00244499,LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,COCA-CN|5|321|0.0155763	1	281	169	3	30686414	.	A	G	281	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=209;VD=209;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGGCTGTATGGTAAGC;RSEQ=AGCCTTTTAAGAAGTTATTC;CSQ=G|splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding||3/7|NM_001024847.2:c.338+7A>G|||||||rs1155705&COSV55442809||1||EntrezGene||YES||||3:g.30686414A>G|0.3701|0.3408|0.342|0.2495|0.6943|0.3853|0.3412|0.3508|0.3627|0.7054|EAS|benign|0&1|1&1,G|splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_003242.6|protein_coding||2/6|NM_003242.6:c.263+7A>G|||||||rs1155705&COSV55442809||1||EntrezGene||||||3:g.30686414A>G|0.3701|0.3408|0.342|0.2495|0.6943|0.3853|0.3412|0.3508|0.3627|0.7054|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:209:209:53,156:0,0:0,209:1:0,2:25.8:1:36.5:1:1:0:60:208:1:0:1	1/1:169:169:52,117:0,0:0,169:1:0,2:35.7:1:36.5:1:1:0:60:83.5:1:0:1.1
    1058. 

  1058. 3	30691872	30691872	A	-	exonic	TGFBR2	.	frameshift deletion	TGFBR2:NM_003242:exon3:c.374delA:p.K128Sfs*35,TGFBR2:NM_001024847:exon4:c.449delA:p.K153Sfs*35	0.056	3.761e-05	0	0	0	0	0.0004	0	0	rs752580104	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	452306	Loeys-Dietz_syndrome|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|not_specified|Cardiovascular_phenotype	MONDO:MONDO:0018954,MedGen:C2697932,OMIM:PS609192,Orphanet:ORPHA60030,SNOMED_CT:446263001|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN169374|MedGen:CN230736	criteria_provided,_conflicting_interpretations	Conflicting_interpretations_of_pathogenicity	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114046655	COCA-CN|1|321|0.00311526	0.5	167	224	3	30691871	.	GA	G	167	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=623;VD=23;AF=0.0369;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.36805;SOR=0.82051;LSEQ=CTCCAAAGTGCATTATGAAG;RSEQ=AAAAAAAAAGCCTGGTGAGA;CSQ=-|frameshift_variant|HIGH|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding|4/8||NM_001024847.2:c.458del|NP_001020018.1:p.Lys153SerfsTer35|831|449|150|E/X|gAa/ga|rs79375991&COSV55453622||1||EntrezGene||YES|||9|3:g.30691881del|0.002484|0.002619|0.0005614|0.002688|0.001594|0.0003203|0.003398|0.002897|0.003316|0.003398|gnomAD_NFE|uncertain_significance&benign&likely_pathogenic|0&1|1&1,-|frameshift_variant|HIGH|TGFBR2|7048|Transcript|NM_003242.6|protein_coding|3/7||NM_003242.6:c.383del|NP_003233.4:p.Lys128SerfsTer35|657|374|125|E/X|gAa/ga|rs79375991&COSV55453622||1||EntrezGene|||||9|3:g.30691881del|0.002484|0.002619|0.0005614|0.002688|0.001594|0.0003203|0.003398|0.002897|0.003316|0.003398|gnomAD_NFE|uncertain_significance&benign&likely_pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:623:23:11,12:313,287:600,23:0.0369:2,2:42.5:1:37:0:0.83217:1.1894:60:46:0.0372:0:0	0/1:224:10:5,5:102,112:214,10:0.0446:2,2:39:1:35.8:1:1:1.1:60:20:0.0446:0.0045:0.1
    1059. 

  1059. 3	30713126	30713126	T	A	intronic	TGFBR2	.	.	.	0.45	0.2595	0.1511	0.4243	0.2167	0.2998	0.2978	0.3006	0.2658	rs11466512	rs11466512	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55442568;OCCURENCE=1(bone),1(stomach),11(soft_tissue),1(pancreas),1(lung),12(large_intestine)	53825	Marfan_syndrome|Loeys-Dietz_syndrome_2|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|not_specified|Cardiovascular_phenotype|none_provided	MONDO:MONDO:0007947,MedGen:C0024796,OMIM:154700,Orphanet:ORPHA284963,Orphanet:ORPHA558,SNOMED_CT:19346006|MONDO:MONDO:0012427,MedGen:C2674574,OMIM:610168|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN169374|MedGen:CN230736|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU585873	LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	231	165	3	30713126	.	T	A	231	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1186;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCTTGTTTTGTTTCCCCA;RSEQ=CAGAATATAACACCAGCAAT;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding||4/7|NM_001024847.2:c.530-4T>A|||||||rs11466512&COSV55442568||1||EntrezGene||YES||||3:g.30713126T>A|0.3004|0.1494|0.4432|0.2006|0.3168|0.2861|0.3111|0.2966|0.2134|0.4432|gnomAD_AMR|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|TGFBR2|7048|Transcript|NM_003242.6|protein_coding||3/6|NM_003242.6:c.455-4T>A|||||||rs11466512&COSV55442568||1||EntrezGene||||||3:g.30713126T>A|0.3004|0.1494|0.4432|0.2006|0.3168|0.2861|0.3111|0.2966|0.2134|0.4432|gnomAD_AMR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1186:0:0,0:791,395:1186,0:0:2,0:37.8:1:35.8:1:1:0:60:41.357:1:0:0.1	1/0:165:83:58,25:60,22:82,83:0.503:2,2:38.3:1:36.3:1:0.73066:1.17439:60:166:0.503:0:1.1
    1060. 

  1060. 3	30713842	30713842	C	T	exonic	TGFBR2	.	synonymous SNV	TGFBR2:NM_003242:exon4:c.C1167T:p.N389N,TGFBR2:NM_001024847:exon5:c.C1242T:p.N414N	0.3	0.0426	0.0320	0.0215	0.0563	0.3201	0.0470	0.0189	0.0399	rs2228048	rs2228048	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55442546;OCCURENCE=2(large_intestine),1(soft_tissue)	53819	Marfan_syndrome|Loeys-Dietz_syndrome_2|Loeys-Dietz_syndrome|Familial_thoracic_aortic_aneurysm_and_aortic_dissection|not_specified|Cardiovascular_phenotype	MONDO:MONDO:0007947,MedGen:C0024796,OMIM:154700,Orphanet:ORPHA284963,Orphanet:ORPHA558,SNOMED_CT:19346006|MONDO:MONDO:0012427,MedGen:C2674574,OMIM:610168|MONDO:MONDO:0018954,MedGen:C2697932,OMIM:PS609192,Orphanet:ORPHA60030,SNOMED_CT:446263001|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387|MedGen:CN169374|MedGen:CN230736	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU764777	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,COCA-CN|2|321|0.00623053	0.25	241	224	3	30713842	.	C	T	241	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2496;VD=1;AF=0.0004;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00054;LSEQ=TCCAATATCCTCGTGAAGAA;RSEQ=GACCTAACCTGCTGCCTGTG;CSQ=T|synonymous_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding|5/8||NM_001024847.2:c.1242C>T|NP_001020018.1:p.Asn414%3D|1624|1242|414|N|aaC/aaT|rs2228048&COSV55442546||1||EntrezGene||YES||||3:g.30713842C>T|0.05502|0.03303|0.01666|0.04467|0.3053|0.04596|0.01449|0.04077|0.1221|0.3053|gnomAD_EAS|benign|0&1|1&1,T|synonymous_variant|LOW|TGFBR2|7048|Transcript|NM_003242.6|protein_coding|4/7||NM_003242.6:c.1167C>T|NP_003233.4:p.Asn389%3D|1450|1167|389|N|aaC/aaT|rs2228048&COSV55442546||1||EntrezGene||||||3:g.30713842C>T|0.05502|0.03303|0.01666|0.04467|0.3053|0.04596|0.01449|0.04077|0.1221|0.3053|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2496:1:1,0:1141,1354:2495,1:0.0004:2,0:37:0:37:0:0.45753:0:60:2:0.0004:0:1	0/1:224:96:33,63:43,84:127,96:0.4286:2,2:33.9:1:36.6:1:1:1.02:60:192:0.4305:0:1.1
    1061. 

  1061. 3	30713860	30713860	G	A	exonic	TGFBR2	.	synonymous SNV	TGFBR2:NM_003242:exon4:c.G1185A:p.L395L,TGFBR2:NM_001024847:exon5:c.G1260A:p.L420L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	200	3	30713860	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2428;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.00576;SOR=0;LSEQ=AACGACCTAACCTGCTGCCT;RSEQ=TGTGACTTTGGGCTTTCCCT;CSQ=A|synonymous_variant|LOW|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding|5/8||NM_001024847.2:c.1260G>A|NP_001020018.1:p.Leu420%3D|1642|1260|420|L|ctG/ctA|COSV55451537||1||EntrezGene||YES||||3:g.30713860G>A|||||||||||||1|1,A|synonymous_variant|LOW|TGFBR2|7048|Transcript|NM_003242.6|protein_coding|4/7||NM_003242.6:c.1185G>A|NP_003233.4:p.Leu395%3D|1468|1185|395|L|ctG/ctA|COSV55451537||1||EntrezGene||||||3:g.30713860G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2428:0:0,0:1072,1355:2427,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:200:2:1,1:69,129:198,2:0.01:2,2:65:1:37:0:1:1.86:60:4:0.01:0:2
    1062. 

  1062. 3	30715615	30715615	A	G	exonic	TGFBR2	.	nonsynonymous SNV	TGFBR2:NM_003242:exon5:c.A1273G:p.M425V,TGFBR2:NM_001024847:exon6:c.A1348G:p.M450V	.	.	.	.	.	.	.	.	.	rs104893817	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	A	1.81	0.478	L	-3.38	0.942	D	-3.98	0.737	D	0.985	0.988	0.978	0.968	D	0.890	0.964	D	0.479	0.948	D	5.862	0.803	27.3	0.996	0.723	0.970	0.718	D	c	0.906	0.895	1.000	0.747	0.722	0.854	0	6.02	0.975	9.325	0.960	1.199	0.960	1.000	0.715	1.000	0.888	16.549	0.842	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain	.	.	.	27556	Loeys-Dietz_syndrome_2|Familial_thoracic_aortic_aneurysm_and_aortic_dissection	MONDO:MONDO:0012427,MedGen:C2674574,OMIM:610168|MONDO:MONDO:0019625,MedGen:C4707243,OMIM:PS607086,Orphanet:ORPHA91387	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	335	3	30715615	.	A	G	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=602;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01615;SOR=0;LSEQ=AGGTGGGAACTGCAAGATAC;RSEQ=TGGCTCCAGAAGTCCTAGAA;CSQ=G|missense_variant|MODERATE|TGFBR2|7048|Transcript|NM_001024847.2|protein_coding|6/8||NM_001024847.2:c.1348A>G|NP_001020018.1:p.Met450Val|1730|1348|450|M/V|Atg/Gtg|rs104893817&CM060084||1||EntrezGene||YES||||3:g.30715615A>G||||||||||||pathogenic||1&1,G|missense_variant|MODERATE|TGFBR2|7048|Transcript|NM_003242.6|protein_coding|5/7||NM_003242.6:c.1273A>G|NP_003233.4:p.Met425Val|1556|1273|425|M/V|Atg/Gtg|rs104893817&CM060084||1||EntrezGene||||||3:g.30715615A>G||||||||||||pathogenic||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:602:0:0,0:343,259:602,0:0:2,0:34.3:1:36.2:1:1:0:60:65.889:1:0:0.1	0/1:335:4:2,2:194,137:331,4:0.0119:2,2:39.2:1:37:0:1:1.41453:60:8:0.0122:0:1.2
    1063. 

  1063. 3	37050394	37050394	C	T	exonic	MLH1	.	synonymous SNV	MLH1:NM_000249:exon6:c.C543T:p.G181G,MLH1:NM_001167617:exon6:c.C249T:p.G83G,MLH1:NM_001258271:exon6:c.C543T:p.G181G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51622998;OCCURENCE=1(pancreas)	621931	Lynch_syndrome|Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0005835,MedGen:C4552100,OMIM:PS120435,Orphanet:ORPHA144|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	reviewed_by_expert_panel	Pathogenic	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU1691932	PACA-CA|1|268|0.00373134	0.25	31	215	3	37050394	.	C	T	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=196;VD=2;AF=0.0102;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.22681;SOR=inf;LSEQ=AAAATTTTGGAAGTTGTTGG;RSEQ=AGGTACAGTCCAAAATCTGG;CSQ=T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_000249.4|protein_coding|6/19||NM_000249.4:c.543C>T|NP_000240.1:p.Gly181%3D|573|543|181|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||YES||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001167617.3|protein_coding|6/19||NM_001167617.3:c.249C>T|NP_001161089.1:p.Gly83%3D|795|249|83|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001167618.3|protein_coding|6/19||NM_001167618.3:c.-181C>T||795|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001167619.3|protein_coding||5/17|NM_001167619.3:c.-179+1840C>T|||||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001258271.2|protein_coding|6/17||NM_001258271.2:c.543C>T|NP_001245200.1:p.Gly181%3D|573|543|181|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001258273.2|protein_coding|5/18||NM_001258273.2:c.-181C>T||482|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001258274.3|protein_coding|7/20||NM_001258274.3:c.-181C>T||945|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354615.2|protein_coding||5/17|NM_001354615.2:c.-179+1840C>T|||||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354616.2|protein_coding||5/17|NM_001354616.2:c.-179+1840C>T|||||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354617.2|protein_coding|6/19||NM_001354617.2:c.-181C>T||568|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354618.2|protein_coding|6/19||NM_001354618.2:c.-181C>T||800|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354619.2|protein_coding|7/20||NM_001354619.2:c.-181C>T||924|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354620.2|protein_coding|6/19||NM_001354620.2:c.249C>T|NP_001341549.1:p.Gly83%3D|563|249|83|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354621.2|protein_coding|6/17||NM_001354621.2:c.-274C>T||800|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354622.2|protein_coding|6/18||NM_001354622.2:c.-387C>T||800|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354623.2|protein_coding|5/17||NM_001354623.2:c.-387C>T||709|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354624.2|protein_coding|6/17||NM_001354624.2:c.-284C>T||573|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354625.2|protein_coding||5/15|NM_001354625.2:c.-282+1840C>T|||||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354626.2|protein_coding|6/17||NM_001354626.2:c.-284C>T||568|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&5_prime_UTR_variant|LOW|MLH1|4292|Transcript|NM_001354627.2|protein_coding|6/17||NM_001354627.2:c.-284C>T||800|||||rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354628.2|protein_coding|6/18||NM_001354628.2:c.543C>T|NP_001341557.1:p.Gly181%3D|573|543|181|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354629.2|protein_coding|5/18||NM_001354629.2:c.444C>T|NP_001341558.1:p.Gly148%3D|474|444|148|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1,T|splice_region_variant&synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354630.2|protein_coding|6/18||NM_001354630.2:c.543C>T|NP_001341559.1:p.Gly181%3D|573|543|181|G|ggC/ggT|rs1481129490&CS173369&COSV51622998||1||EntrezGene||||||3:g.37050394C>T||||||||||||likely_pathogenic&pathogenic|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:196:2:1,1:116,78:194,2:0.0102:2,2:29:0:31:1:1:1.48406:60:4:0.0103:0:1	0/0:215:0:0,0:106,109:215,0:0:2,0:41.7:1:36.2:1:1:0:60:70.667:1:0:0.1
    1064. 

  1064. 3	37053499	37053499	C	T	intronic	MLH1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	220	3	37053499	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=143;VD=2;AF=0.014;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.15453;SOR=inf;LSEQ=GTCTTCTGCTGTTTGTTTAT;RSEQ=AGCAAGGAGAGACAGTAGCT;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_000249.4|protein_coding||7/18|NM_000249.4:c.589-3C>T|||||||||1||EntrezGene||YES||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167617.3|protein_coding||7/18|NM_001167617.3:c.295-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167618.3|protein_coding||7/18|NM_001167618.3:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167619.3|protein_coding||6/17|NM_001167619.3:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258271.2|protein_coding||7/16|NM_001258271.2:c.589-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258273.2|protein_coding||6/17|NM_001258273.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258274.3|protein_coding||8/19|NM_001258274.3:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354615.2|protein_coding||6/17|NM_001354615.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354616.2|protein_coding||6/17|NM_001354616.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354617.2|protein_coding||7/18|NM_001354617.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354618.2|protein_coding||7/18|NM_001354618.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354619.2|protein_coding||8/19|NM_001354619.2:c.-135-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354620.2|protein_coding||7/18|NM_001354620.2:c.295-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354621.2|protein_coding||7/16|NM_001354621.2:c.-228-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354622.2|protein_coding||7/17|NM_001354622.2:c.-341-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354623.2|protein_coding||6/16|NM_001354623.2:c.-341-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354624.2|protein_coding||7/16|NM_001354624.2:c.-238-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354625.2|protein_coding||6/15|NM_001354625.2:c.-238-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354626.2|protein_coding||7/16|NM_001354626.2:c.-238-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354627.2|protein_coding||7/16|NM_001354627.2:c.-238-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354628.2|protein_coding||7/17|NM_001354628.2:c.589-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354629.2|protein_coding||6/17|NM_001354629.2:c.490-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354630.2|protein_coding||7/17|NM_001354630.2:c.589-3C>T|||||||||1||EntrezGene||||||3:g.37053499C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:143:2:1,1:72,69:141,2:0.014:2,2:31:0:37:0:1:1.04318:60:4:0.0141:0:1	0/0:220:0:0,0:99,121:220,0:0:2,0:40.1:1:35.6:1:1:0:60:26.5:1:0:0.1
    1065. 

  1065. 3	37055964	37055964	T	C	exonic	MLH1	.	nonsynonymous SNV	MLH1:NM_000249:exon9:c.T719C:p.F240S,MLH1:NM_001167617:exon9:c.T425C:p.F142S,MLH1:NM_001258271:exon9:c.T719C:p.F240S	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.936	0.504	P	0.795	0.561	P	0.000	0.537	D	1	0.810	D	3.69	0.947	H	-2.64	0.902	D	-5.73	0.885	D	0.909	0.909	0.452	0.899	D	0.603	0.859	D	0.252	0.892	D	5.887	0.807	27.4	0.998	0.894	0.979	0.777	D	c	0.503	0.501	1.000	0.747	0.707	0.730	0	5.7	0.886	3.738	0.545	1.011	0.635	1.000	0.715	0.999	0.750	15.972	0.797	DNA mismatch repair protein, C-terminal|Ribosomal protein S5 domain 2-type fold|Ribosomal protein S5 domain 2-type fold, subgroup;Histidine kinase-like ATPase, C-terminal domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	31	103	3	37055964	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=0;AF=0;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.73571;SOR=0;LSEQ=TGAGGATAAAACCCTAGCCT;RSEQ=CAAAATGAATGGTTACATAT;CSQ=C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_000249.4|protein_coding|9/19||NM_000249.4:c.719T>C|NP_000240.1:p.Phe240Ser|749|719|240|F/S|tTc/tCc|||1||EntrezGene||YES||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001167617.3|protein_coding|9/19||NM_001167617.3:c.425T>C|NP_001161089.1:p.Phe142Ser|971|425|142|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001167618.3|protein_coding|9/19||NM_001167618.3:c.-5T>C||971|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001167619.3|protein_coding|8/18||NM_001167619.3:c.-5T>C||884|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001258271.2|protein_coding|9/17||NM_001258271.2:c.719T>C|NP_001245200.1:p.Phe240Ser|749|719|240|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001258273.2|protein_coding|8/18||NM_001258273.2:c.-5T>C||658|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001258274.3|protein_coding|10/20||NM_001258274.3:c.-5T>C||1121|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354615.2|protein_coding|8/18||NM_001354615.2:c.-5T>C||652|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354616.2|protein_coding|8/18||NM_001354616.2:c.-5T>C||652|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354617.2|protein_coding|9/19||NM_001354617.2:c.-5T>C||744|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354618.2|protein_coding|9/19||NM_001354618.2:c.-5T>C||976|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354619.2|protein_coding|10/20||NM_001354619.2:c.-5T>C||1100|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354620.2|protein_coding|9/19||NM_001354620.2:c.425T>C|NP_001341549.1:p.Phe142Ser|739|425|142|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354621.2|protein_coding||8/16|NM_001354621.2:c.-140+2374T>C|||||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354622.2|protein_coding|9/18||NM_001354622.2:c.-211T>C||976|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354623.2|protein_coding|8/17||NM_001354623.2:c.-211T>C||885|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354624.2|protein_coding|9/17||NM_001354624.2:c.-108T>C||749|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354625.2|protein_coding|8/16||NM_001354625.2:c.-108T>C||647|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354626.2|protein_coding|9/17||NM_001354626.2:c.-108T>C||744|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354627.2|protein_coding|9/17||NM_001354627.2:c.-108T>C||976|||||||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354628.2|protein_coding|9/18||NM_001354628.2:c.719T>C|NP_001341557.1:p.Phe240Ser|749|719|240|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354629.2|protein_coding|8/18||NM_001354629.2:c.620T>C|NP_001341558.1:p.Phe207Ser|650|620|207|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||,C|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354630.2|protein_coding|9/18||NM_001354630.2:c.719T>C|NP_001341559.1:p.Phe240Ser|749|719|240|F/S|tTc/tCc|||1||EntrezGene||||||3:g.37055964T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:17:0:0,0:12,5:17,0:0:2,0:29.6:1:35.6:1:1:0:60:34:1:0:0.1	0/1:103:2:1,1:66,35:101,2:0.0194:2,2:14:1:31:1:1:1.87344:60:4:0.02:0:1
    1066. 

  1066. 3	37055998	37055998	C	A	exonic	MLH1	.	stopgain	MLH1:NM_001167619:exon8:c.C30A:p.Y10X,MLH1:NM_001258273:exon8:c.C30A:p.Y10X,MLH1:NM_000249:exon9:c.C753A:p.Y251X,MLH1:NM_001167617:exon9:c.C459A:p.Y153X,MLH1:NM_001167618:exon9:c.C30A:p.Y10X,MLH1:NM_001258271:exon9:c.C753A:p.Y251X,MLH1:NM_001258274:exon10:c.C30A:p.Y10X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.001	0.397	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.286	0.958	35	0.995	0.703	0.925	0.555	D	c	0.307	0.140	0.788	0.239	0.707	0.730	0	1.92	0.248	0.278	0.184	-0.352	0.070	0.984	0.356	0.980	0.490	9.403	0.374	DNA mismatch repair protein, C-terminal|Ribosomal protein S5 domain 2-type fold|Ribosomal protein S5 domain 2-type fold, subgroup;Histidine kinase-like ATPase, C-terminal domain	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	123	3	37055998	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=34;VD=2;AF=0.0588;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.04581;SOR=inf;LSEQ=TACATATCCAATGCAAACTA;RSEQ=TCAGTGAAGAAGTGCATCTT;CSQ=A|stop_gained|HIGH|MLH1|4292|Transcript|NM_000249.4|protein_coding|9/19||NM_000249.4:c.753C>A|NP_000240.1:p.Tyr251Ter|783|753|251|Y/*|taC/taA|CM117316||1||EntrezGene||YES||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001167617.3|protein_coding|9/19||NM_001167617.3:c.459C>A|NP_001161089.1:p.Tyr153Ter|1005|459|153|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001167618.3|protein_coding|9/19||NM_001167618.3:c.30C>A|NP_001161090.1:p.Tyr10Ter|1005|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001167619.3|protein_coding|8/18||NM_001167619.3:c.30C>A|NP_001161091.1:p.Tyr10Ter|918|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001258271.2|protein_coding|9/17||NM_001258271.2:c.753C>A|NP_001245200.1:p.Tyr251Ter|783|753|251|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001258273.2|protein_coding|8/18||NM_001258273.2:c.30C>A|NP_001245202.1:p.Tyr10Ter|692|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001258274.3|protein_coding|10/20||NM_001258274.3:c.30C>A|NP_001245203.1:p.Tyr10Ter|1155|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354615.2|protein_coding|8/18||NM_001354615.2:c.30C>A|NP_001341544.1:p.Tyr10Ter|686|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354616.2|protein_coding|8/18||NM_001354616.2:c.30C>A|NP_001341545.1:p.Tyr10Ter|686|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354617.2|protein_coding|9/19||NM_001354617.2:c.30C>A|NP_001341546.1:p.Tyr10Ter|778|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354618.2|protein_coding|9/19||NM_001354618.2:c.30C>A|NP_001341547.1:p.Tyr10Ter|1010|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354619.2|protein_coding|10/20||NM_001354619.2:c.30C>A|NP_001341548.1:p.Tyr10Ter|1134|30|10|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354620.2|protein_coding|9/19||NM_001354620.2:c.459C>A|NP_001341549.1:p.Tyr153Ter|773|459|153|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354621.2|protein_coding||8/16|NM_001354621.2:c.-140+2408C>A|||||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354622.2|protein_coding|9/18||NM_001354622.2:c.-177C>A||1010|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354623.2|protein_coding|8/17||NM_001354623.2:c.-177C>A||919|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354624.2|protein_coding|9/17||NM_001354624.2:c.-74C>A||783|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354625.2|protein_coding|8/16||NM_001354625.2:c.-74C>A||681|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354626.2|protein_coding|9/17||NM_001354626.2:c.-74C>A||778|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|5_prime_UTR_variant|MODIFIER|MLH1|4292|Transcript|NM_001354627.2|protein_coding|9/17||NM_001354627.2:c.-74C>A||1010|||||CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354628.2|protein_coding|9/18||NM_001354628.2:c.753C>A|NP_001341557.1:p.Tyr251Ter|783|753|251|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354629.2|protein_coding|8/18||NM_001354629.2:c.654C>A|NP_001341558.1:p.Tyr218Ter|684|654|218|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1,A|stop_gained|HIGH|MLH1|4292|Transcript|NM_001354630.2|protein_coding|9/18||NM_001354630.2:c.753C>A|NP_001341559.1:p.Tyr251Ter|783|753|251|Y/*|taC/taA|CM117316||1||EntrezGene||||||3:g.37055998C>A||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:2:1,1:25,7:32,2:0.0588:2,2:18:0:37:0:0.42068:3.40681:60:4:0.0588:0:1	0/0:123:0:0,0:71,52:123,0:0:2,0:42.3:1:36.4:1:1:0:60:60.5:1:0:0.1
    1067. 

  1067. 3	37067123	37067125	TAC	AAA	intronic	MLH1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	26	51	3	37067123	.	TAC	AAA	26	v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Complex;DP=184;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04637;SOR=0;LSEQ=TTTTTTTTTTTTTTTTTTAA;RSEQ=AGACTTTGCTACCAGGACTT;CSQ=AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_000249.4|protein_coding||11/18|NM_000249.4:c.1039-5_1039-3delinsAAA|||||||||1||EntrezGene||YES||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167617.3|protein_coding||11/18|NM_001167617.3:c.745-5_745-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167618.3|protein_coding||11/18|NM_001167618.3:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167619.3|protein_coding||10/17|NM_001167619.3:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258271.2|protein_coding||11/16|NM_001258271.2:c.1039-5_1039-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258273.2|protein_coding||10/17|NM_001258273.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258274.3|protein_coding||12/19|NM_001258274.3:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354615.2|protein_coding||10/17|NM_001354615.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354616.2|protein_coding||10/17|NM_001354616.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354617.2|protein_coding||11/18|NM_001354617.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354618.2|protein_coding||11/18|NM_001354618.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354619.2|protein_coding||12/19|NM_001354619.2:c.316-5_316-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354620.2|protein_coding||11/18|NM_001354620.2:c.745-5_745-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354621.2|protein_coding||9/16|NM_001354621.2:c.16-5_16-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354622.2|protein_coding||10/17|NM_001354622.2:c.16-5_16-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354623.2|protein_coding||9/16|NM_001354623.2:c.16-5_16-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354624.2|protein_coding||9/16|NM_001354624.2:c.-36-5_-36-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354625.2|protein_coding||8/15|NM_001354625.2:c.-36-5_-36-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354626.2|protein_coding||9/16|NM_001354626.2:c.-36-5_-36-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354627.2|protein_coding||9/16|NM_001354627.2:c.-36-5_-36-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354628.2|protein_coding||11/17|NM_001354628.2:c.1039-5_1039-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354629.2|protein_coding||10/17|NM_001354629.2:c.940-5_940-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||,AAA|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354630.2|protein_coding||11/17|NM_001354630.2:c.1039-5_1039-3delinsAAA|||||||||1||EntrezGene||||||3:g.37067123_37067125delinsAAA||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:184:0:0,0:114,55:169,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:51:2:2,0:35,14:49,2:0.0392:2,0:29.5:1:26.3:1:1:0:60:4:0.0465:0.0196:3
    1068. 

  1068. 3	37090000	37090000	G	A	intronic	MLH1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	152	3	37090000	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=734;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.02927;SOR=0;LSEQ=GTTCCCTTGTCCTTTTTCCT;RSEQ=CAAGCAGGAAGGGAACCTGA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_000249.4|protein_coding||16/18|NM_000249.4:c.1897-8G>A|||||||||1||EntrezGene||YES||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001134369.2|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167617.3|protein_coding||16/18|NM_001167617.3:c.1603-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167618.3|protein_coding||16/18|NM_001167618.3:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001167619.3|protein_coding||15/17|NM_001167619.3:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258271.2|protein_coding||16/16|NM_001258271.2:c.1896+826G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258273.2|protein_coding||15/17|NM_001258273.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001258274.3|protein_coding||17/19|NM_001258274.3:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001282691.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348297.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348298.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348299.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348300.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348301.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348302.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348303.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348304.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348305.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348306.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348307.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348308.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348309.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348310.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348311.1|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354615.2|protein_coding||15/17|NM_001354615.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354616.2|protein_coding||15/17|NM_001354616.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354617.2|protein_coding||16/18|NM_001354617.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354618.2|protein_coding||16/18|NM_001354618.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354619.2|protein_coding||17/19|NM_001354619.2:c.1174-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354620.2|protein_coding||16/18|NM_001354620.2:c.1603-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354621.2|protein_coding||14/16|NM_001354621.2:c.874-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354622.2|protein_coding||15/17|NM_001354622.2:c.874-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354623.2|protein_coding||14/16|NM_001354623.2:c.874-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354624.2|protein_coding||14/16|NM_001354624.2:c.823-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354625.2|protein_coding||13/15|NM_001354625.2:c.823-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354626.2|protein_coding||14/16|NM_001354626.2:c.823-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354627.2|protein_coding||14/16|NM_001354627.2:c.823-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354628.2|protein_coding||16/17|NM_001354628.2:c.1897-395G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354629.2|protein_coding||15/17|NM_001354629.2:c.1798-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|MLH1|4292|Transcript|NM_001354630.2|protein_coding||15/17|NM_001354630.2:c.1732-8G>A|||||||||1||EntrezGene||||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_006309.4|protein_coding|||||||||||4117|-1||EntrezGene||YES||||3:g.37090000G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_017724.2|protein_coding|||||||||||4117|-1||EntrezGene||||||3:g.37090000G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:734:0:0,0:441,292:733,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:152:2:1,1:91,59:150,2:0.0132:2,2:50.5:1:37:0:1:1.5378:60:4:0.0132:0:1
    1069. 

  1069. 3	37090055	37090055	C	T	exonic	MLH1	.	synonymous SNV	MLH1:NM_001167619:exon16:c.C1221T:p.P407P,MLH1:NM_001258273:exon16:c.C1221T:p.P407P,MLH1:NM_000249:exon17:c.C1944T:p.P648P,MLH1:NM_001167617:exon17:c.C1650T:p.P550P,MLH1:NM_001167618:exon17:c.C1221T:p.P407P,MLH1:NM_001258274:exon18:c.C1221T:p.P407P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	190	3	37090055	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1047;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.02349;SOR=0;LSEQ=CTGATTGACAACTATGTGCC;RSEQ=CCTTTGGAGGGACTGCCTAT;CSQ=T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_000249.4|protein_coding|17/19||NM_000249.4:c.1944C>T|NP_000240.1:p.Pro648%3D|1974|1944|648|P|ccC/ccT|CX144050||1||EntrezGene||YES||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001134369.2|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001167617.3|protein_coding|17/19||NM_001167617.3:c.1650C>T|NP_001161089.1:p.Pro550%3D|2196|1650|550|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001167618.3|protein_coding|17/19||NM_001167618.3:c.1221C>T|NP_001161090.1:p.Pro407%3D|2196|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001167619.3|protein_coding|16/18||NM_001167619.3:c.1221C>T|NP_001161091.1:p.Pro407%3D|2109|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258271.2|protein_coding||16/16|NM_001258271.2:c.1896+881C>T|||||||CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001258273.2|protein_coding|16/18||NM_001258273.2:c.1221C>T|NP_001245202.1:p.Pro407%3D|1883|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001258274.3|protein_coding|18/20||NM_001258274.3:c.1221C>T|NP_001245203.1:p.Pro407%3D|2346|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001282691.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348297.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348298.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348299.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348300.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348301.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348302.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348303.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348304.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348305.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348306.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348307.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348308.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348309.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348310.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348311.1|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354615.2|protein_coding|16/18||NM_001354615.2:c.1221C>T|NP_001341544.1:p.Pro407%3D|1877|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354616.2|protein_coding|16/18||NM_001354616.2:c.1221C>T|NP_001341545.1:p.Pro407%3D|1877|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354617.2|protein_coding|17/19||NM_001354617.2:c.1221C>T|NP_001341546.1:p.Pro407%3D|1969|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354618.2|protein_coding|17/19||NM_001354618.2:c.1221C>T|NP_001341547.1:p.Pro407%3D|2201|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354619.2|protein_coding|18/20||NM_001354619.2:c.1221C>T|NP_001341548.1:p.Pro407%3D|2325|1221|407|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354620.2|protein_coding|17/19||NM_001354620.2:c.1650C>T|NP_001341549.1:p.Pro550%3D|1964|1650|550|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354621.2|protein_coding|15/17||NM_001354621.2:c.921C>T|NP_001341550.1:p.Pro307%3D|1994|921|307|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354622.2|protein_coding|16/18||NM_001354622.2:c.921C>T|NP_001341551.1:p.Pro307%3D|2107|921|307|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354623.2|protein_coding|15/17||NM_001354623.2:c.921C>T|NP_001341552.1:p.Pro307%3D|2016|921|307|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354624.2|protein_coding|15/17||NM_001354624.2:c.870C>T|NP_001341553.1:p.Pro290%3D|1726|870|290|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354625.2|protein_coding|14/16||NM_001354625.2:c.870C>T|NP_001341554.1:p.Pro290%3D|1624|870|290|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354626.2|protein_coding|15/17||NM_001354626.2:c.870C>T|NP_001341555.1:p.Pro290%3D|1721|870|290|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354627.2|protein_coding|15/17||NM_001354627.2:c.870C>T|NP_001341556.1:p.Pro290%3D|1953|870|290|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354628.2|protein_coding||16/17|NM_001354628.2:c.1897-340C>T|||||||CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354629.2|protein_coding|16/18||NM_001354629.2:c.1845C>T|NP_001341558.1:p.Pro615%3D|1875|1845|615|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|synonymous_variant|LOW|MLH1|4292|Transcript|NM_001354630.2|protein_coding|16/18||NM_001354630.2:c.1779C>T|NP_001341559.1:p.Pro593%3D|1809|1779|593|P|ccC/ccT|CX144050||1||EntrezGene||||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_006309.4|protein_coding||||||||||CX144050|4062|-1||EntrezGene||YES||||3:g.37090055C>T||||||||||||||1,T|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_017724.2|protein_coding||||||||||CX144050|4062|-1||EntrezGene||||||3:g.37090055C>T||||||||||||||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1047:0:0,0:511,536:1047,0:0:2,0:38.2:1:36.4:1:1:0:60:94.182:1:0:0.1	0/1:190:2:1,1:95,92:187,2:0.0105:2,2:50:1:37:0:1:1.03244:60:4:0.0106:0:1
    1070. 

  1070. 3	37090131	37090131	G	A	intronic	MLH1	.	.	.	0.0001	3.235e-05	0.0001	0	0	0	0	0	0	rs758819869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV104573088;OCCURENCE=1(prostate)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	123	3	37090131	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=765;VD=1;AF=0.0013;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05195;SOR=0.07959;LSEQ=AAGCAGATACTAAGCATTTC;RSEQ=GTACATGCATGTGTGCTGGA;CSQ=A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_000249.4|protein_coding||17/18|NM_000249.4:c.1989+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||YES||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001134369.2|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001167617.3|protein_coding||17/18|NM_001167617.3:c.1695+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001167618.3|protein_coding||17/18|NM_001167618.3:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001167619.3|protein_coding||16/17|NM_001167619.3:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258271.2|protein_coding||16/16|NM_001258271.2:c.1896+957G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258273.2|protein_coding||16/17|NM_001258273.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258274.3|protein_coding||18/19|NM_001258274.3:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001282691.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348297.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348298.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348299.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348300.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348301.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348302.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348303.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348304.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348305.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348306.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348307.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348308.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348309.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348310.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348311.1|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354615.2|protein_coding||16/17|NM_001354615.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354616.2|protein_coding||16/17|NM_001354616.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354617.2|protein_coding||17/18|NM_001354617.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354618.2|protein_coding||17/18|NM_001354618.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354619.2|protein_coding||18/19|NM_001354619.2:c.1266+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354620.2|protein_coding||17/18|NM_001354620.2:c.1695+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354621.2|protein_coding||15/16|NM_001354621.2:c.966+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354622.2|protein_coding||16/17|NM_001354622.2:c.966+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354623.2|protein_coding||15/16|NM_001354623.2:c.966+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354624.2|protein_coding||15/16|NM_001354624.2:c.915+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354625.2|protein_coding||14/15|NM_001354625.2:c.915+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354626.2|protein_coding||15/16|NM_001354626.2:c.915+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354627.2|protein_coding||15/16|NM_001354627.2:c.915+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354628.2|protein_coding||16/17|NM_001354628.2:c.1897-264G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354629.2|protein_coding||16/17|NM_001354629.2:c.1890+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001354630.2|protein_coding||16/17|NM_001354630.2:c.1824+31G>A|||||||rs758819869&COSV104573088||1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_006309.4|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||YES||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1,A|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_017724.2|protein_coding||||||||||rs758819869&COSV104573088|3986|-1||EntrezGene||||||3:g.37090131G>A|1.996e-05|0|2.891e-05|0|0|0|3.527e-05|0|0|3.527e-05|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:765:1:0,1:282,481:763,1:0.0013:2,0:40:0:37:0:1:0:60:2:0.0013:0:1	0/1:123:2:1,1:43,78:121,2:0.0163:2,2:48:1:37:0:1:1.8:60:4:0.0163:0:1
    1071. 

  1071. 3	37090408	37090408	A	G	exonic	MLH1	.	nonsynonymous SNV	MLH1:NM_001167619:exon17:c.A1280G:p.E427G,MLH1:NM_001258273:exon17:c.A1280G:p.E427G,MLH1:NM_000249:exon18:c.A2003G:p.E668G,MLH1:NM_001167617:exon18:c.A1709G:p.E570G,MLH1:NM_001167618:exon18:c.A1280G:p.E427G,MLH1:NM_001258274:exon19:c.A1280G:p.E427G	.	.	.	.	.	.	.	.	.	.	.	0.193	0.224	T	0.004	0.119	B	0.004	0.104	B	0.000	0.537	D	0.999	0.467	D	2.115	0.589	M	-3.32	0.939	D	-2.65	0.579	D	0.695	0.700	0.158	0.852	D	0.708	0.900	D	0.100	0.773	D	2.759	0.393	21.1	0.991	0.525	0.910	0.524	D	c	-0.280	-0.116	1.000	0.480	0.707	0.730	0	4.76	0.600	3.931	0.560	0.203	0.253	1.000	0.715	0.983	0.502	13.376	0.600	DNA mismatch repair protein Mlh1, C-terminal	.	.	.	616881	Hereditary_cancer-predisposing_syndrome|Hereditary_nonpolyposis_colorectal_neoplasms	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0009405	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	172	3	37090408	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=389;VD=0;AF=0;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.09362;SOR=0;LSEQ=GGACCAGGTGAATTGGGACG;RSEQ=AGAAAAGGAATGTTTTGAAA;CSQ=G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_000249.4|protein_coding|18/19||NM_000249.4:c.2003A>G|NP_000240.1:p.Glu668Gly|2033|2003|668|E/G|gAa/gGa|rs1559592416||1||EntrezGene||YES||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001134369.2|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001167617.3|protein_coding|18/19||NM_001167617.3:c.1709A>G|NP_001161089.1:p.Glu570Gly|2255|1709|570|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001167618.3|protein_coding|18/19||NM_001167618.3:c.1280A>G|NP_001161090.1:p.Glu427Gly|2255|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001167619.3|protein_coding|17/18||NM_001167619.3:c.1280A>G|NP_001161091.1:p.Glu427Gly|2168|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|intron_variant|MODIFIER|MLH1|4292|Transcript|NM_001258271.2|protein_coding||16/16|NM_001258271.2:c.1896+1234A>G|||||||rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001258273.2|protein_coding|17/18||NM_001258273.2:c.1280A>G|NP_001245202.1:p.Glu427Gly|1942|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001258274.3|protein_coding|19/20||NM_001258274.3:c.1280A>G|NP_001245203.1:p.Glu427Gly|2405|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001282691.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348297.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348298.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348299.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348300.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348301.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348302.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348303.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348304.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348305.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348306.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348307.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348308.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348309.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348310.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_001348311.1|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354615.2|protein_coding|17/18||NM_001354615.2:c.1280A>G|NP_001341544.1:p.Glu427Gly|1936|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354616.2|protein_coding|17/18||NM_001354616.2:c.1280A>G|NP_001341545.1:p.Glu427Gly|1936|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354617.2|protein_coding|18/19||NM_001354617.2:c.1280A>G|NP_001341546.1:p.Glu427Gly|2028|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354618.2|protein_coding|18/19||NM_001354618.2:c.1280A>G|NP_001341547.1:p.Glu427Gly|2260|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354619.2|protein_coding|19/20||NM_001354619.2:c.1280A>G|NP_001341548.1:p.Glu427Gly|2384|1280|427|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354620.2|protein_coding|18/19||NM_001354620.2:c.1709A>G|NP_001341549.1:p.Glu570Gly|2023|1709|570|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354621.2|protein_coding|16/17||NM_001354621.2:c.980A>G|NP_001341550.1:p.Glu327Gly|2053|980|327|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354622.2|protein_coding|17/18||NM_001354622.2:c.980A>G|NP_001341551.1:p.Glu327Gly|2166|980|327|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354623.2|protein_coding|16/17||NM_001354623.2:c.980A>G|NP_001341552.1:p.Glu327Gly|2075|980|327|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354624.2|protein_coding|16/17||NM_001354624.2:c.929A>G|NP_001341553.1:p.Glu310Gly|1785|929|310|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354625.2|protein_coding|15/16||NM_001354625.2:c.929A>G|NP_001341554.1:p.Glu310Gly|1683|929|310|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354626.2|protein_coding|16/17||NM_001354626.2:c.929A>G|NP_001341555.1:p.Glu310Gly|1780|929|310|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354627.2|protein_coding|16/17||NM_001354627.2:c.929A>G|NP_001341556.1:p.Glu310Gly|2012|929|310|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354628.2|protein_coding|17/18||NM_001354628.2:c.1910A>G|NP_001341557.1:p.Glu637Gly|1940|1910|637|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354629.2|protein_coding|17/18||NM_001354629.2:c.1904A>G|NP_001341558.1:p.Glu635Gly|1934|1904|635|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|missense_variant|MODERATE|MLH1|4292|Transcript|NM_001354630.2|protein_coding|17/18||NM_001354630.2:c.1838A>G|NP_001341559.1:p.Glu613Gly|1868|1838|613|E/G|gAa/gGa|rs1559592416||1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_006309.4|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||YES||||3:g.37090408A>G||||||||||||uncertain_significance||1,G|downstream_gene_variant|MODIFIER|LRRFIP2|9209|Transcript|NM_017724.2|protein_coding||||||||||rs1559592416|3709|-1||EntrezGene||||||3:g.37090408A>G||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:389:0:0,0:238,151:389,0:0:2,0:34.1:1:36.4:1:1:0:60:388:1:0:0.2	0/1:172:2:1,1:111,59:170,2:0.0116:2,2:22.5:1:37:0:1:1.87407:60:4:0.0119:0:1
    1072. 

  1072. 3	38180524	38180524	G	T	intronic	MYD88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	165	3	38180524	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1340;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01195;SOR=0;LSEQ=CTGGGACCCAGCATTGGTGA;RSEQ=GACGTCCCCTTCCTGGCCTC;CSQ=T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NM_001130410.2|protein_coding|||||||||||1906|-1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172566.2|protein_coding||1/2|NM_001172566.2:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172567.2|protein_coding||1/4|NM_001172567.2:c.328+5G>T|||||||||1||EntrezGene||YES||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172568.2|protein_coding||1/3|NM_001172568.2:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172569.3|protein_coding||1/3|NM_001172569.3:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001365876.1|protein_coding||1/4|NM_001365876.1:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001365877.1|protein_coding||1/3|NM_001365877.1:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001374787.1|protein_coding||1/4|NM_001374787.1:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|MYD88|4615|Transcript|NM_001374788.1|protein_coding|||||||||||718|1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NM_001607.4|protein_coding|||||||||||1906|-1||EntrezGene||YES||||3:g.38180524G>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_002468.5|protein_coding||1/4|NM_002468.5:c.328+5G>T|||||||||1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NR_024024.2|misc_RNA|||||||||||1906|-1||EntrezGene||||||3:g.38180524G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|MYD88|4615|Transcript|NR_164663.1|misc_RNA|||||||||||718|1||EntrezGene||||||3:g.38180524G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1340:0:0,0:431,909:1340,0:0:2,0:35:1:36.7:1:1:0:60:334:1:0:0.1	0/1:165:2:1,1:50,113:163,2:0.0121:2,2:34:1:37:0:0.52395:2.25:60:4:0.0123:0:1
    1073. 

  1073. 3	38182606	38182606	C	T	intronic	MYD88	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	183	3	38182606	.	C	T	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2312;VD=1;AF=0.0004;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.01528;SOR=0.03931;LSEQ=AGGGCCTGATGCCAGCATGG;RSEQ=ACCCCTTGGCTTGCAGGTGC;CSQ=T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NM_001130410.2|protein_coding||||||||||rs1183374933|3988|-1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172566.2|protein_coding||2/2|NM_001172566.2:c.421-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172567.2|protein_coding||4/4|NM_001172567.2:c.761-17C>T|||||||rs1183374933||1||EntrezGene||YES||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172568.2|protein_coding||3/3|NM_001172568.2:c.602-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001172569.3|protein_coding||3/3|NM_001172569.3:c.556-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001365876.1|protein_coding||4/4|NM_001365876.1:c.718-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001365877.1|protein_coding||3/3|NM_001365877.1:c.583-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001374787.1|protein_coding||4/4|NM_001374787.1:c.694-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_001374788.1|protein_coding||4/4|NM_001374788.1:c.269-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NM_001607.4|protein_coding||||||||||rs1183374933|3988|-1||EntrezGene||YES||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant|LOW|MYD88|4615|Transcript|NM_002468.5|protein_coding||4/4|NM_002468.5:c.737-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|upstream_gene_variant|MODIFIER|ACAA1|30|Transcript|NR_024024.2|misc_RNA||||||||||rs1183374933|3988|-1||EntrezGene||||||3:g.38182606C>T||||||||||||||,T|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|MYD88|4615|Transcript|NR_164663.1|misc_RNA||4/4|NR_164663.1:n.420-17C>T|||||||rs1183374933||1||EntrezGene||||||3:g.38182606C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2312:1:0,1:1445,866:2311,1:0.0004:2,0:51:0:37:0:0.375:0:60:2:0.0004:0:1	0/1:183:2:1,1:116,65:181,2:0.0109:2,2:28.5:1:37:0:1:1.77857:60:4:0.011:0:1
    1074. 

  1074. 3	41265549	41265549	C	G	UTR5	CTNNB1	NM_001330729:c.-476C>G;NM_001098210:c.-11C>G;NM_001904:c.-11C>G;NM_001098209:c.-11C>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	136	3	41265549	.	C	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=260;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.11738;SOR=0;LSEQ=ATACAACTGTTTTGAAAATC;RSEQ=AGCGTGGACAATGGCTACTC;CSQ=G|5_prime_UTR_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|2/16||NM_001098209.2:c.-11C>G||204|||||||1||EntrezGene||||||3:g.41265549C>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|2/16||NM_001098210.2:c.-11C>G||204|||||||1||EntrezGene||||||3:g.41265549C>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|2/17||NM_001330729.2:c.-164C>G||204|||||||1||EntrezGene||||||3:g.41265549C>G||||||||||||||,G|5_prime_UTR_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|2/15||NM_001904.4:c.-11C>G||204|||||||1||EntrezGene||YES||||3:g.41265549C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:260:0:0,0:176,84:260,0:0:2,0:30.6:1:36.2:1:1:0:60:129:1:0:0.1	0/1:136:2:1,1:81,53:134,2:0.0147:2,2:52:0:37:0:1:1.52336:60:4:0.0149:0:1
    1075. 

  1075. 3	41266011	41266011	T	C	intronic	CTNNB1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	159	3	41266011	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.57789;SOR=0;LSEQ=ATGCTAATACTGTTTCGTAT;RSEQ=TATAGCTGATTTGATGGAGT;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding||2/15|NM_001098209.2:c.14-6T>C|||||||||1||EntrezGene||||||3:g.41266011T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding||2/15|NM_001098210.2:c.14-6T>C|||||||||1||EntrezGene||||||3:g.41266011T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding||3/16|NM_001330729.2:c.-8-6T>C|||||||||1||EntrezGene||||||3:g.41266011T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|CTNNB1|1499|Transcript|NM_001904.4|protein_coding||2/14|NM_001904.4:c.14-6T>C|||||||||1||EntrezGene||YES||||3:g.41266011T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:50:0:0,0:33,17:50,0:0:2,0:32.3:1:36.5:1:1:0:60:100:1:0:0.5	0/1:159:2:1,1:116,41:157,2:0.0126:2,2:21.5:1:37:0:0.45976:2.80741:60:4:0.0129:0:1
    1076. 

  1076. 3	41266040	41266040	G	A	exonic	CTNNB1	.	nonsynonymous SNV	CTNNB1:NM_001098209:exon3:c.G37A:p.A13T,CTNNB1:NM_001098210:exon3:c.G37A:p.A13T,CTNNB1:NM_001904:exon3:c.G37A:p.A13T,CTNNB1:NM_001330729:exon4:c.G16A:p.A6T	.	.	.	.	.	.	.	.	.	rs121913394	.	0.024	0.477	D	0.204	0.281	B	0.062	0.255	B	0.000	0.843	D	1	0.810	D	0	0.065	N	0.89	0.456	T	-0.54	0.740	N	0.174	0.780	-1.061	0.115	T	0.086	0.334	T	0.012	0.304	T	2.230	0.329	17.70	0.981	0.381	0.977	0.766	D	c	0.159	0.372	1.0	0.983	0.707	0.730	0	5.76	0.907	10.003	0.997	1.048	0.713	1.000	0.715	1.000	0.888	19.960	0.972	.	.	.	ID=COSV62704902;OCCURENCE=2(oesophagus),1(stomach),1(skin)	363102	Melanoma	Human_Phenotype_Ontology:HP:0002861,Human_Phenotype_Ontology:HP:0002887,Human_Phenotype_Ontology:HP:0006777,Human_Phenotype_Ontology:HP:0007474,MONDO:MONDO:0005105,MeSH:D008545,MedGen:C0025202,SNOMED_CT:2092003,SNOMED_CT:372244006	no_assertion_criteria_provided	Likely_pathogenic	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	204	3	41266040	.	G	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.40666;SOR=0;LSEQ=ATTTGATGGAGTTGGACATG;RSEQ=CCATGGAACCAGACAGAAAA;CSQ=A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|3/16||NM_001098209.2:c.37G>A|NP_001091679.1:p.Ala13Thr|251|37|13|A/T|Gcc/Acc|rs121913394&COSV62704902||1||EntrezGene||||||3:g.41266040G>A||||||||||||likely_pathogenic|0&1|1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|3/16||NM_001098210.2:c.37G>A|NP_001091680.1:p.Ala13Thr|251|37|13|A/T|Gcc/Acc|rs121913394&COSV62704902||1||EntrezGene||||||3:g.41266040G>A||||||||||||likely_pathogenic|0&1|1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|4/17||NM_001330729.2:c.16G>A|NP_001317658.1:p.Ala6Thr|383|16|6|A/T|Gcc/Acc|rs121913394&COSV62704902||1||EntrezGene||||||3:g.41266040G>A||||||||||||likely_pathogenic|0&1|1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|3/15||NM_001904.4:c.37G>A|NP_001895.1:p.Ala13Thr|251|37|13|A/T|Gcc/Acc|rs121913394&COSV62704902||1||EntrezGene||YES||||3:g.41266040G>A||||||||||||likely_pathogenic|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:71:0:0,0:41,29:70,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:204:3:2,1:136,65:201,3:0.0147:2,2:37.3:1:37:0:1:1.04592:60:6:0.015:0:1
    1077. 

  1077. 3	41268677	41268678	AT	-	intronic	CTNNB1	.	.	.	0.15	0	0	0	0	0	0	0	0	rs139158008	rs139158008	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112740961	PRAD-CA|1|306|0.00326797,LINC-JP|2|394|0.00507614,GACA-JP|2|585|0.0034188	0.5	85	174	3	41268676	.	GAT	G	85	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=6;VD=2;AF=0.3333;SHIFT3=12;MSI=7;MSILEN=2;SSF=0.01813;SOR=16.0837;LSEQ=CAAGATTCCTTGACTAACAA;RSEQ=ATATATATATATCTTTCTAG;CSQ=-|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding||6/15|NM_001098209.2:c.937-10_937-9del|||||||rs139158008||1||EntrezGene||||||3:g.41268689_41268690del|0.001776|0.001977|0.0006759|0.0005206|0.001599|0.004676|0.001829|0.00107|0.001645|0.004676|gnomAD_FIN|||,-|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding||6/15|NM_001098210.2:c.937-10_937-9del|||||||rs139158008||1||EntrezGene||||||3:g.41268689_41268690del|0.001776|0.001977|0.0006759|0.0005206|0.001599|0.004676|0.001829|0.00107|0.001645|0.004676|gnomAD_FIN|||,-|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding||7/16|NM_001330729.2:c.916-10_916-9del|||||||rs139158008||1||EntrezGene||||||3:g.41268689_41268690del|0.001776|0.001977|0.0006759|0.0005206|0.001599|0.004676|0.001829|0.00107|0.001645|0.004676|gnomAD_FIN|||,-|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001904.4|protein_coding||6/14|NM_001904.4:c.937-10_937-9del|||||||rs139158008||1||EntrezGene||YES||||3:g.41268689_41268690del|0.001776|0.001977|0.0006759|0.0005206|0.001599|0.004676|0.001829|0.00107|0.001645|0.004676|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:6:2:1,1:4,0:4,2:0.3333:0,2:15:0:37:0:0.33333:0:60:4:0.3333:0:0	0/1:174:5:5,0:114,55:169,5:0.0287:2,0:44.6:1:37:0:0.18075:0:60:10:0.0291:0:0
    1078. 

  1078. 3	41268887	41268887	A	G	intronic	CTNNB1	.	.	.	.	.	.	.	.	.	.	.	.	rs936946422	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	124	3	41268887	.	A	G	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.95313;SOR=0;LSEQ=GTCTTGTGTATAGCATCTGC;RSEQ=GTTCTAATTAGATTACTTTT;CSQ=G|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding||7/15|NM_001098209.2:c.1081+44A>G|||||||rs936946422||1||EntrezGene||||||3:g.41268887A>G||||||||||||||,G|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding||7/15|NM_001098210.2:c.1081+44A>G|||||||rs936946422||1||EntrezGene||||||3:g.41268887A>G||||||||||||||,G|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding||8/16|NM_001330729.2:c.1060+44A>G|||||||rs936946422||1||EntrezGene||||||3:g.41268887A>G||||||||||||||,G|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001904.4|protein_coding||7/14|NM_001904.4:c.1081+44A>G|||||||rs936946422||1||EntrezGene||YES||||3:g.41268887A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:0,3:3,0:0:0,0:22.3:1:37:0:1:0:60:6:1:0:0	0/1:124:2:1,1:34,88:122,2:0.0161:2,2:23.5:1:37:0:0.48649:2.57:60:4:0.0161:0:1
    1079. 

  1079. 3	41275640	41275640	G	A	exonic	CTNNB1	.	nonsynonymous SNV	CTNNB1:NM_001098209:exon10:c.G1535A:p.G512E,CTNNB1:NM_001098210:exon10:c.G1535A:p.G512E,CTNNB1:NM_001904:exon10:c.G1535A:p.G512E,CTNNB1:NM_001330729:exon11:c.G1514A:p.G505E	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.971	D	0.000	0.843	D	1	0.810	D	3.495	0.929	M	-0.0	0.626	T	-7.56	0.952	D	0.948	0.944	0.341	0.882	D	0.584	0.850	D	0.200	0.867	D	6.155	0.849	28.5	0.998	0.923	0.996	0.981	D	c	1.081	1.020	1.0	0.983	0.672	0.522	0	5.86	0.939	10.003	0.997	1.048	0.713	1.000	0.715	0.996	0.625	20.186	0.982	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	163	3	41275640	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=407;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.08142;SOR=0;LSEQ=TGTTTTTCAGGCTACTGTTG;RSEQ=ATTGATTCGAAATCTTGCCC;CSQ=A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|10/16||NM_001098209.2:c.1535G>A|NP_001091679.1:p.Gly512Glu|1749|1535|512|G/E|gGa/gAa|COSV62717927||1||EntrezGene||||||3:g.41275640G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|10/16||NM_001098210.2:c.1535G>A|NP_001091680.1:p.Gly512Glu|1749|1535|512|G/E|gGa/gAa|COSV62717927||1||EntrezGene||||||3:g.41275640G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|11/17||NM_001330729.2:c.1514G>A|NP_001317658.1:p.Gly505Glu|1881|1514|505|G/E|gGa/gAa|COSV62717927||1||EntrezGene||||||3:g.41275640G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|10/15||NM_001904.4:c.1535G>A|NP_001895.1:p.Gly512Glu|1749|1535|512|G/E|gGa/gAa|COSV62717927||1||EntrezGene||YES||||3:g.41275640G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:407:0:0,0:266,140:406,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:163:2:1,1:108,52:160,2:0.0123:2,2:26:1:37:0:0.54865:2.06679:60:4:0.0124:0:1
    1080. 

  1080. 3	41277254	41277254	G	A	exonic	CTNNB1	.	nonsynonymous SNV	CTNNB1:NM_001098209:exon11:c.G1723A:p.G575R,CTNNB1:NM_001098210:exon11:c.G1723A:p.G575R,CTNNB1:NM_001904:exon11:c.G1723A:p.G575R,CTNNB1:NM_001330729:exon12:c.G1702A:p.G568R	.	.	.	.	.	.	.	.	.	rs797044875	.	0.001	0.784	D	1.0	0.899	D	0.995	0.971	D	0.000	0.843	D	1	0.810	D	3.435	0.922	M	-0.13	0.648	T	-6.84	0.930	D	0.981	0.984	0.309	0.877	D	0.568	0.843	D	0.236	0.885	D	7.613	0.954	34	0.999	0.998	0.995	0.969	D	c	1.056	0.997	1.0	0.983	0.722	0.854	0	5.62	0.857	10.003	0.997	1.048	0.713	1.000	0.715	0.999	0.750	19.661	0.958	Armadillo-like helical|Armadillo-type fold	.	.	ID=COSV62690253;OCCURENCE=1(stomach),2(large_intestine)	205241	Inborn_genetic_diseases	MeSH:D030342,MedGen:C0950123	criteria_provided,_single_submitter	Likely_pathogenic	Likely pathogenic	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	MU5877306	STAD-US|1|439|0.0022779	0.25	37	274	3	41277254	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=142;VD=2;AF=0.0141;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11598;SOR=inf;LSEQ=AAATAGTTGAAGGTTGTACC;RSEQ=GAGCCCTTCACATCCTAGCT;CSQ=A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|11/16||NM_001098209.2:c.1723G>A|NP_001091679.1:p.Gly575Arg|1937|1723|575|G/R|Gga/Aga|rs797044875&CM162169&COSV62690253||1||EntrezGene||||||3:g.41277254G>A||||||||||||likely_pathogenic|0&0&1|1&1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|11/16||NM_001098210.2:c.1723G>A|NP_001091680.1:p.Gly575Arg|1937|1723|575|G/R|Gga/Aga|rs797044875&CM162169&COSV62690253||1||EntrezGene||||||3:g.41277254G>A||||||||||||likely_pathogenic|0&0&1|1&1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|12/17||NM_001330729.2:c.1702G>A|NP_001317658.1:p.Gly568Arg|2069|1702|568|G/R|Gga/Aga|rs797044875&CM162169&COSV62690253||1||EntrezGene||||||3:g.41277254G>A||||||||||||likely_pathogenic|0&0&1|1&1&1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|11/15||NM_001904.4:c.1723G>A|NP_001895.1:p.Gly575Arg|1937|1723|575|G/R|Gga/Aga|rs797044875&CM162169&COSV62690253||1||EntrezGene||YES||||3:g.41277254G>A||||||||||||likely_pathogenic|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:142:2:1,1:68,72:140,2:0.0141:2,2:23:0:37:0:1:1.06:60:4:0.0141:0:1	0/0:274:0:0,0:137,137:274,0:0:2,0:38.5:1:36.4:1:1:0:60:273:1:0:0.1
    1081. 

  1081. 3	41277353	41277353	G	T	intronic	CTNNB1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	147	3	41277353	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=32;VD=2;AF=0.0625;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.03113;SOR=inf;LSEQ=AGGTATGTTTTAAGTGAAGT;RSEQ=TTCTAGGTTTTATGTCCATA;CSQ=T|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding||11/15|NM_001098209.2:c.1803+19G>T|||||||||1||EntrezGene||||||3:g.41277353G>T||||||||||||||,T|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding||11/15|NM_001098210.2:c.1803+19G>T|||||||||1||EntrezGene||||||3:g.41277353G>T||||||||||||||,T|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding||12/16|NM_001330729.2:c.1782+19G>T|||||||||1||EntrezGene||||||3:g.41277353G>T||||||||||||||,T|intron_variant|MODIFIER|CTNNB1|1499|Transcript|NM_001904.4|protein_coding||11/14|NM_001904.4:c.1803+19G>T|||||||||1||EntrezGene||YES||||3:g.41277353G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:32:2:1,1:7,23:30,2:0.0625:2,2:57:1:37:0:0.44355:3.14:60:4:0.0645:0:1	0/0:147:0:0,0:48,99:147,0:0:2,0:38:1:36:1:1:0:60:35.75:1:0:0.2
    1082. 

  1082. 3	41279564	41279564	G	A	exonic	CTNNB1	.	nonsynonymous SNV	CTNNB1:NM_001098209:exon14:c.G2134A:p.D712N,CTNNB1:NM_001098210:exon14:c.G2134A:p.D712N,CTNNB1:NM_001904:exon14:c.G2134A:p.D712N,CTNNB1:NM_001330729:exon15:c.G2113A:p.D705N	.	.	.	.	.	.	.	.	.	.	.	0.511	0.075	T	0.06	0.217	B	0.031	0.206	B	0.000	0.843	D	1.000	0.588	D	0.55	0.145	N	0.77	0.496	T	0.08	0.060	N	0.029	0.017	-1.008	0.277	T	0.119	0.418	T	0.025	0.481	T	3.234	0.448	22.8	0.992	0.540	0.966	0.697	D	c	0.035	0.227	1.000	0.747	0.719	0.830	0	5.21	0.719	7.758	0.840	0.998	0.613	1.000	0.715	1.000	0.888	18.762	0.918	.	.	.	ID=COSV62709278;OCCURENCE=1(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU1909636	UCEC-US|1|531|0.00188324	0.25	37	119	3	41279564	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=126;VD=2;AF=0.0159;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.26347;SOR=inf;LSEQ=AACCCCTTGGATATCGCCAG;RSEQ=ATGGTATGTGTCTCATATTT;CSQ=A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|14/16||NM_001098209.2:c.2134G>A|NP_001091679.1:p.Asp712Asn|2348|2134|712|D/N|Gat/Aat|COSV62709278||1||EntrezGene||||||3:g.41279564G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|14/16||NM_001098210.2:c.2134G>A|NP_001091680.1:p.Asp712Asn|2348|2134|712|D/N|Gat/Aat|COSV62709278||1||EntrezGene||||||3:g.41279564G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|15/17||NM_001330729.2:c.2113G>A|NP_001317658.1:p.Asp705Asn|2480|2113|705|D/N|Gat/Aat|COSV62709278||1||EntrezGene||||||3:g.41279564G>A|||||||||||||1|1,A|missense_variant|MODERATE|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|14/15||NM_001904.4:c.2134G>A|NP_001895.1:p.Asp712Asn|2348|2134|712|D/N|Gat/Aat|COSV62709278||1||EntrezGene||YES||||3:g.41279564G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:126:2:1,1:71,53:124,2:0.0159:2,2:5:0:37:0:1:1.33646:60:4:0.016:0:1	0/0:119:0:0,0:56,63:119,0:0:2,0:37.9:1:36.6:1:1:0:60:118:1:0:0.1
    1083. 

  1083. 3	41280827	41280827	C	T	exonic	CTNNB1	.	synonymous SNV	CTNNB1:NM_001098209:exon15:c.C2340T:p.D780D,CTNNB1:NM_001098210:exon15:c.C2340T:p.D780D,CTNNB1:NM_001904:exon15:c.C2340T:p.D780D,CTNNB1:NM_001330729:exon16:c.C2319T:p.D773D	0.17	0.0114	0.0032	0.1277	0	0.1233	0.0003	0.0005	0.0112	rs2293303	rs2293303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62704170;OCCURENCE=2(meninges),2(large_intestine)	134317	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	1	1	MU82252279	COCA-CN|1|321|0.00311526	0.25	183	72	3	41280827	.	C	T	183	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=193;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCCTGGTTTGATACTGA;RSEQ=CTGTAAATCATCCTTTAGGT;CSQ=T|synonymous_variant|LOW|CTNNB1|1499|Transcript|NM_001098209.2|protein_coding|15/16||NM_001098209.2:c.2340C>T|NP_001091679.1:p.Asp780%3D|2554|2340|780|D|gaC/gaT|rs2293303&COSV62704170||1||EntrezGene||||||3:g.41280827C>T|0.03171|0.003453|0.1483|0|0.1371|0|0.0003203|0.02163|0.002979|0.1483|gnomAD_AMR|benign|0&1|1&1,T|synonymous_variant|LOW|CTNNB1|1499|Transcript|NM_001098210.2|protein_coding|15/16||NM_001098210.2:c.2340C>T|NP_001091680.1:p.Asp780%3D|2554|2340|780|D|gaC/gaT|rs2293303&COSV62704170||1||EntrezGene||||||3:g.41280827C>T|0.03171|0.003453|0.1483|0|0.1371|0|0.0003203|0.02163|0.002979|0.1483|gnomAD_AMR|benign|0&1|1&1,T|synonymous_variant|LOW|CTNNB1|1499|Transcript|NM_001330729.2|protein_coding|16/17||NM_001330729.2:c.2319C>T|NP_001317658.1:p.Asp773%3D|2686|2319|773|D|gaC/gaT|rs2293303&COSV62704170||1||EntrezGene||||||3:g.41280827C>T|0.03171|0.003453|0.1483|0|0.1371|0|0.0003203|0.02163|0.002979|0.1483|gnomAD_AMR|benign|0&1|1&1,T|synonymous_variant|LOW|CTNNB1|1499|Transcript|NM_001904.4|protein_coding|15/15||NM_001904.4:c.2340C>T|NP_001895.1:p.Asp780%3D|2554|2340|780|D|gaC/gaT|rs2293303&COSV62704170||1||EntrezGene||YES||||3:g.41280827C>T|0.03171|0.003453|0.1483|0|0.1371|0|0.0003203|0.02163|0.002979|0.1483|gnomAD_AMR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:193:0:0,0:40,153:193,0:0:2,0:26.8:1:36.6:1:1:0:60:192:1:0:0	0/1:72:32:4,28:8,32:40,32:0.4444:2,2:36.1:1:36.6:1:0.52922:1.73679:60:64:0.4507:0:1.1
    1084. 

  1084. 3	47084154	47084154	G	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon16:c.C7003T:p.P2335S,SETD2:NM_014159:exon17:c.C7135T:p.P2379S	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	1.0	0.899	D	0.997	0.850	D	0.000	0.523	D	1	0.810	D	1.04	0.263	L	-2.86	0.914	D	-3.63	0.697	D	0.407	0.465	0.728	0.935	D	0.817	0.939	D	0.093	0.761	D	6.434	0.888	29.8	0.999	0.974	0.972	0.734	D	c	0.839	0.843	1.0	0.983	0.707	0.730	0	5.51	0.817	9.926	0.988	0.883	0.387	1.000	0.715	0.995	0.604	19.414	0.947	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	220	3	47084154	.	G	A	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=185;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.08598;SOR=0;LSEQ=TTTGGGAGGAGAGGGGGGCG;RSEQ=CAGATCCAAGAGATTATTTG;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|16/20||NM_001349370.3:c.7003C>T|NP_001336299.1:p.Pro2335Ser|7308|7003|2335|P/S|Ccg/Tcg|||-1||EntrezGene||||||3:g.47084154G>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|17/21||NM_014159.7:c.7135C>T|NP_054878.5:p.Pro2379Ser|7324|7135|2379|P/S|Ccg/Tcg|||-1||EntrezGene||YES||||3:g.47084154G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|18/22||NR_146158.3:n.7492C>T||7492|||||||-1||EntrezGene||||||3:g.47084154G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:185:0:0,0:63,121:184,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:220:4:2,2:88,128:216,4:0.0182:2,2:50.8:1:37:0:1:1.45:60:8:0.0185:0:1
    1085. 

  1085. 3	47098301	47098301	A	T	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	200	3	47098301	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=127;VD=2;AF=0.0157;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.15011;SOR=inf;LSEQ=GCAGAAAAGAAAAGTTTCAG;RSEQ=ATTAGTTACCTGTACAATTG;CSQ=T|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||14/19|NM_001349370.3:c.6831+10T>A|||||||||-1||EntrezGene||||||3:g.47098301A>T||||||||||||||,T|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||15/20|NM_014159.7:c.6963+10T>A|||||||||-1||EntrezGene||YES||||3:g.47098301A>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||16/21|NR_146158.3:n.7320+10T>A|||||||||-1||EntrezGene||||||3:g.47098301A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:127:2:2,0:97,28:125,2:0.0157:2,0:28:1:37:0:1:0:60:4:0.0157:0:1	0/0:200:0:0,0:157,43:200,0:0:2,0:33.4:1:36.3:1:1:0:60:199:1:0:0.2
    1086. 

  1086. 3	47103862	47103863	TT	-	intronic	SETD2	.	.	.	0.03	0.6596	0.7455	0.7056	0.5584	0.6946	0.6539	0.6054	0.6421	rs10589946	rs10589946	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	428201	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	222	119	3	47103861	.	GTT	G	222	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=155;VD=65;AF=0.4194;SHIFT3=12;MSI=14;MSILEN=1;SSF=0.00438;SOR=2.04484;LSEQ=GGGAAAAGGGTGGTTTGTTT;RSEQ=TTTTTTTTTTTTAAGTTTAT;CSQ=-|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||12/19|NM_001349370.3:c.5978-27_5978-26del|||||||rs10589946||-1||EntrezGene||||||3:g.47103874_47103875del|0.5931|0.6739|0.7014|0.5355|0.6351|0.5961|0.5634|0.5695|0.5461|0.7126|AFR|likely_benign||1,-|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||13/20|NM_014159.7:c.6110-27_6110-26del|||||||rs10589946||-1||EntrezGene||YES||||3:g.47103874_47103875del|0.5931|0.6739|0.7014|0.5355|0.6351|0.5961|0.5634|0.5695|0.5461|0.7126|AFR|likely_benign||1,-|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||14/21|NR_146158.3:n.6467-27_6467-26del|||||||rs10589946||-1||EntrezGene||||||3:g.47103874_47103875del|0.5931|0.6739|0.7014|0.5355|0.6351|0.5961|0.5634|0.5695|0.5461|0.7126|AFR|likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:155:65:14,51:22,53:75,65:0.4194:2,2:34.8:1:36.9:1:0.33565:1.50768:60:130:0.4248:0.0065:0.2	0/1:119:31:10,21:26,55:81,31:0.2605:2,2:46.5:1:36.6:1:1:1.01:60:62:0.265:0:0.3
    1087. 

  1087. 3	47108564	47108564	G	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon12:c.C5973A:p.N1991K,SETD2:NM_014159:exon13:c.C6105A:p.N2035K	.	.	.	.	.	.	.	.	.	.	.	0.043	0.413	D	0.042	0.201	B	0.061	0.254	B	0.122	0.190	N	0.998	0.224	N	1.1	0.281	L	2.15	0.193	T	0.08	0.060	N	0.027	0.012	-0.993	0.319	T	0.025	0.109	T	0.005	0.122	T	2.459	0.357	19.20	0.977	0.347	0.836	0.424	D	c	-0.639	-0.468	0.991	0.324	0.732	0.924	0	1.75	0.236	2.249	0.426	0.142	0.226	1.000	0.715	0.999	0.750	9.338	0.370	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	203	3	47108564	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=25;VD=2;AF=0.08;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.01159;SOR=inf;LSEQ=ATCTCTGAATACCTACTTGT;RSEQ=TTTTCCTTTTCAGTTTGACT;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|12/20||NM_001349370.3:c.5973C>A|NP_001336299.1:p.Asn1991Lys|6278|5973|1991|N/K|aaC/aaA|||-1||EntrezGene||||||3:g.47108564G>T||||||||||||||,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|13/21||NM_014159.7:c.6105C>A|NP_054878.5:p.Asn2035Lys|6294|6105|2035|N/K|aaC/aaA|||-1||EntrezGene||YES||||3:g.47108564G>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|14/22||NR_146158.3:n.6462C>A||6462|||||||-1||EntrezGene||||||3:g.47108564G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:25:2:1,1:13,10:23,2:0.08:2,2:13:0:37:0:1:1.28628:60:4:0.08:0:1	0/0:203:0:0,0:117,86:203,0:0:2,0:24:0:11:0:1:0:60:0:0:0:3
    1088. 

  1088. 3	47125385	47125385	G	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon11:c.C5753T:p.P1918L,SETD2:NM_014159:exon12:c.C5885T:p.P1962L	0.61	0.4931	0.2820	0.4771	0.4933	0.5424	0.6158	0.5774	0.5767	rs4082155	rs4082155	0.311	0.139	T	0.001	0.067	B	0.002	0.063	B	0.655	0.105	N	0.090	0.364	P	0.895	0.225	L	1.98	0.219	T	-0.3	0.119	N	0.195	0.239	-0.947	0.416	T	0.000	0.000	T	.	.	.	1.276	0.218	12.14	0.939	0.234	0.565	0.299	D	c	-0.703	-0.512	1.000	0.747	0.731	0.878	0	2.94	0.330	0.296	0.187	0.135	0.219	0.092	0.224	0.998	0.697	5.284	0.149	.	ENSG00000114650.14|ENSG00000160796.12|ENSG00000076201.10|ENSG00000160796.12|ENSG00000160796.12|ENSG00000114650.14|ENSG00000160796.12|ENSG00000076201.10|ENSG00000160796.12|ENSG00000114650.14	Cells_Transformed_fibroblasts|Esophagus_Muscularis|Esophagus_Muscularis|Muscle_Skeletal|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Testis|Testis|Thyroid|Whole_Blood	ID=COSV57428846;OCCURENCE=16(meninges),1(large_intestine),1(stomach),2(haematopoietic_and_lymphoid_tissue),15(soft_tissue),5(prostate)	138941	not_specified|not_provided	MedGen:CN169374|MedGen:CN517202	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU585924	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579	0.75	366	243	3	47125385	.	G	A	366	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1122;VD=1113;AF=0.992;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=116.064;LSEQ=TTGTGCCGTTGCTCTCTTTG;RSEQ=GCTCTATTTCAGCGTCAGCT;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|11/20||NM_001349370.3:c.5753C>T|NP_001336299.1:p.Pro1918Leu|6058|5753|1918|P/L|cCc/cTc|rs4082155&COSV57428846||-1||EntrezGene||||||3:g.47125385G>A|0.538|0.2801|0.502|0.5201|0.5423|0.6137|0.5696|0.5564|0.5446|0.6137|gnomAD_FIN|not_provided&benign|0&1|1&1,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|12/21||NM_014159.7:c.5885C>T|NP_054878.5:p.Pro1962Leu|6074|5885|1962|P/L|cCc/cTc|rs4082155&COSV57428846||-1||EntrezGene||YES||||3:g.47125385G>A|0.538|0.2801|0.502|0.5201|0.5423|0.6137|0.5696|0.5564|0.5446|0.6137|gnomAD_FIN|not_provided&benign|0&1|1&1,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|12/22||NR_146158.3:n.6074C>T||6074|||||rs4082155&COSV57428846||-1||EntrezGene||||||3:g.47125385G>A|0.538|0.2801|0.502|0.5201|0.5423|0.6137|0.5696|0.5564|0.5446|0.6137|gnomAD_FIN|not_provided&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1122:1113:642,471:0,0:0,1113:0.992:0,2:34.1:1:36.2:1:1:0:60:91.75:0.9946:0:1.1	1/0:243:125:72,53:65,53:118,125:0.5144:2,2:34.8:1:36:1:0.70006:1.11:60:40.667:0.5236:0:1
    1089. 

  1089. 3	47125848	47125848	G	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon11:c.C5290T:p.P1764S,SETD2:NM_014159:exon12:c.C5422T:p.P1808S	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.996	0.832	D	0.000	0.537	D	1	0.810	D	2.465	0.718	M	-3.68	0.953	D	-7.81	0.959	D	0.167	0.768	1.024	0.976	D	0.909	0.970	D	0.280	0.902	D	5.725	0.782	26.9	0.999	0.968	0.992	0.928	D	c	0.872	0.816	1.000	0.747	0.722	0.854	0	4.56	0.555	9.257	0.947	1.048	0.713	1.000	0.715	0.994	0.587	17.896	0.888	.	.	.	ID=COSV57432191;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	133	3	47125848	.	G	A	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=3;AF=0.0204;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1433;SOR=inf;LSEQ=CATATTTTTAGTAGGAATGG;RSEQ=CAAGTGTTCCAAAGTCTTTA;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|11/20||NM_001349370.3:c.5290C>T|NP_001336299.1:p.Pro1764Ser|5595|5290|1764|P/S|Ccc/Tcc|COSV57432191||-1||EntrezGene||||||3:g.47125848G>A|||||||||||||1|1,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|12/21||NM_014159.7:c.5422C>T|NP_054878.5:p.Pro1808Ser|5611|5422|1808|P/S|Ccc/Tcc|COSV57432191||-1||EntrezGene||YES||||3:g.47125848G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|12/22||NR_146158.3:n.5611C>T||5611|||||COSV57432191||-1||EntrezGene||||||3:g.47125848G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:147:3:1,2:23,121:144,3:0.0204:2,2:20.7:1:37:0:0.41654:2.61:60:6:0.0208:0:1.3	0/0:133:0:0,0:21,112:133,0:0:2,0:33.4:1:35.8:1:1:0:60:32.25:1:0:0.1
    1090. 

  1090. 3	47127632	47127632	G	A	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	154	3	47127632	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=85;VD=2;AF=0.0235;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12552;SOR=inf;LSEQ=ATTATCACATATCCACAACC;RSEQ=AGGCAATCAATATAACAGTT;CSQ=A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||10/19|NM_001349370.3:c.5265+53C>T|||||||||-1||EntrezGene||||||3:g.47127632G>A||||||||||||||,A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||11/20|NM_014159.7:c.5397+53C>T|||||||||-1||EntrezGene||YES||||3:g.47127632G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||11/21|NR_146158.3:n.5586+53C>T|||||||||-1||EntrezGene||||||3:g.47127632G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:85:2:1,1:65,17:82,2:0.0235:2,2:18.5:1:37:0:0.38468:3.74436:60:4:0.0241:0:1	0/0:154:0:0,0:114,40:154,0:0:2,0:38.5:1:36.1:1:1:0:60:37.5:1:0:0.1
    1091. 

  1091. 3	47129635	47129635	C	A	exonic	SETD2	.	stopgain	SETD2:NM_001349370:exon9:c.G5113T:p.E1705X,SETD2:NM_014159:exon10:c.G5245T:p.E1749X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.002	0.370	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.094	0.980	38	0.996	0.760	0.979	0.781	D	c	0.791	0.615	1.000	0.402	0.732	0.924	0	3.57	0.399	7.323	0.782	0.935	0.490	1.000	0.715	1.000	0.888	14.793	0.693	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	175	3	47129635	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=2;AF=0.0187;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.14313;SOR=inf;LSEQ=CAGACAGGTAAGTTTCTGCT;RSEQ=CAAAGTTTCAATTCTAACCA;CSQ=A|stop_gained|HIGH|SETD2|29072|Transcript|NM_001349370.3|protein_coding|9/20||NM_001349370.3:c.5113G>T|NP_001336299.1:p.Glu1705Ter|5418|5113|1705|E/*|Gag/Tag|||-1||EntrezGene||||||3:g.47129635C>A||||||||||||||,A|stop_gained|HIGH|SETD2|29072|Transcript|NM_014159.7|protein_coding|10/21||NM_014159.7:c.5245G>T|NP_054878.5:p.Glu1749Ter|5434|5245|1749|E/*|Gag/Tag|||-1||EntrezGene||YES||||3:g.47129635C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|10/22||NR_146158.3:n.5434G>T||5434|||||||-1||EntrezGene||||||3:g.47129635C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:59,46:105,2:0.0187:2,2:33.5:1:37:0:1:1.27959:60:4:0.0189:0:1	0/0:175:0:0,0:90,85:175,0:0:2,0:37.9:1:36.7:1:1:0:60:350:1:0:0.1
    1092. 

  1092. 3	47129661	47129661	C	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon9:c.G5087A:p.R1696Q,SETD2:NM_014159:exon10:c.G5219A:p.R1740Q	.	.	.	.	.	.	.	.	.	.	.	0.03	0.453	D	1.0	0.899	D	0.992	0.790	D	0.000	0.473	D	1.000	0.588	D	2.02	0.555	M	-2.84	0.913	D	-3.91	0.730	D	0.26	0.755	0.805	0.945	D	0.824	0.941	D	0.073	0.718	D	7.916	0.956	35	0.999	0.999	0.978	0.772	D	c	0.765	0.717	1.000	0.747	0.732	0.924	0	4.46	0.534	7.323	0.782	0.935	0.490	1.000	0.715	1.000	0.888	17.675	0.881	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	183	3	47129661	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=127;VD=2;AF=0.0157;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.16705;SOR=inf;LSEQ=TTTCAATTCTAACCATTAGC;RSEQ=GGGATAAGCTGAGCACCTGG;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|9/20||NM_001349370.3:c.5087G>A|NP_001336299.1:p.Arg1696Gln|5392|5087|1696|R/Q|cGg/cAg|||-1||EntrezGene||||||3:g.47129661C>T||||||||||||||,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|10/21||NM_014159.7:c.5219G>A|NP_054878.5:p.Arg1740Gln|5408|5219|1740|R/Q|cGg/cAg|||-1||EntrezGene||YES||||3:g.47129661C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|10/22||NR_146158.3:n.5408G>A||5408|||||||-1||EntrezGene||||||3:g.47129661C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:127:2:1,1:69,56:125,2:0.0157:2,2:47:0:37:0:1:1.2301:60:4:0.016:0:1	0/0:183:0:0,0:81,102:183,0:0:2,0:39.3:1:36.1:1:1:0:60:44.75:1:0:0.1
    1093. 

  1093. 3	47129759	47129759	C	A	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	87	3	47129759	.	C	A	37	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=60;VD=2;AF=0.0333;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.36287;SOR=2.94347;LSEQ=TACCACAGCAAATAAAAATA;RSEQ=CTTTTTATAAAACAACAACA;CSQ=A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||8/19|NM_001349370.3:c.5011-22G>T|||||||||-1||EntrezGene||||||3:g.47129759C>A||||||||||||||,A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||9/20|NM_014159.7:c.5143-22G>T|||||||||-1||EntrezGene||YES||||3:g.47129759C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||9/21|NR_146158.3:n.5332-22G>T|||||||||-1||EntrezGene||||||3:g.47129759C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:60:2:1,1:19,39:58,2:0.0333:2,2:39:1:37:0:1:2.03:60:4:0.0357:0:1	0/1:87:1:0,1:25,61:86,1:0.0115:2,0:6:0:25:0:1:0:60:2:0.0128:0:2
    1094. 

  1094. 3	47129781	47129781	-	A	intronic	SETD2	.	.	.	0.15	0.0132	0.0369	0.0148	0	0	0.0144	0.0009	0.0015	rs777027080	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112245826	BTCA-SG|3|71|0.0422535	0.5	102	67	3	47129781	.	C	CA	102	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=37;VD=1;AF=0.027;SHIFT3=11;MSI=12;MSILEN=1;SSF=0.21475;SOR=0.28516;LSEQ=TTTTTATAAAACAACAACAA;RSEQ=AAAAAAAAAAACCAAAAACC;CSQ=A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||8/19|NM_001349370.3:c.5011-45dup|||||||rs748501527||-1||EntrezGene||||||3:g.47129792dup|0.1424|0.1856|0.1914|0.1862|0.1976|0.09781|0.115|0.1644|0.1737|0.1976|gnomAD_EAS|||,A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||9/20|NM_014159.7:c.5143-45dup|||||||rs748501527||-1||EntrezGene||YES||||3:g.47129792dup|0.1424|0.1856|0.1914|0.1862|0.1976|0.09781|0.115|0.1644|0.1737|0.1976|gnomAD_EAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||9/21|NR_146158.3:n.5332-45dup|||||||rs748501527||-1||EntrezGene||||||3:g.47129792dup|0.1424|0.1856|0.1914|0.1862|0.1976|0.09781|0.115|0.1644|0.1737|0.1976|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:1:0,1:11,22:33,1:0.027:2,0:72.5:0:39.5:0:1:0:64:2:0.0323:0:0	0/1:67:6:2,4:14,44:58,6:0.0896:2,2:43.4:1:39.5:0:0.63458:1.56:64:12:0.1034:0:0.4
    1095. 

  1095. 3	47139548	47139548	C	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon8:c.G4907A:p.C1636Y,SETD2:NM_014159:exon9:c.G5039A:p.C1680Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.629	D	1	0.810	D	4.045	0.971	H	-7.58	0.999	D	-10.78	0.992	D	0.601	0.984	0.916	0.959	D	0.997	0.999	D	0.547	0.958	D	6.648	0.912	32	0.998	0.878	0.988	0.866	D	c	1.019	0.927	1.0	0.983	0.707	0.730	0	5.29	0.743	7.702	0.834	0.935	0.490	1.000	0.715	0.996	0.625	19.124	0.933	Post-SET domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	3	47139548	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=109;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.3687;SOR=0;LSEQ=CCCGGCAATTGGCTGATCCG;RSEQ=AGAAACATTTCTGGGCTTCT;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|8/20||NM_001349370.3:c.4907G>A|NP_001336299.1:p.Cys1636Tyr|5212|4907|1636|C/Y|tGc/tAc|COSV104633435||-1||EntrezGene||||||3:g.47139548C>T|||||||||||||1|1,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|9/21||NM_014159.7:c.5039G>A|NP_054878.5:p.Cys1680Tyr|5228|5039|1680|C/Y|tGc/tAc|COSV104633435||-1||EntrezGene||YES||||3:g.47139548C>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|9/22||NR_146158.3:n.5228G>A||5228|||||COSV104633435||-1||EntrezGene||||||3:g.47139548C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:109:0:0,0:47,62:109,0:0:2,0:37.7:1:36.3:1:1:0:60:108:1:0:0	0/1:169:2:1,1:78,89:167,2:0.0118:2,2:52.5:1:37:0:1:1.14:60:4:0.0118:0:1
    1096. 

  1096. 3	47139562	47139562	G	A	exonic	SETD2	.	synonymous SNV	SETD2:NM_001349370:exon8:c.C4893T:p.A1631A,SETD2:NM_014159:exon9:c.C5025T:p.A1675A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	734096	Luscan-lumish_syndrome	MONDO:MONDO:0014791,MedGen:C4085873,OMIM:616831	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	153	3	47139562	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=89;VD=2;AF=0.0225;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.13429;SOR=inf;LSEQ=GATCCGCAGAAACATTTCTG;RSEQ=GCTTCTTTTCTGTTCAAAGA;CSQ=A|synonymous_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding|8/20||NM_001349370.3:c.4893C>T|NP_001336299.1:p.Ala1631%3D|5198|4893|1631|A|gcC/gcT|rs1293494337||-1||EntrezGene||||||3:g.47139562G>A|7.958e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|likely_benign||1,A|synonymous_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding|9/21||NM_014159.7:c.5025C>T|NP_054878.5:p.Ala1675%3D|5214|5025|1675|A|gcC/gcT|rs1293494337||-1||EntrezGene||YES||||3:g.47139562G>A|7.958e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|likely_benign||1,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|9/22||NR_146158.3:n.5214C>T||5214|||||rs1293494337||-1||EntrezGene||||||3:g.47139562G>A|7.958e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|likely_benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:89:2:1,1:35,52:87,2:0.0225:2,2:48:0:37:0:1:1.48:60:4:0.0225:0:1	0/0:153:0:0,0:69,84:153,0:0:2,0:34.3:1:36.5:1:1:0:60:306:1:0:0.1
    1097. 

  1097. 3	47139578	47139578	A	-	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	115	3	47139577	.	CA	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=71;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.38099;SOR=0;LSEQ=TTCTGGGCTTCTTTTCTGTT;RSEQ=AAGAGCATAGGAAAGAAGTC;CSQ=-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding||7/19|NM_001349370.3:c.4884-7del|||||||||-1||EntrezGene||||||3:g.47139580del||||||||||||||,-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding||8/20|NM_014159.7:c.5016-7del|||||||||-1||EntrezGene||YES||||3:g.47139580del||||||||||||||,-|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|SETD2|29072|Transcript|NR_146158.3|misc_RNA||8/21|NR_146158.3:n.5205-7del|||||||||-1||EntrezGene||||||3:g.47139580del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:71:0:0,0:28,43:71,0:0:2,0:33.3:1:36.3:1:1:0:60:142:1:0:0.1	0/1:115:2:1,1:45,68:113,2:0.0174:2,2:35.5:1:37:0:1:1.51:60:4:0.0175:0:0
    1098. 

  1098. 3	47144833	47144833	T	C	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	139	3	47144833	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.67561;SOR=0;LSEQ=ACTCTAAATCCACCTCAACT;RSEQ=ACTTTTTGGGTTTCACAATT;CSQ=C|splice_donor_region_variant&intron_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding||6/19|NM_001349370.3:c.4785+3A>G|||||||||-1||EntrezGene||||||3:g.47144833T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding||7/20|NM_014159.7:c.4917+3A>G|||||||||-1||EntrezGene||YES||||3:g.47144833T>C||||||||||||||,C|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|SETD2|29072|Transcript|NR_146158.3|misc_RNA||7/21|NR_146158.3:n.5106+3A>G|||||||||-1||EntrezGene||||||3:g.47144833T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:18,12:30,0:0:2,0:41.9:1:36.6:1:1:0:60:60:1:0:0.1	0/1:139:2:1,1:78,59:137,2:0.0144:2,2:41:1:37:0:1:1.31933:60:4:0.0145:0:1
    1099. 

  1099. 3	47147487	47147487	C	T	exonic	SETD2	.	synonymous SNV	SETD2:NM_001349370:exon5:c.G4707A:p.E1569E,SETD2:NM_014159:exon6:c.G4839A:p.E1613E	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	167	3	47147487	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=425;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07923;SOR=0;LSEQ=AACATATCCAAGCTGCTTAC;RSEQ=TCATCATTCTTCAGGGCCAT;CSQ=T|splice_region_variant&synonymous_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding|5/20||NM_001349370.3:c.4707G>A|NP_001336299.1:p.Glu1569%3D|5012|4707|1569|E|gaG/gaA|||-1||EntrezGene||||||3:g.47147487C>T||||||||||||||,T|splice_region_variant&synonymous_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding|6/21||NM_014159.7:c.4839G>A|NP_054878.5:p.Glu1613%3D|5028|4839|1613|E|gaG/gaA|||-1||EntrezGene||YES||||3:g.47147487C>T||||||||||||||,T|splice_region_variant&non_coding_transcript_exon_variant|LOW|SETD2|29072|Transcript|NR_146158.3|misc_RNA|6/22||NR_146158.3:n.5028G>A||5028|||||||-1||EntrezGene||||||3:g.47147487C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:425:0:0,0:187,238:425,0:0:2,0:40.9:1:35.4:1:1:0:60:27.333:1:0:0.3	0/1:167:2:1,1:87,78:165,2:0.012:2,2:60:1:37:0:1:1.11465:60:4:0.0129:0:1
    1100. 

  1100. 3	47147544	47147544	C	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon5:c.G4650T:p.K1550N,SETD2:NM_014159:exon6:c.G4782T:p.K1594N	.	.	.	.	.	.	.	.	.	.	.	0.014	0.531	D	1.0	0.899	D	0.994	0.916	D	0.000	0.559	D	1	0.810	D	1.865	0.494	L	-1.38	0.803	T	-3.17	0.643	D	0.224	0.421	-0.096	0.802	T	0.543	0.832	D	0.206	0.871	D	5.481	0.744	26.2	0.998	0.896	0.864	0.454	D	c	0.026	-0.078	0.987	0.312	0.719	0.830	0	-0.237	0.124	0.344	0.196	-0.797	0.032	0.993	0.376	0.915	0.391	9.700	0.392	SET domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	184	3	47147544	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=343;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.12147;SOR=0;LSEQ=TTTTTGTTTCGTGCATACTC;RSEQ=TTCACTCGAGCTTTAAACTC;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|5/20||NM_001349370.3:c.4650G>T|NP_001336299.1:p.Lys1550Asn|4955|4650|1550|K/N|aaG/aaT|||-1||EntrezGene||||||3:g.47147544C>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|6/21||NM_014159.7:c.4782G>T|NP_054878.5:p.Lys1594Asn|4971|4782|1594|K/N|aaG/aaT|||-1||EntrezGene||YES||||3:g.47147544C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|6/22||NR_146158.3:n.4971G>T||4971|||||||-1||EntrezGene||||||3:g.47147544C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:343:0:0,0:147,196:343,0:0:2,0:34.9:1:36:1:1:0:60:56.167:1:0:0.1	0/1:184:2:1,1:90,92:182,2:0.0109:2,2:29.5:1:37:0:1:1.02:60:4:0.0112:0:1
    1101. 

  1101. 3	47147636	47147636	C	T	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	125	3	47147636	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=79;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37429;SOR=0;LSEQ=AACCAAAAGGAAAAAAATAG;RSEQ=ACTTCCTACCTAGGAGCAGT;CSQ=T|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||4/19|NM_001349370.3:c.4584-26G>A|||||||||-1||EntrezGene||||||3:g.47147636C>T||||||||||||||,T|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||5/20|NM_014159.7:c.4716-26G>A|||||||||-1||EntrezGene||YES||||3:g.47147636C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||5/21|NR_146158.3:n.4905-26G>A|||||||||-1||EntrezGene||||||3:g.47147636C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:79:0:0,0:19,60:79,0:0:2,0:29.7:1:35.7:1:1:0:60:25.333:1:0:0.2	0/1:125:2:1,1:52,71:123,2:0.016:2,2:45.5:1:37:0:1:1.36:60:4:0.0165:0:1
    1102. 

  1102. 3	47158094	47158094	A	G	intronic	SETD2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	116	3	47158094	.	A	G	31	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.95001;SOR=0;LSEQ=GAAGTGTTGAGCAAAAGCCG;RSEQ=GTATTCTAATTTACTTACCA;CSQ=G|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||3/19|NM_001349370.3:c.4454+19T>C|||||||||-1||EntrezGene||||||3:g.47158094A>G||||||||||||||,G|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||4/20|NM_014159.7:c.4586+19T>C|||||||||-1||EntrezGene||YES||||3:g.47158094A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||4/21|NR_146158.3:n.4775+19T>C|||||||||-1||EntrezGene||||||3:g.47158094A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:3,0:3,0:0:0,0:28:1:37:0:1:0:60:6:1:0:0	0/1:116:2:1,1:69,45:114,2:0.0172:2,2:39:1:31:1:1:1.52748:60:4:0.0172:0:1
    1103. 

  1103. 3	47161890	47161890	C	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.G4104T:p.E1368D,SETD2:NM_014159:exon3:c.G4236T:p.E1412D	.	.	.	.	.	.	.	.	.	.	.	0.033	0.443	D	0.898	0.475	P	0.674	0.514	P	0.000	0.559	D	1.000	0.497	D	1.905	0.510	L	-2.74	0.907	D	-1.05	0.275	N	0.283	0.563	0.334	0.881	D	0.665	0.884	D	0.015	0.359	T	3.331	0.459	22.9	0.998	0.927	0.811	0.403	D	c	0.323	0.366	1.000	0.423	0.732	0.924	0	4.22	0.490	0.599	0.236	0.935	0.490	0.998	0.411	1.000	0.888	14.300	0.658	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	104	3	47161890	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=2;SSF=0.45463;SOR=0;LSEQ=CCATCACTTTCAGAATCACT;RSEQ=TCTATTTCCTGCCTCCTTTT;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.4104G>T|NP_001336299.1:p.Glu1368Asp|4409|4104|1368|E/D|gaG/gaT|||-1||EntrezGene||||||3:g.47161890C>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.4236G>T|NP_054878.5:p.Glu1412Asp|4425|4236|1412|E/D|gaG/gaT|||-1||EntrezGene||YES||||3:g.47161890C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.4425G>T||4425|||||||-1||EntrezGene||||||3:g.47161890C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:50:0:0,0:18,32:50,0:0:2,0:25.3:1:36.5:1:1:0:60:100:1:0:0.1	0/1:104:2:1,1:46,56:102,2:0.0192:2,2:13.5:1:37:0:1:1.22:60:4:0.0192:0:1
    1104. 

  1104. 3	47162661	47162661	A	G	exonic	SETD2	.	synonymous SNV	SETD2:NM_001349370:exon2:c.T3333C:p.N1111N,SETD2:NM_014159:exon3:c.T3465C:p.N1155N	0.78	0.6568	0.7570	0.6945	0.5667	0.6937	0.6316	0.6017	0.6337	rs6767907	rs6767907	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57430115;OCCURENCE=1(breast),16(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(urinary_tract),1(lung)	576751	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU18259588	LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611,BRCA-KR|1|50|0.02	0.75	312	243	3	47162661	.	A	G	312	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=382;VD=381;AF=0.9974;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=399.726;LSEQ=TGAGAAAGTTCAGGCAGGCG;RSEQ=TTATCTATTTGTTTTCTACT;CSQ=G|synonymous_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.3333T>C|NP_001336299.1:p.Asn1111%3D|3638|3333|1111|N|aaT/aaC|rs6767907&COSV57430115||-1||EntrezGene||||||3:g.47162661A>G|0.6375|0.766|0.7551|0.5939|0.6787|0.6326|0.5938|0.6222|0.5961|0.7837|AFR|benign|0&1|1&1,G|synonymous_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.3465T>C|NP_054878.5:p.Asn1155%3D|3654|3465|1155|N|aaT/aaC|rs6767907&COSV57430115||-1||EntrezGene||YES||||3:g.47162661A>G|0.6375|0.766|0.7551|0.5939|0.6787|0.6326|0.5938|0.6222|0.5961|0.7837|AFR|benign|0&1|1&1,G|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.3654T>C||3654|||||rs6767907&COSV57430115||-1||EntrezGene||||||3:g.47162661A>G|0.6375|0.766|0.7551|0.5939|0.6787|0.6326|0.5938|0.6222|0.5961|0.7837|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:382:381:120,261:0,0:0,381:0.9974:0,2:30:1:36.4:1:1:0:60:126:1:0:1.1	0/1:243:118:50,68:59,66:125,118:0.4856:2,2:38.7:1:36.3:1:0.51897:1.21477:60:58:0.4813:0:1.1
    1105. 

  1105. 3	47162956	47162956	T	C	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.A3038G:p.D1013G,SETD2:NM_014159:exon3:c.A3170G:p.D1057G	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	1.0	0.899	D	0.996	0.832	D	0.000	0.629	D	1	0.810	D	1.1	0.281	L	-3.3	0.938	D	-1.86	0.871	N	0.258	0.561	0.815	0.946	D	0.807	0.935	D	0.220	0.878	D	4.444	0.595	24.2	0.998	0.906	0.998	0.996	D	c	0.611	0.628	1.000	0.747	0.732	0.924	0	5.03	0.669	7.321	0.782	1.061	0.807	1.000	0.715	0.999	0.750	14.940	0.705	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	190	3	47162956	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=159;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.29567;SOR=0;LSEQ=TTCTTGGAATACTGCTATCA;RSEQ=CCGAATCTGTATCTTCTGAA;CSQ=C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.3038A>G|NP_001336299.1:p.Asp1013Gly|3343|3038|1013|D/G|gAt/gGt|rs189671317&COSV57435736||-1||EntrezGene||||||3:g.47162956T>C|3.987e-06|0|0|0|0|0|0|0.0001636|0|0.0001636|gnomAD_OTH||0&1|0&1,C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.3170A>G|NP_054878.5:p.Asp1057Gly|3359|3170|1057|D/G|gAt/gGt|rs189671317&COSV57435736||-1||EntrezGene||YES||||3:g.47162956T>C|3.987e-06|0|0|0|0|0|0|0.0001636|0|0.0001636|gnomAD_OTH||0&1|0&1,C|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.3359A>G||3359|||||rs189671317&COSV57435736||-1||EntrezGene||||||3:g.47162956T>C|3.987e-06|0|0|0|0|0|0|0.0001636|0|0.0001636|gnomAD_OTH||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:159:0:0,0:71,88:159,0:0:2,0:36:1:36.7:1:1:0:60:318:1:0:0.1	0/1:190:2:1,1:80,108:188,2:0.0105:2,2:43:1:37:0:1:1.35:60:4:0.0106:0:1
    1106. 

  1106. 3	47163035	47163035	C	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.G2959T:p.V987L,SETD2:NM_014159:exon3:c.G3091T:p.V1031L	.	.	.	.	.	.	.	.	.	.	.	0.005	0.632	D	0.029	0.185	B	0.008	0.127	B	0.003	0.353	N	0.999	0.217	N	0.895	0.225	L	-2.39	0.884	D	-0.23	0.299	N	0.123	0.490	-0.706	0.602	T	0.421	0.766	T	0.017	0.383	T	1.727	0.269	14.56	0.967	0.301	0.461	0.274	N	c	-0.347	-0.185	1.000	0.454	0.732	0.924	0	5.03	0.669	0.246	0.178	0.935	0.490	0.174	0.238	0.999	0.750	6.595	0.217	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	162	3	47163035	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=101;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.37852;SOR=0;LSEQ=ATCTTCATGAACTGTAGACA;RSEQ=AATTTCTGGGGCATGACCAC;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2959G>T|NP_001336299.1:p.Val987Leu|3264|2959|987|V/L|Gtg/Ttg|||-1||EntrezGene||||||3:g.47163035C>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.3091G>T|NP_054878.5:p.Val1031Leu|3280|3091|1031|V/L|Gtg/Ttg|||-1||EntrezGene||YES||||3:g.47163035C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.3280G>T||3280|||||||-1||EntrezGene||||||3:g.47163035C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:101:0:0,0:35,66:101,0:0:2,0:35:1:36.4:1:1:0:60:202:1:0:0.1	0/1:162:2:1,1:71,89:160,2:0.0123:2,2:43.5:1:37:0:1:1.25:60:4:0.0124:0:1
    1107. 

  1107. 3	47163037	47163037	A	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.T2957A:p.I986N,SETD2:NM_014159:exon3:c.T3089A:p.I1030N	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.947	0.515	P	0.36	0.414	B	0.009	0.306	N	0.731	0.337	D	0.55	0.145	N	-2.65	0.902	D	-1.21	0.750	N	0.275	0.472	0.322	0.879	D	0.517	0.819	D	0.109	0.786	D	5.082	0.685	25.3	0.991	0.523	0.990	0.895	D	c	0.251	0.354	1.000	0.747	0.732	0.924	0	5.03	0.669	5.054	0.639	1.199	0.960	1.000	0.715	0.999	0.750	14.940	0.705	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	159	3	47163037	.	A	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=102;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.3702;SOR=0;LSEQ=CTTCATGAACTGTAGACACA;RSEQ=TTTCTGGGGCATGACCACTA;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2957T>A|NP_001336299.1:p.Ile986Asn|3262|2957|986|I/N|aTt/aAt|||-1||EntrezGene||||||3:g.47163037A>T||||||||||||||,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.3089T>A|NP_054878.5:p.Ile1030Asn|3278|3089|1030|I/N|aTt/aAt|||-1||EntrezGene||YES||||3:g.47163037A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.3278T>A||3278|||||||-1||EntrezGene||||||3:g.47163037A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:102:0:0,0:35,66:101,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:159:2:1,1:68,89:157,2:0.0126:2,2:37:1:37:0:1:1.31:60:4:0.0127:0:1
    1108. 

  1108. 3	47163337	47163337	A	G	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.T2657C:p.V886A,SETD2:NM_014159:exon3:c.T2789C:p.V930A	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.039	0.197	B	0.007	0.121	B	0.085	0.024	N	1	0.090	N	0.345	0.112	N	-2.43	0.887	D	-0.53	0.309	N	0.191	0.234	-0.637	0.633	T	0.405	0.755	T	0.014	0.341	T	0.838	0.174	9.695	0.963	0.287	0.241	0.221	N	c	-0.945	-0.912	0.984	0.306	0.732	0.924	0	0.872	0.182	0.771	0.261	0.582	0.286	0.002	0.151	0.986	0.517	2.296	0.039	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	197	3	47163337	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=98;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.4452;SOR=0;LSEQ=GAAGGTCACTACCTACTTCT;RSEQ=CTATTGTTTCTTTCCCTGCA;CSQ=G|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2657T>C|NP_001336299.1:p.Val886Ala|2962|2657|886|V/A|gTa/gCa|||-1||EntrezGene||||||3:g.47163337A>G||||||||||||||,G|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.2789T>C|NP_054878.5:p.Val930Ala|2978|2789|930|V/A|gTa/gCa|||-1||EntrezGene||YES||||3:g.47163337A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2978T>C||2978|||||||-1||EntrezGene||||||3:g.47163337A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:98:0:0,0:52,46:98,0:0:2,0:39.1:1:36:1:1:0:60:48:1:0:0	0/1:197:2:1,1:102,93:195,2:0.0102:2,2:26.5:1:31:1:1:1.09626:60:4:0.0104:0:1
    1109. 

  1109. 3	47163352	47163352	C	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.G2642T:p.G881V,SETD2:NM_014159:exon3:c.G2774T:p.G925V	.	.	.	.	.	.	.	.	.	.	.	0.256	0.174	T	0.0	0.026	B	0.001	0.040	B	0.329	0.141	N	0.982	0.398	D	0.205	0.094	N	-2.32	0.878	D	-0.9	0.443	N	0.304	0.372	-0.821	0.539	T	0.276	0.648	T	0.027	0.502	D	1.120	0.202	11.32	0.839	0.145	0.545	0.294	D	c	-0.641	-0.486	0.987	0.311	0.732	0.924	0	1.79	0.239	0.669	0.246	0.007	0.138	0.812	0.296	0.922	0.397	2.668	0.047	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	187	3	47163352	.	C	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=105;VD=2;AF=0.019;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.12851;SOR=inf;LSEQ=CTTCTACTATTGTTTCTTTC;RSEQ=CTGCATGCTTTAAAAACTCT;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2642G>T|NP_001336299.1:p.Gly881Val|2947|2642|881|G/V|gGg/gTg|||-1||EntrezGene||||||3:g.47163352C>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.2774G>T|NP_054878.5:p.Gly925Val|2963|2774|925|G/V|gGg/gTg|||-1||EntrezGene||YES||||3:g.47163352C>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2963G>T||2963|||||||-1||EntrezGene||||||3:g.47163352C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:105:2:1,1:54,49:103,2:0.019:2,2:5:0:37:0:1:1.10102:60:4:0.0192:0:1	0/0:187:0:0,0:94,93:187,0:0:2,0:37.5:1:35.4:1:1:0:60:25.714:1:0:0.1
    1110. 

  1110. 3	47163567	47163567	C	T	exonic	SETD2	.	synonymous SNV	SETD2:NM_001349370:exon2:c.G2427A:p.K809K,SETD2:NM_014159:exon3:c.G2559A:p.K853K	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	142	3	47163567	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=20;VD=2;AF=0.1;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01457;SOR=inf;LSEQ=CTAGTGCTACCGATGCTCTG;RSEQ=TTATATTCTTCACATGCAAA;CSQ=T|synonymous_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2427G>A|NP_001336299.1:p.Lys809%3D|2732|2427|809|K|aaG/aaA|||-1||EntrezGene||||||3:g.47163567C>T||||||||||||||,T|synonymous_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.2559G>A|NP_054878.5:p.Lys853%3D|2748|2559|853|K|aaG/aaA|||-1||EntrezGene||YES||||3:g.47163567C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2748G>A||2748|||||||-1||EntrezGene||||||3:g.47163567C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:20:2:1,1:6,12:18,2:0.1:2,2:38.5:1:37:0:1:1.93:60:4:0.1:0:1	0/0:142:0:0,0:56,86:142,0:0:2,0:38.3:1:35.4:1:1:0:60:22.667:1:0:0.1
    1111. 

  1111. 3	47163668	47163668	A	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.T2326A:p.S776T,SETD2:NM_014159:exon3:c.T2458A:p.S820T	.	.	.	.	.	.	.	.	.	.	.	0.258	0.167	T	0.024	0.178	B	0.005	0.104	B	0.012	0.292	N	0.974	0.255	N	0.805	0.203	L	-2.33	0.879	D	-0.25	0.293	N	0.157	0.290	-0.843	0.525	T	0.307	0.678	T	0.010	0.260	T	0.272	0.120	5.422	0.879	0.170	0.652	0.324	D	c	-0.292	-0.069	0.998	0.366	0.732	0.924	0	3.96	0.449	2.899	0.481	1.199	0.960	1.000	0.715	1.000	0.888	5.131	0.141	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	109	3	47163668	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00522;SOR=inf;LSEQ=ATTCATAAAGCTATTTGAAG;RSEQ=AATCTTCATAACTGAAGGCT;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.2326T>A|NP_001336299.1:p.Ser776Thr|2631|2326|776|S/T|Tct/Act|||-1||EntrezGene||||||3:g.47163668A>T||||||||||||||,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.2458T>A|NP_054878.5:p.Ser820Thr|2647|2458|820|S/T|Tct/Act|||-1||EntrezGene||YES||||3:g.47163668A>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2647T>A||2647|||||||-1||EntrezGene||||||3:g.47163668A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:9:2:1,1:6,1:7,2:0.2222:2,2:8.5:1:37:0:0.41667:4.58262:60:4:0.2222:0:1.5	0/0:109:0:0,0:59,50:109,0:0:2,0:33.6:1:36.3:1:1:0:60:108:1:0:0.2
    1112. 

  1112. 3	47164184	47164184	T	C	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.A1810G:p.S604G,SETD2:NM_014159:exon3:c.A1942G:p.S648G	.	.	.	.	.	.	.	.	.	.	.	0.036	0.433	D	0.997	0.689	D	0.97	0.706	D	0.000	0.504	D	0.932	0.370	D	0.895	0.225	L	-2.96	0.920	D	-1.6	0.617	N	0.141	0.352	0.778	0.941	D	0.772	0.923	D	0.066	0.698	D	2.912	0.411	21.9	0.996	0.759	0.969	0.715	D	c	0.538	0.568	1.000	0.747	0.707	0.730	0	5.44	0.793	4.163	0.577	0.153	0.239	1.000	0.715	0.998	0.697	15.665	0.769	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	57	3	47164184	.	T	C	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTCTAATTCCTTAATAC;RSEQ=ATCATGGCTATCATGTGTTA;CSQ=C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1810A>G|NP_001336299.1:p.Ser604Gly|2115|1810|604|S/G|Agt/Ggt|||-1||EntrezGene||||||3:g.47164184T>C||||||||||||||,C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1942A>G|NP_054878.5:p.Ser648Gly|2131|1942|648|S/G|Agt/Ggt|||-1||EntrezGene||YES||||3:g.47164184T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2131A>G||2131|||||||-1||EntrezGene||||||3:g.47164184T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:57:2:1,1:14,41:55,2:0.0351:2,2:46.5:1:37:0:0.46053:2.86:60:4:0.0357:0:1
    1113. 

  1113. 3	47164281	47164281	T	C	exonic	SETD2	.	synonymous SNV	SETD2:NM_001349370:exon2:c.A1713G:p.P571P,SETD2:NM_014159:exon3:c.A1845G:p.P615P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	42	3	47164281	.	T	C	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAATCGATTTGATGGAGC;RSEQ=GGAGACCCAGCCTTTTCTCT;CSQ=C|synonymous_variant|LOW|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1713A>G|NP_001336299.1:p.Pro571%3D|2018|1713|571|P|ccA/ccG|||-1||EntrezGene||||||3:g.47164281T>C||||||||||||||,C|synonymous_variant|LOW|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1845A>G|NP_054878.5:p.Pro615%3D|2034|1845|615|P|ccA/ccG|||-1||EntrezGene||YES||||3:g.47164281T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.2034A>G||2034|||||||-1||EntrezGene||||||3:g.47164281T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:42:2:1,1:27,13:40,2:0.0476:2,2:44:1:37:0:1:2.03815:60:4:0.0476:0:1
    1114. 

  1114. 3	47164594	47164594	G	T	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.C1400A:p.S467Y,SETD2:NM_014159:exon3:c.C1532A:p.S511Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.91	0.483	P	0.507	0.460	P	0.001	0.411	D	0.932	0.370	D	1.01	0.254	L	2.53	0.140	T	-2.27	0.784	N	0.253	0.467	-1.087	0.060	T	0.034	0.147	T	0.006	0.172	T	1.911	0.291	15.66	0.989	0.472	0.977	0.760	D	c	0.372	0.442	1.000	0.747	0.707	0.730	0	4.79	0.608	4.047	0.569	1.048	0.713	1.000	0.715	1.000	0.888	16.930	0.860	.	.	.	ID=COSV57444536;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	206	3	47164594	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=19;VD=2;AF=0.1053;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00679;SOR=inf;LSEQ=ATTCTCTTTCTAGTTTTGAA;RSEQ=AATACTTGCCTCTTCTTTCC;CSQ=T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1400C>A|NP_001336299.1:p.Ser467Tyr|1705|1400|467|S/Y|tCt/tAt|COSV57444536||-1||EntrezGene||||||3:g.47164594G>T|||||||||||||1|1,T|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1532C>A|NP_054878.5:p.Ser511Tyr|1721|1532|511|S/Y|tCt/tAt|COSV57444536||-1||EntrezGene||YES||||3:g.47164594G>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.1721C>A||1721|||||COSV57444536||-1||EntrezGene||||||3:g.47164594G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:19:2:1,1:8,9:17,2:0.1053:2,2:35:1:37:0:1:1.12:60:4:0.1053:0:1	0/0:206:0:0,0:89,117:206,0:0:2,0:36.1:1:35.5:1:1:0:60:28.429:1:0:0.1
    1115. 

  1115. 3	47164718	47164718	A	G	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.T1276C:p.S426P,SETD2:NM_014159:exon3:c.T1408C:p.S470P	.	.	.	.	.	.	.	.	.	.	.	0.134	0.263	T	0.071	0.224	B	0.019	0.176	B	.	.	.	0.924	0.368	D	0.83	0.210	L	2.45	0.150	T	-1.07	0.625	N	0.314	0.404	-1.046	0.156	T	0.022	0.096	T	0.006	0.156	T	2.024	0.304	16.36	0.957	0.270	0.966	0.697	D	c	-0.265	-0.073	1.000	0.747	0.719	0.830	0	3.86	0.435	4.264	0.584	0.237	0.263	1.000	0.715	0.998	0.697	10.209	0.421	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	211	3	47164718	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=2;AF=0.0345;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04586;SOR=inf;LSEQ=ATGAGATGAGGTACGCCTTG;RSEQ=GTATGTCTTCTTATACTCTT;CSQ=G|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1276T>C|NP_001336299.1:p.Ser426Pro|1581|1276|426|S/P|Tca/Cca|||-1||EntrezGene||||||3:g.47164718A>G||||||||||||||,G|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1408T>C|NP_054878.5:p.Ser470Pro|1597|1408|470|S/P|Tca/Cca|||-1||EntrezGene||YES||||3:g.47164718A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.1597T>C||1597|||||||-1||EntrezGene||||||3:g.47164718A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:58:2:1,1:30,26:56,2:0.0345:2,2:11.5:1:37:0:1:1.15099:60:4:0.0345:0:1.5	0/0:211:0:0,0:109,102:211,0:0:2,0:36.3:1:36.3:1:1:0:60:69.333:1:0:0.1
    1116. 

  1116. 3	47164846	47164846	T	C	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.A1148G:p.Y383C,SETD2:NM_014159:exon3:c.A1280G:p.Y427C	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.998	0.875	D	.	.	.	1.000	0.537	D	1.935	0.520	L	2.32	0.166	T	-2.97	0.928	D	0.298	0.699	-1.075	0.082	T	0.072	0.291	T	0.014	0.339	T	4.867	0.654	24.9	0.997	0.816	0.988	0.869	D	c	0.564	0.583	1.000	0.747	0.707	0.730	0	5.0	0.661	5.650	0.674	1.061	0.807	1.000	0.715	1.000	0.888	15.166	0.724	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	234	3	47164846	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=2;AF=0.0136;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.14824;SOR=inf;LSEQ=AGCGACGATCAGAGTCATAA;RSEQ=AATGAGATCGTTCTGACCTG;CSQ=C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1148A>G|NP_001336299.1:p.Tyr383Cys|1453|1148|383|Y/C|tAt/tGt|||-1||EntrezGene||||||3:g.47164846T>C||||||||||||||,C|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1280A>G|NP_054878.5:p.Tyr427Cys|1469|1280|427|Y/C|tAt/tGt|||-1||EntrezGene||YES||||3:g.47164846T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.1469A>G||1469|||||||-1||EntrezGene||||||3:g.47164846T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:147:2:1,1:75,70:145,2:0.0136:2,2:57.5:1:37:0:1:1.07089:60:4:0.0138:0:1	0/0:234:0:0,0:111,123:234,0:0:2,0:36.5:1:36.2:1:1:0:60:77:1:0:0.1
    1117. 

  1117. 3	47164912	47164912	G	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_001349370:exon2:c.C1082T:p.S361F,SETD2:NM_014159:exon3:c.C1214T:p.S405F	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.997	0.850	D	.	.	.	0.995	0.426	D	1.935	0.520	L	2.24	0.179	T	-2.26	0.769	N	0.228	0.464	-1.114	0.028	T	0.073	0.296	T	0.014	0.345	T	5.291	0.716	25.7	0.998	0.850	0.991	0.913	D	c	0.660	0.691	1.000	0.747	0.707	0.730	0	5.0	0.661	5.337	0.655	1.048	0.713	1.000	0.715	0.998	0.697	18.856	0.922	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	208	3	47164912	.	G	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=109;VD=2;AF=0.0183;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.11752;SOR=inf;LSEQ=CTCTCTCAGACCTAGAGTGA;RSEQ=ATCTGCTCCGCCGTCGCTCT;CSQ=A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.1082C>T|NP_001336299.1:p.Ser361Phe|1387|1082|361|S/F|tCt/tTt|||-1||EntrezGene||||||3:g.47164912G>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1214C>T|NP_054878.5:p.Ser405Phe|1403|1214|405|S/F|tCt/tTt|||-1||EntrezGene||YES||||3:g.47164912G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.1403C>T||1403|||||||-1||EntrezGene||||||3:g.47164912G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:109:2:1,1:40,67:107,2:0.0183:2,2:39:1:31:1:1:1.67:60:4:0.0185:0:3.5	0/0:208:0:0,0:87,121:208,0:0:2,0:38.1:1:36.4:1:1:0:60:68.333:1:0:0.2
    1118. 

  1118. 3	47165068	47165068	T	-	exonic	SETD2	.	frameshift deletion	SETD2:NM_001349370:exon2:c.926delA:p.K309Rfs*6,SETD2:NM_014159:exon3:c.1058delA:p.K353Rfs*6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	81	3	47165067	.	CT	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=12;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.75736;SOR=0;LSEQ=CTTTTTAAAGGTGCTGAGCT;RSEQ=TTTTAAAATCTCTTTCCTTT;CSQ=-|frameshift_variant|HIGH|SETD2|29072|Transcript|NM_001349370.3|protein_coding|2/20||NM_001349370.3:c.926del|NP_001336299.1:p.Lys309ArgfsTer6|1231|926|309|K/X|aAg/ag|||-1||EntrezGene||||||3:g.47165072del||||||||||||||,-|frameshift_variant|HIGH|SETD2|29072|Transcript|NM_014159.7|protein_coding|3/21||NM_014159.7:c.1058del|NP_054878.5:p.Lys353ArgfsTer6|1247|1058|353|K/X|aAg/ag|||-1||EntrezGene||YES||||3:g.47165072del||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|3/22||NR_146158.3:n.1247del||1247|||||||-1||EntrezGene||||||3:g.47165072del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:5,7:12,0:0:2,0:42.2:1:34.8:1:1:0:60:11:1:0:0.2	0/1:81:2:1,1:31,48:79,2:0.0247:2,2:40.5:1:37:0:1:1.54:60:4:0.0247:0:0
    1119. 

  1119. 3	47205285	47205285	G	A	intronic	SETD2	.	.	.	.	3.287e-05	0.0001	0	0	0	0	0	0	rs930834099	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	32	3	47205285	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=2;AF=0.0101;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.74161;SOR=inf;LSEQ=GCCACCCGTCAGGACGCGCC;RSEQ=CCCTCGGCTGGGGATAAGGC;CSQ=A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding||1/19|NM_001349370.3:c.-46+59C>T|||||||rs930834099||-1||EntrezGene||||||3:g.47205285G>A||||||||||||||,A|intron_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding||1/20|NM_014159.7:c.71+59C>T|||||||rs930834099||-1||EntrezGene||YES||||3:g.47205285G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|KIF9-AS1|285352|Transcript|NR_033373.1|lncRNA||||||||||rs930834099|575|1||EntrezGene||YES||||3:g.47205285G>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA||1/21|NR_146158.3:n.260+59C>T|||||||rs930834099||-1||EntrezGene||||||3:g.47205285G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:199:2:1,1:116,81:197,2:0.0101:2,2:31.5:1:37:0:1:1.42943:60:4:0.0102:0:1	0/0:32:0:0,0:16,16:32,0:0:2,0:38:1:36.2:1:1:0:60:31:1:0:0.1
    1120. 

  1120. 3	47205393	47205393	G	A	exonic	SETD2	.	nonsynonymous SNV	SETD2:NM_014159:exon1:c.C22T:p.P8S	.	.	.	.	.	.	.	.	.	.	.	0.011	0.555	D	0.001	0.067	B	0.001	0.040	B	.	.	.	0.997	0.229	N	0.345	0.112	N	-2.39	0.884	D	-0.43	0.144	N	0.205	0.251	-0.616	0.642	T	0.387	0.742	T	0.713	0.977	D	2.882	0.407	21.8	0.998	0.876	0.162	0.191	N	c	-0.567	-0.445	1.000	0.747	0.267	0.040	1	2.05	0.257	1.525	0.353	0.789	0.320	1.000	0.715	0.996	0.625	5.469	0.158	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	38	3	47205393	.	G	A	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=299;VD=3;AF=0.01;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.69764;SOR=inf;LSEQ=ATCCCCCATCTTCGGAGGCG;RSEQ=CTGCGGCTGCAGCTGCTTCA;CSQ=A|5_prime_UTR_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding|1/20||NM_001349370.3:c.-95C>T||211|||||||-1||EntrezGene||||||3:g.47205393G>A||||||||||||||,A|missense_variant|MODERATE|SETD2|29072|Transcript|NM_014159.7|protein_coding|1/21||NM_014159.7:c.22C>T|NP_054878.5:p.Pro8Ser|211|22|8|P/S|Ccg/Tcg|||-1||EntrezGene||YES||||3:g.47205393G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|KIF9-AS1|285352|Transcript|NR_033373.1|lncRNA|||||||||||467|1||EntrezGene||YES||||3:g.47205393G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|1/22||NR_146158.3:n.211C>T||211|||||||-1||EntrezGene||||||3:g.47205393G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:299:3:1,2:141,155:296,3:0.01:2,2:54.3:1:37:0:1:1.81586:60:6:0.0101:0:1	0/0:38:0:0,0:19,19:38,0:0:2,0:33.3:1:36.7:1:1:0:60:76:1:0:0.1
    1121. 

  1121. 3	47205491	47205491	G	A	upstream	KIF9-AS1;SETD2	dist=369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	17	3	47205491	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.67869;SOR=inf;LSEQ=GGAGGGGAGGGGAGGAGGCC;RSEQ=CAGGTCCGACCGCGGCGGCG;CSQ=A|5_prime_UTR_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding|1/20||NM_001349370.3:c.-193C>T||113|||||||-1||EntrezGene||||||3:g.47205491G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding|1/21||NM_014159.7:c.-77C>T||113|||||||-1||EntrezGene||YES||||3:g.47205491G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|KIF9-AS1|285352|Transcript|NR_033373.1|lncRNA|||||||||||369|1||EntrezGene||YES||||3:g.47205491G>A||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|1/22||NR_146158.3:n.113C>T||113|||||||-1||EntrezGene||||||3:g.47205491G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:19,58:77,2:0.025:2,2:53:1:37:0:0.44466:3:60:4:0.0253:0:1.5	0/0:17:0:0,0:5,12:17,0:0:2,0:38.8:1:36.3:1:1:0:60:34:1:0:0.1
    1122. 

  1122. 3	47205503	47205511	GCGGCGGCG	-	upstream	KIF9-AS1;SETD2	dist=349	.	.	0.99	0.6537	0.7440	0.6948	0.5870	0.6857	0.6437	0.5996	0.6300	rs545985439	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	199	14	3	47205502	.	CGCGGCGGCG	C	199	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=67;VD=45;AF=0.6716;SHIFT3=23;MSI=10;MSILEN=3;SSF=0.00896;SOR=5.00321;LSEQ=GAGGAGGCCGCAGGTCCGAC;RSEQ=GCGGCGGCGGCGGCGGCGGC;CSQ=-|5_prime_UTR_variant|MODIFIER|SETD2|29072|Transcript|NM_001349370.3|protein_coding|1/20||NM_001349370.3:c.-213_-205del||93-101|||||rs76496241||-1||EntrezGene||||||3:g.47205526_47205534del||||||||||0.9856|AFR|||,-|5_prime_UTR_variant|MODIFIER|SETD2|29072|Transcript|NM_014159.7|protein_coding|1/21||NM_014159.7:c.-97_-89del||93-101|||||rs76496241||-1||EntrezGene||YES||||3:g.47205526_47205534del||||||||||0.9856|AFR|||,-|upstream_gene_variant|MODIFIER|KIF9-AS1|285352|Transcript|NR_033373.1|lncRNA||||||||||rs76496241|349|1||EntrezGene||YES||||3:g.47205526_47205534del||||||||||0.9856|AFR|||,-|non_coding_transcript_exon_variant|MODIFIER|SETD2|29072|Transcript|NR_146158.3|misc_RNA|1/22||NR_146158.3:n.93_101del||93-101|||||rs76496241||-1||EntrezGene||||||3:g.47205526_47205534del||||||||||0.9856|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:67:45:1,44:14,8:22,45:0.6716:2,1:50.3:1:36.4:1:0:69.8547:60:44:0.6667:0.0149:0.1	0/1:14:4:0,4:4,6:10,4:0.2857:2,0:41.8:1:36.5:1:0.25075:0:60:8:0.2857:0.0714:0
    1123. 

  1123. 3	49397824	49397824	-	A	intronic	RHOA	.	.	.	0.0034	0.0003	0.0006	0.0012	0	0	0	7.479e-05	0	rs761095111	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU115494633	PRAD-CA|2|306|0.00653595	0.25	189	344	3	49397824	.	G	GA	189	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=1386;VD=33;AF=0.0238;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.05222;SOR=2.77122;LSEQ=TTTCACCGGCTCCTAGCAAA;RSEQ=AAAAAAAAATAGTCCTTTTA;CSQ=A|upstream_gene_variant|MODIFIER|GPX1|2876|Transcript|NM_000581.4|protein_coding||||||||||rs761095111|2038|-1||EntrezGene||YES||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313941.2|protein_coding||5/5|NM_001313941.2:c.409-10dup|||||||rs761095111||-1||EntrezGene||YES||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313943.2|protein_coding||5/5|NM_001313943.2:c.548-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313944.2|protein_coding||4/4|NM_001313944.2:c.349-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313945.2|protein_coding||4/4|NM_001313945.2:c.166-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313946.2|protein_coding||2/2|NM_001313946.2:c.157-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001313947.2|protein_coding||3/3|NM_001313947.2:c.*15-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|upstream_gene_variant|MODIFIER|GPX1|2876|Transcript|NM_001329455.2|protein_coding||||||||||rs761095111|2038|-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|upstream_gene_variant|MODIFIER|GPX1|2876|Transcript|NM_001329502.2|protein_coding||||||||||rs761095111|2038|-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|upstream_gene_variant|MODIFIER|GPX1|2876|Transcript|NM_001329503.2|protein_coding||||||||||rs761095111|2038|-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|RHOA|387|Transcript|NM_001664.4|protein_coding||4/4|NM_001664.4:c.409-10dup|||||||rs761095111||-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||,A|upstream_gene_variant|MODIFIER|GPX1|2876|Transcript|NM_201397.3|protein_coding||||||||||rs761095111|2038|-1||EntrezGene||||||3:g.49397833dup|0.001194|0.0006528|0.002622|0.0008436|0.0008697|0.0009159|0.0009069|0.002523|0.001592|0.002622|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1386:33:7,26:364,846:1210,33:0.0238:2,2:30.2:1:37.6:1:0.33713:1.59756:61.3:66:0.0282:0.0022:0.1	0/0:344:3:1,2:120,200:320,3:0.0087:2,2:29.8:1:39:0:1:1.1993:63.2:6:0.0102:0:0
    1124. 

  1124. 3	49721718	49721718	C	T	intronic	MST1	.	.	.	.	.	.	.	.	.	.	.	.	.	rs74938297	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	0	3	49721718	.	C	T	31	d5;v3;pSTD;Q0	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=2;AF=0.5;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGCCCCCCATACCCTTC;RSEQ=AGGGCTGGCCCAGGGCCCTG;CSQ=T|downstream_gene_variant|MODIFIER|APEH|327|Transcript|NM_001640.4|protein_coding|||||||||||314|1||EntrezGene||YES||||3:g.49721718C>T||||||||||||||,T|intron_variant|MODIFIER|MST1|4485|Transcript|NM_020998.3|protein_coding||17/17|NM_020998.3:c.2016+29G>A|||||||||-1||EntrezGene||YES||||3:g.49721718C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|MST1|4485|Transcript|NR_146060.1|misc_RNA||16/16|NR_146060.1:n.1969+29G>A|||||||||-1||EntrezGene||||||3:g.49721718C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:1,1:1,1:2,2:0.5:2,2:43:0:31:1:1:1:0:4:0.5:0:2	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1125. 

  1125. 3	49721740	49721740	C	T	intronic	MST1	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs748213082	rs75704976	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	0	3	49721740	.	C	T	37	d5;v3;pSTD;Q0	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=2;AF=0.5;SHIFT3=0;MSI=2;MSILEN=3;SSF=1;SOR=0;LSEQ=GGGCTGGCCCAGGGCCCTGC;RSEQ=ACCAACCTCACAGGCCCCCA;CSQ=T|downstream_gene_variant|MODIFIER|APEH|327|Transcript|NM_001640.4|protein_coding||||||||||rs748213082|336|1||EntrezGene||YES||||3:g.49721740C>T|4.049e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|splice_region_variant&intron_variant|LOW|MST1|4485|Transcript|NM_020998.3|protein_coding||17/17|NM_020998.3:c.2016+7G>A|||||||rs748213082||-1||EntrezGene||YES||||3:g.49721740C>T|4.049e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|MST1|4485|Transcript|NR_146060.1|misc_RNA||16/16|NR_146060.1:n.1969+7G>A|||||||rs748213082||-1||EntrezGene||||||3:g.49721740C>T|4.049e-06|0|0|0|0|0|0|0|3.267e-05|3.267e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:4:2:1,1:1,1:2,2:0.5:2,2:21:0:37:0:1:1:0:4:0.5:0:2	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1126. 

  1126. 3	49723379	49723379	T	C	exonic	MST1	.	synonymous SNV	MST1:NM_020998:exon10:c.A1164G:p.A388A	0.14	0.0002	0.0001	0	0	0.0014	0	0.0001	0	rs4052580	rs4052580	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56535178;OCCURENCE=1(skin),1(thymus)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU17737893	SKCA-BR|1|100|0.01	0.25	58	0	3	49723379	.	T	C	58	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=3;AF=0.6;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCGCGGTACTGCTCCCC;RSEQ=GCGCCGTGGTAGCAGTCTGT;CSQ=C|downstream_gene_variant|MODIFIER|APEH|327|Transcript|NM_001640.4|protein_coding||||||||||rs4052580&COSV56535178|1975|1||EntrezGene||YES||||3:g.49723379T>C|0.005463|0.009553|0.003849|0.001963|0.009697|0.008825|0.005427|0.004341|0.002619|0.009697|gnomAD_EAS||0&1|0&1,C|synonymous_variant|LOW|MST1|4485|Transcript|NM_020998.3|protein_coding|10/18||NM_020998.3:c.1164A>G|NP_066278.3:p.Ala388%3D|1236|1164|388|A|gcA/gcG|rs4052580&COSV56535178||-1||EntrezGene||YES||||3:g.49723379T>C|0.005463|0.009553|0.003849|0.001963|0.009697|0.008825|0.005427|0.004341|0.002619|0.009697|gnomAD_EAS||0&1|0&1,C|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NM_022064.5|protein_coding||||||||||rs4052580&COSV56535178|3611|1||EntrezGene||YES||||3:g.49723379T>C|0.005463|0.009553|0.003849|0.001963|0.009697|0.008825|0.005427|0.004341|0.002619|0.009697|gnomAD_EAS||0&1|0&1,C|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NR_135218.2|misc_RNA||||||||||rs4052580&COSV56535178|3611|1||EntrezGene||||||3:g.49723379T>C|0.005463|0.009553|0.003849|0.001963|0.009697|0.008825|0.005427|0.004341|0.002619|0.009697|gnomAD_EAS||0&1|0&1,C|non_coding_transcript_exon_variant|MODIFIER|MST1|4485|Transcript|NR_146060.1|misc_RNA|10/17||NR_146060.1:n.1236A>G||1236|||||rs4052580&COSV56535178||-1||EntrezGene||||||3:g.49723379T>C|0.005463|0.009553|0.003849|0.001963|0.009697|0.008825|0.005427|0.004341|0.002619|0.009697|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:5:3:1,2:0,2:2,3:0.6:0,2:23.7:1:37:0:1:0:13:6:0.6:0:2.3	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1127. 

  1127. 3	49723784	49723784	C	A	exonic	MST1	.	synonymous SNV	MST1:NM_020998:exon8:c.G978T:p.P326P	0.66	0.4461	0.3271	0.5537	0.3973	0.9428	0.4230	0.4640	0.4705	rs9713651	rs77898053	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56535754;OCCURENCE=2(large_intestine),1(NS),2(thyroid),2(eye)	698177	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU119849	COCA-CN|5|321|0.0155763	0.5	37	0	3	49723784	.	C	A	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTAAATCGGTGCTGATG;RSEQ=GGGATTTGCGCGTCCCAACG;CSQ=A|downstream_gene_variant|MODIFIER|APEH|327|Transcript|NM_001640.4|protein_coding||||||||||rs9713651&COSV56535754|2380|1||EntrezGene||YES||||3:g.49723784C>A|0.4578|0.3038|0.5341|0.3456|0.7703|0.3775|0.4179|0.4532|0.5179|0.7703|gnomAD_EAS|likely_benign|0&1|1&1,A|synonymous_variant|LOW|MST1|4485|Transcript|NM_020998.3|protein_coding|8/18||NM_020998.3:c.978G>T|NP_066278.3:p.Pro326%3D|1050|978|326|P|ccG/ccT|rs9713651&COSV56535754||-1||EntrezGene||YES||||3:g.49723784C>A|0.4578|0.3038|0.5341|0.3456|0.7703|0.3775|0.4179|0.4532|0.5179|0.7703|gnomAD_EAS|likely_benign|0&1|1&1,A|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NM_022064.5|protein_coding||||||||||rs9713651&COSV56535754|3206|1||EntrezGene||YES||||3:g.49723784C>A|0.4578|0.3038|0.5341|0.3456|0.7703|0.3775|0.4179|0.4532|0.5179|0.7703|gnomAD_EAS|likely_benign|0&1|1&1,A|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NR_135218.2|misc_RNA||||||||||rs9713651&COSV56535754|3206|1||EntrezGene||||||3:g.49723784C>A|0.4578|0.3038|0.5341|0.3456|0.7703|0.3775|0.4179|0.4532|0.5179|0.7703|gnomAD_EAS|likely_benign|0&1|1&1,A|non_coding_transcript_exon_variant|MODIFIER|MST1|4485|Transcript|NR_146060.1|misc_RNA|8/17||NR_146060.1:n.1050G>T||1050|||||rs9713651&COSV56535754||-1||EntrezGene||||||3:g.49723784C>A|0.4578|0.3038|0.5341|0.3456|0.7703|0.3775|0.4179|0.4532|0.5179|0.7703|gnomAD_EAS|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:37:0:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1128. 

  1128. 3	49724808	49724808	T	C	exonic	MST1	.	synonymous SNV	MST1:NM_020998:exon4:c.A459G:p.P153P	0.99	0.8201	0.7258	0.8819	0.8079	0.9963	0.8986	0.8320	0.8599	rs3020779	rs3020779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU81762505	COCA-CN|5|321|0.0155763	0.5	95	0	3	49724808	.	T	C	95	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=6;AF=1;SHIFT3=2;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTCACTTGTGATCATT;RSEQ=GGGAACTTGTGGCTCCAAGC;CSQ=C|downstream_gene_variant|MODIFIER|APEH|327|Transcript|NM_001640.4|protein_coding||||||||||rs3020779|3404|1||EntrezGene||YES||||3:g.49724808T>C|0.8634|0.729|0.9111|0.8502|0.993|0.9096|0.8184|0.8419|0.9447|0.993|gnomAD_EAS|||,C|synonymous_variant|LOW|MST1|4485|Transcript|NM_020998.3|protein_coding|4/18||NM_020998.3:c.459A>G|NP_066278.3:p.Pro153%3D|531|459|153|P|ccA/ccG|rs3020779||-1||EntrezGene||YES||||3:g.49724808T>C|0.8634|0.729|0.9111|0.8502|0.993|0.9096|0.8184|0.8419|0.9447|0.993|gnomAD_EAS|||,C|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NM_022064.5|protein_coding||||||||||rs3020779|2182|1||EntrezGene||YES||||3:g.49724808T>C|0.8634|0.729|0.9111|0.8502|0.993|0.9096|0.8184|0.8419|0.9447|0.993|gnomAD_EAS|||,C|upstream_gene_variant|MODIFIER|RNF123|63891|Transcript|NR_135218.2|misc_RNA||||||||||rs3020779|2182|1||EntrezGene||||||3:g.49724808T>C|0.8634|0.729|0.9111|0.8502|0.993|0.9096|0.8184|0.8419|0.9447|0.993|gnomAD_EAS|||,C|non_coding_transcript_exon_variant|MODIFIER|MST1|4485|Transcript|NR_146060.1|misc_RNA|4/17||NR_146060.1:n.531A>G||531|||||rs3020779||-1||EntrezGene||||||3:g.49724808T>C|0.8634|0.729|0.9111|0.8502|0.993|0.9096|0.8184|0.8419|0.9447|0.993|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:6:6:4,2:0,0:0,6:1:0,2:54.3:1:37:0:1:0:60:12:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1129. 

  1129. 3	49928691	49928691	T	C	exonic	MST1R	.	nonsynonymous SNV	MST1R:NM_001318913:exon15:c.A3265G:p.S1089G,MST1R:NM_001244937:exon16:c.A3436G:p.S1146G,MST1R:NM_002447:exon17:c.A3583G:p.S1195G	1.	1.0000	0.9999	1	1	1	1	1	1	rs7433231	rs7433231	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56564120;OCCURENCE=23(upper_aerodigestive_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU81762617	COCA-CN|5|321|0.0155763	0.5	103	0	3	49928691	.	T	C	103	PASS	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=7;AF=1;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCCAGGTACTCCATGC;RSEQ=GCGGGCTACCTGCAGGCCAA;CSQ=C|missense_variant|MODERATE|MST1R|4486|Transcript|NM_001244937.3|protein_coding|16/19||NM_001244937.3:c.3436A>G|NP_001231866.1:p.Ser1146Gly|3700|3436|1146|S/G|Agc/Ggc|rs7433231&COSV56564120||-1||EntrezGene||||||3:g.49928691T>C|1|1|1|1|0.9999|1|1|1|1|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|missense_variant|MODERATE|MST1R|4486|Transcript|NM_001318913.2|protein_coding|15/18||NM_001318913.2:c.3265A>G|NP_001305842.1:p.Ser1089Gly|3529|3265|1089|S/G|Agc/Ggc|rs7433231&COSV56564120||-1||EntrezGene||||||3:g.49928691T>C|1|1|1|1|0.9999|1|1|1|1|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|missense_variant|MODERATE|MST1R|4486|Transcript|NM_002447.4|protein_coding|17/20||NM_002447.4:c.3583A>G|NP_002438.2:p.Ser1195Gly|3847|3583|1195|S/G|Agc/Ggc|rs7433231&COSV56564120||-1||EntrezGene||YES||||3:g.49928691T>C|1|1|1|1|0.9999|1|1|1|1|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,C|non_coding_transcript_exon_variant|MODIFIER|MST1R|4486|Transcript|NR_134919.2|misc_RNA|17/20||NR_134919.2:n.3783A>G||3783|||||rs7433231&COSV56564120||-1||EntrezGene||||||3:g.49928691T>C|1|1|1|1|0.9999|1|1|1|1|1|AFR&AMR&EAS&EUR&SAS&gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:7:7:2,5:0,0:0,7:1:0,2:40.7:1:37:0:1:0:60:14:1:0:2.3	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1130. 

  1130. 3	49935537	49935537	G	A	exonic	MST1R	.	synonymous SNV	MST1R:NM_001318913:exon3:c.C1509T:p.V503V,MST1R:NM_001244937:exon5:c.C1827T:p.V609V,MST1R:NM_002447:exon5:c.C1827T:p.V609V	0.015	0.0013	0	0	0	0.0062	0.0029	0.0011	0.0031	rs56273948	rs56273948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56567233;OCCURENCE=1(oesophagus)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	1	.	.	0.5	85	1	3	49935537	.	G	A	85	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.16667;SOR=inf;LSEQ=CAGGGACTTTGGCCCACAGT;RSEQ=ACCTGATGGGTTCCCTCAGG;CSQ=A|synonymous_variant|LOW|MST1R|4486|Transcript|NM_001244937.3|protein_coding|5/19||NM_001244937.3:c.1827C>T|NP_001231866.1:p.Val609%3D|2091|1827|609|V|gtC/gtT|rs56273948&COSV56567233||-1||EntrezGene||||||3:g.49935537G>A|0.001297|0|5.782e-05|0|0.008535|0.00425|0.000563|0.001792|0|0.0149|EAS||0&1|0&1,A|synonymous_variant|LOW|MST1R|4486|Transcript|NM_001318913.2|protein_coding|3/18||NM_001318913.2:c.1509C>T|NP_001305842.1:p.Val503%3D|1773|1509|503|V|gtC/gtT|rs56273948&COSV56567233||-1||EntrezGene||||||3:g.49935537G>A|0.001297|0|5.782e-05|0|0.008535|0.00425|0.000563|0.001792|0|0.0149|EAS||0&1|0&1,A|synonymous_variant|LOW|MST1R|4486|Transcript|NM_002447.4|protein_coding|5/20||NM_002447.4:c.1827C>T|NP_002438.2:p.Val609%3D|2091|1827|609|V|gtC/gtT|rs56273948&COSV56567233||-1||EntrezGene||YES||||3:g.49935537G>A|0.001297|0|5.782e-05|0|0.008535|0.00425|0.000563|0.001792|0|0.0149|EAS||0&1|0&1,A|non_coding_transcript_exon_variant|MODIFIER|MST1R|4486|Transcript|NR_134919.2|misc_RNA|5/20||NR_134919.2:n.2091C>T||2091|||||rs56273948&COSV56567233||-1||EntrezGene||||||3:g.49935537G>A|0.001297|0|5.782e-05|0|0.008535|0.00425|0.000563|0.001792|0|0.0149|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:5:5:3,2:0,0:0,5:1:0,2:38.2:1:37:0:1:0:60:10:1:0:1	0/0:1:0:0,0:0,1:1,0:0:0,0:53:0:37:0:1:0:60:2:1:0:0
    1131. 

  1131. 3	51977522	51977522	A	G	exonic	PARP3	.	nonsynonymous SNV	PARP3:NM_001003931:exon2:c.A172G:p.T58A,PARP3:NM_005485:exon2:c.A151G:p.T51A	.	.	.	.	.	.	.	.	.	.	.	0.574	0.063	T	0.0	0.026	B	0.0	0.013	B	0.001	0.007	N	1	0.090	N	-0.315	0.036	N	2.34	0.164	T	0.17	0.103	N	0.128	0.146	-1.038	0.181	T	0.014	0.057	T	0.002	0.041	T	-3.055	0.001	0.001	0.352	0.022	0.009	0.034	N	c	-2.118	-2.225	1.0	0.983	0.507	0.198	0	-10.1	0.003	-3.047	0.007	-0.293	0.083	0.000	0.063	0.000	0.016	3.345	0.067	WGR domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	81	3	51977522	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1118;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00451;SOR=0;LSEQ=GCATAATCCGCGTGGATCCA;RSEQ=CATGTCCACTCAGCAGCAAC;CSQ=G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001003931.4|protein_coding|2/11||NM_001003931.4:c.151A>G|NP_001003931.4:p.Thr51Ala|499|151|51|T/A|Aca/Gca|||1||EntrezGene||||||3:g.51977522A>G||||||||||||||,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001370239.1|protein_coding|3/12||NM_001370239.1:c.151A>G|NP_001357168.1:p.Thr51Ala|621|151|51|T/A|Aca/Gca|||1||EntrezGene||||||3:g.51977522A>G||||||||||||||,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001370240.1|protein_coding|2/11||NM_001370240.1:c.151A>G|NP_001357169.1:p.Thr51Ala|842|151|51|T/A|Aca/Gca|||1||EntrezGene||YES||||3:g.51977522A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|RRP9|9136|Transcript|NM_004704.5|protein_coding|||||||||||1602|-1||EntrezGene||YES||||3:g.51977522A>G||||||||||||||,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_005485.6|protein_coding|2/11||NM_005485.6:c.151A>G|NP_005476.4:p.Thr51Ala|504|151|51|T/A|Aca/Gca|||1||EntrezGene||||||3:g.51977522A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1118:0:0,0:511,607:1118,0:0:2,0:37.5:1:35.9:1:1:0:60:54.9:1:0:0.1	0/1:81:2:1,1:37,42:79,2:0.0247:2,2:17:0:37:0:1:1.13:60:4:0.025:0:1
    1132. 

  1132. 3	51978093	51978093	C	A	intronic	PARP3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	147	3	51978093	.	C	A	44	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2830;VD=1;AF=0.0004;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.00046;SOR=0.01707;LSEQ=CCAGCCTGCCCCCCACCTCC;RSEQ=CTCTGGCCCAGGTGTATGAG;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PARP3|10039|Transcript|NM_001003931.4|protein_coding||2/10|NM_001003931.4:c.184-12C>A|||||||||1||EntrezGene||||||3:g.51978093C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PARP3|10039|Transcript|NM_001370239.1|protein_coding||3/11|NM_001370239.1:c.184-12C>A|||||||||1||EntrezGene||||||3:g.51978093C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PARP3|10039|Transcript|NM_001370240.1|protein_coding||2/10|NM_001370240.1:c.184-12C>A|||||||||1||EntrezGene||YES||||3:g.51978093C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|RRP9|9136|Transcript|NM_004704.5|protein_coding|||||||||||2173|-1||EntrezGene||YES||||3:g.51978093C>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PARP3|10039|Transcript|NM_005485.6|protein_coding||2/10|NM_005485.6:c.184-12C>A|||||||||1||EntrezGene||||||3:g.51978093C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2830:1:0,1:1622,1207:2829,1:0.0004:2,0:71:0:11:0:0.42686:0:60:0:0:0:4	0/1:147:3:1,2:90,54:144,3:0.0204:2,2:59.3:1:28.3:1:0.55786:3.30524:60:2:0.0137:0:2.3
    1133. 

  1133. 3	51978220	51978220	A	G	exonic	PARP3	.	nonsynonymous SNV	PARP3:NM_001003931:exon3:c.A320G:p.H107R,PARP3:NM_005485:exon3:c.A299G:p.H100R	1.	0.9937	0.9977	0.9928	1	1	0.9946	0.9907	0.9908	rs28547534	rs28547534	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51755714;OCCURENCE=1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU4565297	COCA-CN|5|321|0.0155763	1	442	230	3	51978220	.	A	G	442	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4516;VD=4497;AF=0.9958;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.27082;SOR=2.07573;LSEQ=CTTCTTCACCTGCTGGAACC;RSEQ=CTGGGGCCGTGTGGTGAGTG;CSQ=G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001003931.4|protein_coding|3/11||NM_001003931.4:c.299A>G|NP_001003931.4:p.His100Arg|647|299|100|H/R|cAc/cGc|rs28547534&COSV51755714||1||EntrezGene||||||3:g.51978220A>G|0.993|0.998|0.9973|0.9983|0.9999|0.9952|0.9892|0.9919|0.9926|1|AFR&EAS||0&1|0&1,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001370239.1|protein_coding|4/12||NM_001370239.1:c.299A>G|NP_001357168.1:p.His100Arg|769|299|100|H/R|cAc/cGc|rs28547534&COSV51755714||1||EntrezGene||||||3:g.51978220A>G|0.993|0.998|0.9973|0.9983|0.9999|0.9952|0.9892|0.9919|0.9926|1|AFR&EAS||0&1|0&1,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_001370240.1|protein_coding|3/11||NM_001370240.1:c.299A>G|NP_001357169.1:p.His100Arg|990|299|100|H/R|cAc/cGc|rs28547534&COSV51755714||1||EntrezGene||YES||||3:g.51978220A>G|0.993|0.998|0.9973|0.9983|0.9999|0.9952|0.9892|0.9919|0.9926|1|AFR&EAS||0&1|0&1,G|upstream_gene_variant|MODIFIER|RRP9|9136|Transcript|NM_004704.5|protein_coding||||||||||rs28547534&COSV51755714|2300|-1||EntrezGene||YES||||3:g.51978220A>G|0.993|0.998|0.9973|0.9983|0.9999|0.9952|0.9892|0.9919|0.9926|1|AFR&EAS||0&1|0&1,G|missense_variant|MODERATE|PARP3|10039|Transcript|NM_005485.6|protein_coding|3/11||NM_005485.6:c.299A>G|NP_005476.4:p.His100Arg|652|299|100|H/R|cAc/cGc|rs28547534&COSV51755714||1||EntrezGene||||||3:g.51978220A>G|0.993|0.998|0.9973|0.9983|0.9999|0.9952|0.9892|0.9919|0.9926|1|AFR&EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4516:4497:2204,2293:5,7:12,4497:0.9958:2,2:38.2:1:36.5:1:0.77467:1.35:60:127.486:0.9964:0:1.1	1/1:230:228:129,99:0,0:0,228:0.9913:0,2:40.4:1:36.7:1:1:0:60:456:0.9956:0:1.1
    1134. 

  1134. 3	51979588	51979588	C	-	exonic	PARP3	.	frameshift deletion	PARP3:NM_001003931:exon7:c.960delC:p.L322Wfs*15,PARP3:NM_005485:exon7:c.939delC:p.L315Wfs*15	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	49	160	3	51979587	.	AC	A	49	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1713;VD=0;AF=0;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.00061;SOR=0;LSEQ=GACGGTGGAGGAGGTGCCAC;RSEQ=CCCCTGGACCGAGACTACCA;CSQ=-|frameshift_variant|HIGH|PARP3|10039|Transcript|NM_001003931.4|protein_coding|7/11||NM_001003931.4:c.943del|NP_001003931.4:p.Leu315TrpfsTer15|1287|939|313|H/X|caC/ca|||1||EntrezGene|||||4|3:g.51979592del||||||||||||||,-|frameshift_variant|HIGH|PARP3|10039|Transcript|NM_001370239.1|protein_coding|8/12||NM_001370239.1:c.943del|NP_001357168.1:p.Leu315TrpfsTer15|1409|939|313|H/X|caC/ca|||1||EntrezGene|||||4|3:g.51979592del||||||||||||||,-|frameshift_variant|HIGH|PARP3|10039|Transcript|NM_001370240.1|protein_coding|7/11||NM_001370240.1:c.943del|NP_001357169.1:p.Leu315TrpfsTer15|1630|939|313|H/X|caC/ca|||1||EntrezGene||YES|||4|3:g.51979592del||||||||||||||,-|upstream_gene_variant|MODIFIER|RRP9|9136|Transcript|NM_004704.5|protein_coding|||||||||||3668|-1||EntrezGene||YES||||3:g.51979592del||||||||||||||,-|frameshift_variant|HIGH|PARP3|10039|Transcript|NM_005485.6|protein_coding|7/11||NM_005485.6:c.943del|NP_005476.4:p.Leu315TrpfsTer15|1292|939|313|H/X|caC/ca|||1||EntrezGene|||||4|3:g.51979592del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1713:0:0,0:934,779:1713,0:0:2,0:39.5:1:36.7:1:1:0:60:284.5:1:0:0.1	0/1:160:3:1,2:89,68:157,3:0.0187:2,2:55:1:31.4:1:0.58152:2.60213:60:2:0.0126:0.0063:0
    1135. 

  1135. 3	51979600	51979600	A	G	exonic	PARP3	.	synonymous SNV	PARP3:NM_001003931:exon7:c.A972G:p.R324R,PARP3:NM_005485:exon7:c.A951G:p.R317R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	170	3	51979600	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1794;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00745;SOR=0;LSEQ=GTGCCACACCCCCTGGACCG;RSEQ=GACTACCAGCTTCTCAAGTG;CSQ=G|synonymous_variant|LOW|PARP3|10039|Transcript|NM_001003931.4|protein_coding|7/11||NM_001003931.4:c.951A>G|NP_001003931.4:p.Arg317%3D|1299|951|317|R|cgA/cgG|||1||EntrezGene||||||3:g.51979600A>G||||||||||||||,G|synonymous_variant|LOW|PARP3|10039|Transcript|NM_001370239.1|protein_coding|8/12||NM_001370239.1:c.951A>G|NP_001357168.1:p.Arg317%3D|1421|951|317|R|cgA/cgG|||1||EntrezGene||||||3:g.51979600A>G||||||||||||||,G|synonymous_variant|LOW|PARP3|10039|Transcript|NM_001370240.1|protein_coding|7/11||NM_001370240.1:c.951A>G|NP_001357169.1:p.Arg317%3D|1642|951|317|R|cgA/cgG|||1||EntrezGene||YES||||3:g.51979600A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|RRP9|9136|Transcript|NM_004704.5|protein_coding|||||||||||3680|-1||EntrezGene||YES||||3:g.51979600A>G||||||||||||||,G|synonymous_variant|LOW|PARP3|10039|Transcript|NM_005485.6|protein_coding|7/11||NM_005485.6:c.951A>G|NP_005476.4:p.Arg317%3D|1304|951|317|R|cgA/cgG|||1||EntrezGene||||||3:g.51979600A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1794:0:0,0:946,848:1794,0:0:2,0:37.9:1:36.4:1:1:0:60:111.125:1:0:0.1	0/1:170:2:1,1:87,81:168,2:0.0118:2,2:36.5:1:31:1:1:1.07359:60:4:0.0118:0:1.5
    1136. 

  1136. 3	52436275	52436275	G	A	UTR3	BAP1	NM_004656:c.*29C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	110	3	52436275	.	G	A	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=753;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01612;SOR=0;LSEQ=GTGAGGGCCACACGGCAAGA;RSEQ=TGGGCTGCAGAGTCAGGGCC;CSQ=A|3_prime_UTR_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding|17/17||NM_004656.4:c.*29C>T||2349|||||||-1||EntrezGene||YES||||3:g.52436275G>A||||||||||||||,A|downstream_gene_variant|MODIFIER|DNAH1|25981|Transcript|NM_015512.5|protein_coding|||||||||||1767|1||EntrezGene||YES||||3:g.52436275G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:753:0:0,0:485,267:752,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:110:2:1,1:62,46:108,2:0.0182:2,2:49:1:31:1:1:1.34411:60:4:0.0182:0:1
    1137. 

  1137. 3	52436368	52436368	A	G	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon17:c.T2126C:p.L709P	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.998	0.715	D	0.995	0.818	D	0.000	0.843	D	1	0.810	D	0.695	0.181	N	0.9	0.453	T	-2.55	0.551	D	0.441	0.819	-0.856	0.515	T	0.194	0.548	T	0.060	0.681	D	6.017	0.828	27.9	0.998	0.918	0.982	0.808	D	c	0.376	0.492	1.000	0.747	0.707	0.730	0	5.52	0.821	9.255	0.947	1.199	0.960	1.000	0.715	0.998	0.697	15.624	0.765	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	143	3	52436368	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1281;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01002;SOR=0;LSEQ=CAGGCTTCCGCTGCTTGTGG;RSEQ=GCCGGCCGATGCTGACCCCT;CSQ=G|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|17/17||NM_004656.4:c.2126T>C|NP_004647.1:p.Leu709Pro|2256|2126|709|L/P|cTc/cCc|||-1||EntrezGene||YES||||3:g.52436368A>G||||||||||||||,G|downstream_gene_variant|MODIFIER|DNAH1|25981|Transcript|NM_015512.5|protein_coding|||||||||||1860|1||EntrezGene||YES||||3:g.52436368A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1281:0:0,0:681,599:1280,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:143:2:1,1:82,59:141,2:0.014:2,2:37.5:1:37:0:1:1.38656:60:4:0.014:0:1
    1138. 

  1138. 3	52436977	52436977	C	A	intronic	BAP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	17	193	3	52436977	.	C	A	17	f0.01;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2507;VD=3;AF=0.0012;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04402;SOR=0.11462;LSEQ=CTAGAGGCAAGGATGAGCAG;RSEQ=GAGTCCATGCCTATCAAGGC;CSQ=A|intron_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding||14/16|NM_004656.4:c.1891-90G>T|||||||COSV56242045||-1||EntrezGene||YES||||3:g.52436977C>A|||||||||||||1|1,A|downstream_gene_variant|MODIFIER|DNAH1|25981|Transcript|NM_015512.5|protein_coding||||||||||COSV56242045|2469|1||EntrezGene||YES||||3:g.52436977C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2507:3:2,1:1030,1474:2504,3:0.0012:2,2:28.3:1:11:0:0.57229:2.86:60:0:0:0:2.3	0/1:193:2:1,1:80,111:191,2:0.0104:2,2:50:1:37:0:1:1.39:60:4:0.0106:0:1
    1139. 

  1139. 3	52437303	52437303	C	T	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon14:c.G1741A:p.G581S	0.0001	.	.	.	.	.	.	.	.	rs779252716	.	0.293	0.152	T	0.001	0.067	B	0.001	0.040	B	0.002	0.376	N	0.935	0.371	D	0	0.065	N	0.57	0.544	T	0.05	0.064	N	0.124	0.152	-1.018	0.245	T	0.059	0.248	T	0.003	0.069	T	1.392	0.231	12.75	0.983	0.395	0.679	0.333	D	c	-0.274	-0.010	1.000	0.747	0.707	0.730	0	5.06	0.677	1.481	0.349	0.935	0.490	1.000	0.715	0.998	0.697	6.754	0.225	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	.	482507	Hereditary_cancer-predisposing_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	182	3	52437303	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1854;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00795;SOR=0;LSEQ=TCTGATGGAGGGCGAGGAAC;RSEQ=CTTCCCACCCTCTGGGAAGA;CSQ=T|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|14/17||NM_004656.4:c.1741G>A|NP_004647.1:p.Gly581Ser|1871|1741|581|G/S|Ggt/Agt|rs779252716||-1||EntrezGene||YES||||3:g.52437303C>T|3.982e-06|0|0|0|5.437e-05|0|0|0|0|5.437e-05|gnomAD_EAS|uncertain_significance||1,T|downstream_gene_variant|MODIFIER|DNAH1|25981|Transcript|NM_015512.5|protein_coding||||||||||rs779252716|2795|1||EntrezGene||YES||||3:g.52437303C>T|3.982e-06|0|0|0|5.437e-05|0|0|0|0|5.437e-05|gnomAD_EAS|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1854:0:0,0:1008,846:1854,0:0:2,0:36:1:36.6:1:1:0:60:205:1:0:0.1	0/1:182:2:1,1:99,81:180,2:0.011:2,2:60:1:37:0:1:1.22086:60:4:0.0111:0:1
    1140. 

  1140. 3	52437750	52437750	C	A	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon13:c.G1411T:p.A471S	.	.	.	.	.	.	.	.	.	.	.	0.016	0.518	D	0.478	0.348	P	0.158	0.330	B	0.000	0.454	D	0.965	0.384	D	0	0.065	N	0.47	0.565	T	0.06	0.063	N	0.22	0.270	-1.018	0.245	T	0.100	0.373	T	0.009	0.239	T	2.373	0.346	18.64	0.994	0.614	0.961	0.675	D	c	0.115	0.315	1.000	0.747	0.707	0.730	0	6.05	0.981	4.083	0.571	0.935	0.490	1.000	0.715	0.554	0.280	18.789	0.919	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	395	323	3	52437750	.	C	A	395	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=3938;VD=1953;AF=0.4959;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGCCACAGCCGGACTCCCAG;RSEQ=CCCGCTGCTAGTCTTGATGG;CSQ=A|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|13/17||NM_004656.4:c.1411G>T|NP_004647.1:p.Ala471Ser|1541|1411|471|A/S|Gct/Tct|COSV56230132||-1||EntrezGene||YES||||3:g.52437750C>A|||||||||||||1|1,A|downstream_gene_variant|MODIFIER|DNAH1|25981|Transcript|NM_015512.5|protein_coding||||||||||COSV56230132|3242|1||EntrezGene||YES||||3:g.52437750C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3938:1953:927,1026:938,1039:1977,1953:0.4959:2,2:36.3:1:36.2:1:1:1:60:87.773:0.4954:0:1.1	0/0:323:0:0,0:132,191:323,0:0:2,0:33.5:1:36.7:1:1:0:60:646:1:0:0.1
    1141. 

  1141. 3	52440238	52440241	TGGG	GGGC	intronic	BAP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	147	125	3	52440238	.	TGGG	GGGC	147	Bias	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Complex;DP=1449;VD=43;AF=0.0297;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.02709;SOR=inf;LSEQ=GAATGCAGGGAGGGTTGGGC;RSEQ=CAGAGGCCAGGAAGAAAGGG;CSQ=GGGC|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||4435|1||EntrezGene||||||3:g.52440238_52440241delinsGGGC||||||||||||||,GGGC|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||4435|1||EntrezGene||||||3:g.52440238_52440241delinsGGGC||||||||||||||,GGGC|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||4435|1||EntrezGene||YES||||3:g.52440238_52440241delinsGGGC||||||||||||||,GGGC|intron_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding||9/16|NM_004656.4:c.783+28_783+31delinsGCCC|||||||||-1||EntrezGene||YES||||3:g.52440238_52440241delinsGGGC||||||||||||||,GGGC|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||4435|1||EntrezGene||||||3:g.52440238_52440241delinsGGGC||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1449:43:0,43:957,389:1346,43:0.0297:2,1:47.1:1:27.1:1:0:0:60:42:0.0351:0.029:0.1	0/0:125:0:0,0:86,34:120,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1142. 

  1142. 3	52440861	52440861	C	G	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon8:c.G643C:p.G215R	.	.	.	.	.	.	.	.	.	.	.	0.02	0.506	D	1.0	0.899	D	0.99	0.774	D	0.000	0.843	D	1	0.810	D	2.085	0.579	M	1.0	0.414	T	-5.55	0.862	D	0.967	0.967	-0.747	0.581	T	0.247	0.617	T	0.030	0.529	D	7.080	0.941	33	0.999	0.975	0.996	0.973	D	c	0.828	0.843	1.0	0.983	0.707	0.730	0	6.04	0.980	7.867	0.854	0.935	0.490	1.000	0.715	0.286	0.235	20.200	0.983	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	172	3	52440861	.	C	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1785;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00768;SOR=0;LSEQ=TTACCCTGCAGTGGCGAGGC;RSEQ=GATACGCTCCATGATGACCC;CSQ=G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||3815|1||EntrezGene||||||3:g.52440861C>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||3815|1||EntrezGene||||||3:g.52440861C>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||3815|1||EntrezGene||YES||||3:g.52440861C>G||||||||||||||,G|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|8/17||NM_004656.4:c.643G>C|NP_004647.1:p.Gly215Arg|773|643|215|G/R|Ggc/Cgc|||-1||EntrezGene||YES||||3:g.52440861C>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||3815|1||EntrezGene||||||3:g.52440861C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1785:0:0,0:969,816:1785,0:0:2,0:36.9:1:36.6:1:1:0:60:118:1:0:0.1	0/1:172:2:1,1:98,71:169,2:0.0116:2,2:47:1:37:0:1:1.37762:60:4:0.0118:0:1
    1143. 

  1143. 3	52440882	52440882	G	A	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon8:c.C622T:p.R208W	.	.	.	.	.	.	.	.	.	.	.	0.015	0.524	D	0.977	0.566	D	0.725	0.532	P	0.000	0.843	D	1	0.810	D	2.71	0.795	M	0.89	0.456	T	-6.05	0.922	D	0.931	0.929	-0.522	0.679	T	0.199	0.555	T	0.101	0.775	D	5.945	0.816	27.6	0.999	0.938	0.933	0.575	D	c	0.120	0.061	1.000	0.446	0.707	0.730	0	0.425	0.156	0.957	0.286	-0.354	0.069	0.959	0.333	0.964	0.448	17.416	0.873	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	ID=COSV56241066;OCCURENCE=2(breast)	943683	Tumor_susceptibility_linked_to_germline_BAP1_mutations	MONDO:MONDO:0013692,MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	191	3	52440882	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1902;VD=1;AF=0.0005;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02337;SOR=0.04988;LSEQ=GATACGCTCCATGATGACCC;RSEQ=CCGGGCCTTGTCTGTCCACT;CSQ=A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding||||||||||COSV56240437&COSV56241066&COSV56242266|3794|1||EntrezGene||||||3:g.52440882G>A|||||||||||||1&1&1|1&1&1,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding||||||||||COSV56240437&COSV56241066&COSV56242266|3794|1||EntrezGene||||||3:g.52440882G>A|||||||||||||1&1&1|1&1&1,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding||||||||||COSV56240437&COSV56241066&COSV56242266|3794|1||EntrezGene||YES||||3:g.52440882G>A|||||||||||||1&1&1|1&1&1,A|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|8/17||NM_004656.4:c.622C>T|NP_004647.1:p.Arg208Trp|752|622|208|R/W|Cgg/Tgg|COSV56240437&COSV56241066&COSV56242266||-1||EntrezGene||YES||||3:g.52440882G>A|||||||||||||1&1&1|1&1&1,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding||||||||||COSV56240437&COSV56241066&COSV56242266|3794|1||EntrezGene||||||3:g.52440882G>A|||||||||||||1&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1902:1:1,0:993,908:1901,1:0.0005:2,0:34:0:37:0:1:0:60:2:0.0005:0:1	0/1:191:2:1,1:103,86:189,2:0.0105:2,2:46.5:1:37:0:1:1.19653:60:4:0.0106:0:1
    1144. 

  1144. 3	52441438	52441438	G	A	exonic	BAP1	.	synonymous SNV	BAP1:NM_004656:exon6:c.C414T:p.A138A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	181	3	52441438	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2086;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.00634;SOR=0;LSEQ=GCATGGCTATTATGGGCCTT;RSEQ=GCCAACTCCGGGGCATTGCC;CSQ=A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||3238|1||EntrezGene||||||3:g.52441438G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||3238|1||EntrezGene||||||3:g.52441438G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||3238|1||EntrezGene||YES||||3:g.52441438G>A||||||||||||||,A|synonymous_variant|LOW|BAP1|8314|Transcript|NM_004656.4|protein_coding|6/17||NM_004656.4:c.414C>T|NP_004647.1:p.Ala138%3D|544|414|138|A|gcC/gcT|||-1||EntrezGene||YES||||3:g.52441438G>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||3238|1||EntrezGene||||||3:g.52441438G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2086:0:0,0:967,1117:2084,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:181:2:1,1:66,113:179,2:0.011:2,2:32.5:1:37:0:1:1.71:60:4:0.0111:0:1.5
    1145. 

  1145. 3	52442054	52442054	C	T	exonic	BAP1	.	nonsynonymous SNV	BAP1:NM_004656:exon5:c.G295A:p.V99M	.	.	.	.	.	.	.	.	.	.	.	0.004	0.912	D	1.0	0.899	D	0.997	0.850	D	0.000	0.843	D	1	0.810	D	3.235	0.898	M	0.39	0.574	T	-2.54	0.567	D	0.891	0.881	-0.042	0.814	T	0.430	0.772	T	0.065	0.697	D	7.164	0.944	34	0.999	0.977	0.988	0.867	D	c	0.914	0.866	1.0	0.983	0.707	0.730	0	5.49	0.809	7.657	0.826	0.935	0.490	1.000	0.715	0.985	0.512	19.369	0.944	Peptidase C12, ubiquitin carboxyl-terminal hydrolase	.	.	ID=COSV56236367;OCCURENCE=1(peritoneum),3(stomach)	1004912	Tumor_susceptibility_linked_to_germline_BAP1_mutations	MONDO:MONDO:0013692,MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU5895724	GACA-JP|1|585|0.0017094,STAD-US|2|439|0.00455581	0.25	37	144	3	52442054	.	C	T	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2078;VD=1;AF=0.0005;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.01198;SOR=0.03432;LSEQ=GCTGCTGCAGTTCAGGAGCA;RSEQ=GCTCAGCAAGGCATGAGTTG;CSQ=T|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding||||||||||COSV56236367|2622|1||EntrezGene||||||3:g.52442054C>T|||||||||||||1|1,T|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding||||||||||COSV56236367|2622|1||EntrezGene||||||3:g.52442054C>T|||||||||||||1|1,T|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding||||||||||COSV56236367|2622|1||EntrezGene||YES||||3:g.52442054C>T|||||||||||||1|1,T|missense_variant|MODERATE|BAP1|8314|Transcript|NM_004656.4|protein_coding|5/17||NM_004656.4:c.295G>A|NP_004647.1:p.Val99Met|425|295|99|V/M|Gtg/Atg|COSV56236367||-1||EntrezGene||YES||||3:g.52442054C>T|||||||||||||1|1,T|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding||||||||||COSV56236367|2622|1||EntrezGene||||||3:g.52442054C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2078:1:0,1:926,1150:2076,1:0.0005:2,0:11:0:37:0:1:0:60:2:0.0005:0:1	0/1:144:2:1,1:59,83:142,2:0.0139:2,2:35:0:37:0:1:1.4:60:4:0.014:0:1
    1146. 

  1146. 3	52442117	52442117	C	A	intronic	BAP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	109	3	52442117	.	C	A	37	v3;f0.01;pSTD;q22.5;SN1.5;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1441;VD=1;AF=0.0007;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01403;SOR=0.03738;LSEQ=TGAAACCAAGAATAGTCACC;RSEQ=ATACACAGCACCCCTCACTG;CSQ=A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||2559|1||EntrezGene||||||3:g.52442117C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||2559|1||EntrezGene||||||3:g.52442117C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||2559|1||EntrezGene||YES||||3:g.52442117C>A||||||||||||||,A|intron_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding||4/16|NM_004656.4:c.256-24G>T|||||||||-1||EntrezGene||YES||||3:g.52442117C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||2559|1||EntrezGene||||||3:g.52442117C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1441:1:0,1:537,903:1440,1:0.0007:2,0:19:0:11:0:1:0:60:0:0:0:6	0/1:109:2:1,1:39,68:107,2:0.0183:2,2:39:1:37:0:1:1.73:60:4:0.0185:0:1
    1147. 

  1147. 3	52442450	52442450	A	G	intronic	BAP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	176	3	52442450	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2210;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00541;SOR=0;LSEQ=TTCCCAAGCAAAAACATGGC;RSEQ=GCATCCCACCCTCCAAACAA;CSQ=G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||2226|1||EntrezGene||||||3:g.52442450A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||2226|1||EntrezGene||||||3:g.52442450A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||2226|1||EntrezGene||YES||||3:g.52442450A>G||||||||||||||,G|intron_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding||4/16|NM_004656.4:c.255+40T>C|||||||||-1||EntrezGene||YES||||3:g.52442450A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||2226|1||EntrezGene||||||3:g.52442450A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2210:0:0,0:1356,854:2210,0:0:2,0:36.2:1:36.3:1:1:0:60:115.316:1:0:0.2	0/1:176:2:1,1:115,58:173,2:0.0114:2,2:23.5:1:37:0:1:1.97448:60:4:0.0115:0:1
    1148. 

  1148. 3	52442669	52442669	C	A	intronic	BAP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	162	3	52442669	.	C	A	37	v3;f0.01;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1914;VD=2;AF=0.001;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0327;SOR=0.08392;LSEQ=ATCAGCCAAAGGGGAGAAGA;RSEQ=AATCAGCATTCCCTTCTTTC;CSQ=A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001278221.3|protein_coding|||||||||||2007|1||EntrezGene||||||3:g.52442669C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321126.2|protein_coding|||||||||||2007|1||EntrezGene||||||3:g.52442669C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_001321127.2|protein_coding|||||||||||2007|1||EntrezGene||YES||||3:g.52442669C>A||||||||||||||,A|intron_variant|MODIFIER|BAP1|8314|Transcript|NM_004656.4|protein_coding||3/16|NM_004656.4:c.123-47G>T|||||||||-1||EntrezGene||YES||||3:g.52442669C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|PHF7|51533|Transcript|NM_016483.7|protein_coding|||||||||||2007|1||EntrezGene||||||3:g.52442669C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1914:2:2,0:753,1158:1911,2:0.001:2,0:10.5:1:18:1:0.15564:0:60:1:0.0005:0:5	0/1:162:2:1,1:48,112:160,2:0.0123:2,2:33:1:37:0:0.51476:2.32:60:4:0.0125:0:1
    1149. 

  1149. 3	52582106	52582106	G	T	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon30:c.C4878A:p.R1626R,PBRM1:NM_018313:exon30:c.C4722A:p.R1574R,PBRM1:NM_181042:exon30:c.C4722A:p.R1574R,PBRM1:NM_001350079:exon31:c.C4710A:p.R1570R,PBRM1:NM_001350074:exon32:c.C4830A:p.R1610R,PBRM1:NM_001350076:exon32:c.C4827A:p.R1609R,PBRM1:NM_001350078:exon32:c.C4830A:p.R1610R,PBRM1:NM_001350077:exon33:c.C4821A:p.R1607R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	44	240	3	52582106	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=430;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04559;SOR=0;LSEQ=TTTTCTAGGTTGTATGCTTG;RSEQ=CGAATGTTGAGGGTGTCCCG;CSQ=T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|32/32||NM_001350074.2:c.4830C>A|NP_001337003.1:p.Arg1610%3D|5214|4830|1610|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|30/30||NM_001350075.2:c.4878C>A|NP_001337004.1:p.Arg1626%3D|5058|4878|1626|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|32/32||NM_001350076.2:c.4827C>A|NP_001337005.1:p.Arg1609%3D|5212|4827|1609|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|33/33||NM_001350077.2:c.4821C>A|NP_001337006.1:p.Arg1607%3D|5264|4821|1607|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|32/32||NM_001350078.2:c.4830C>A|NP_001337007.1:p.Arg1610%3D|5215|4830|1610|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|31/31||NM_001350079.2:c.4710C>A|NP_001337008.1:p.Arg1570%3D|5095|4710|1570|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|31/31||NM_001366070.2:c.4830C>A|NP_001352999.1:p.Arg1610%3D|5073|4830|1610|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|31/31||NM_001366071.2:c.4950C>A|NP_001353000.1:p.Arg1650%3D|5193|4950|1650|R|cgC/cgA|||-1||EntrezGene||YES||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|30/30||NM_001366072.2:c.4785C>A|NP_001353001.1:p.Arg1595%3D|5028|4785|1595|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|30/30||NM_001366073.2:c.4776C>A|NP_001353002.1:p.Arg1592%3D|5019|4776|1592|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|31/31||NM_001366074.2:c.4773C>A|NP_001353003.1:p.Arg1591%3D|5158|4773|1591|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|31/31||NM_001366075.2:c.4755C>A|NP_001353004.1:p.Arg1585%3D|4998|4755|1585|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|30/30||NM_001366076.2:c.4725C>A|NP_001353005.1:p.Arg1575%3D|4968|4725|1575|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|30/30||NM_018313.5:c.4722C>A|NP_060783.3:p.Arg1574%3D|4899|4722|1574|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|30/30||NM_181042.5:c.4722C>A|NP_851385.1:p.Arg1574%3D|5041|4722|1574|R|cgC/cgA|||-1||EntrezGene||||||3:g.52582106G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:430:0:0,0:291,139:430,0:0:2,0:31.3:1:36.1:1:1:0:60:60.429:1:0:0.1	0/1:240:3:1,2:135,102:237,3:0.0125:2,2:51.3:1:28.3:1:0.58039:2.63645:60:2:0.0087:0:2
    1150. 

  1150. 3	52584431	52584431	-	CTC	intronic	PBRM1	.	.	.	0.62	0.5078	0.5459	0.6007	0.5099	0.4317	0.4392	0.5060	0.4898	rs34372721	rs34372721	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114065483	COCA-CN|1|321|0.00311526	0.75	326	169	3	52584431	.	T	TCTC	326	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=502;VD=500;AF=0.996;SHIFT3=2;MSI=2;MSILEN=1;SSF=0;SOR=341.928;LSEQ=AAAGGCTTATTTAGAAGGAA;RSEQ=CTTACCTGCCAGTGTCTGAT;CSQ=CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||31/31|NM_001350074.2:c.4684+5_4684+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||29/29|NM_001350075.2:c.4732+5_4732+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||31/31|NM_001350076.2:c.4681+5_4681+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||32/32|NM_001350077.2:c.4675+5_4675+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||31/31|NM_001350078.2:c.4684+5_4684+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||30/30|NM_001350079.2:c.4564+5_4564+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||30/30|NM_001366070.2:c.4684+5_4684+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||30/30|NM_001366071.2:c.4804+5_4804+6insGAG|||||||rs34372721||-1||EntrezGene||YES||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||29/29|NM_001366072.2:c.4639+5_4639+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||29/29|NM_001366073.2:c.4630+5_4630+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||30/30|NM_001366074.2:c.4627+5_4627+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||30/30|NM_001366075.2:c.4609+5_4609+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||29/29|NM_001366076.2:c.4579+5_4579+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding||29/29|NM_018313.5:c.4576+5_4576+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||,CTC|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding||29/29|NM_181042.5:c.4576+5_4576+6insGAG|||||||rs34372721||-1||EntrezGene||||||3:g.52584433_52584434insCCT|0.4907|0.5366|0.6074|0.4966|0.4329|0.4769|0.5046|0.4805|0.2859|0.6095|AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:502:500:363,137:0,1:1,500:0.996:0,2:25.1:1:36.4:1:0.27545:0:60:1000:0.998:0.3486:0.1	0/1:169:71:48,23:69,29:98,71:0.4201:2,2:39.4:1:36.6:1:0.73725:1.13919:60:142:0.4201:0.0533:0
    1151. 

  1151. 3	52584787	52584787	T	C	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon28:c.A4491G:p.P1497P,PBRM1:NM_018313:exon28:c.A4335G:p.P1445P,PBRM1:NM_181042:exon28:c.A4335G:p.P1445P,PBRM1:NM_001350079:exon29:c.A4323G:p.P1441P,PBRM1:NM_001350074:exon30:c.A4443G:p.P1481P,PBRM1:NM_001350076:exon30:c.A4440G:p.P1480P,PBRM1:NM_001350078:exon30:c.A4443G:p.P1481P,PBRM1:NM_001350077:exon31:c.A4434G:p.P1478P	0.54	0.3415	0.1782	0.4904	0.4396	0.4148	0.3605	0.4115	0.3781	rs2251219	rs2251219	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56259388;OCCURENCE=98(meninges),3(haematopoietic_and_lymphoid_tissue),16(soft_tissue),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU11667185	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.75	344	184	3	52584787	.	T	C	344	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=672;VD=668;AF=0.994;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=184.283;LSEQ=TGTCCATATGGACTTCCACC;RSEQ=GGTGCTGGAGTCCCTACCAT;CSQ=C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|30/32||NM_001350074.2:c.4443A>G|NP_001337003.1:p.Pro1481%3D|4827|4443|1481|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|28/30||NM_001350075.2:c.4491A>G|NP_001337004.1:p.Pro1497%3D|4671|4491|1497|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|30/32||NM_001350076.2:c.4440A>G|NP_001337005.1:p.Pro1480%3D|4825|4440|1480|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|31/33||NM_001350077.2:c.4434A>G|NP_001337006.1:p.Pro1478%3D|4877|4434|1478|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|30/32||NM_001350078.2:c.4443A>G|NP_001337007.1:p.Pro1481%3D|4828|4443|1481|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|29/31||NM_001350079.2:c.4323A>G|NP_001337008.1:p.Pro1441%3D|4708|4323|1441|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|29/31||NM_001366070.2:c.4443A>G|NP_001352999.1:p.Pro1481%3D|4686|4443|1481|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|29/31||NM_001366071.2:c.4563A>G|NP_001353000.1:p.Pro1521%3D|4806|4563|1521|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||YES||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|28/30||NM_001366072.2:c.4398A>G|NP_001353001.1:p.Pro1466%3D|4641|4398|1466|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|28/30||NM_001366073.2:c.4389A>G|NP_001353002.1:p.Pro1463%3D|4632|4389|1463|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|29/31||NM_001366074.2:c.4386A>G|NP_001353003.1:p.Pro1462%3D|4771|4386|1462|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|29/31||NM_001366075.2:c.4368A>G|NP_001353004.1:p.Pro1456%3D|4611|4368|1456|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|28/30||NM_001366076.2:c.4338A>G|NP_001353005.1:p.Pro1446%3D|4581|4338|1446|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|28/30||NM_018313.5:c.4335A>G|NP_060783.3:p.Pro1445%3D|4512|4335|1445|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|28/30||NM_181042.5:c.4335A>G|NP_851385.1:p.Pro1445%3D|4654|4335|1445|P|ccA/ccG|rs2251219&COSV56259388||-1||EntrezGene||||||3:g.52584787T>C|0.391|0.1704|0.5337|0.4514|0.4273|0.4057|0.4056|0.389|0.2426|0.5337|gnomAD_AMR||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:672:668:270,398:0,0:0,668:0.994:0,2:37.5:1:36.7:1:1:0:60:166:0.997:0:1.6	0/1:184:87:43,44:43,54:97,87:0.4728:2,2:42.1:1:36.4:1:0.5545:1.23:60:174:0.4728:0:1.6
    1152. 

  1152. 3	52592374	52592374	C	T	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	178	3	52592374	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=648;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.04623;SOR=0;LSEQ=CGGGGAGAAGCACTCGGCTG;RSEQ=TGTTGCTGTGCTGCTCGCTC;CSQ=T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||29/31|NM_001350074.2:c.4396+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||26/29|NM_001350075.2:c.4288+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||29/31|NM_001350076.2:c.4393+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||30/32|NM_001350077.2:c.4387+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||29/31|NM_001350078.2:c.4396+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||28/30|NM_001350079.2:c.4276+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||28/30|NM_001366070.2:c.4396+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|28/31||NM_001366071.2:c.4407G>A|NP_001353000.1:p.Gln1469%3D|4650|4407|1469|Q|caG/caA|||-1||EntrezGene||YES||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||27/29|NM_001366072.2:c.4351+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||27/29|NM_001366073.2:c.4342+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||28/30|NM_001366074.2:c.4339+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||28/30|NM_001366075.2:c.4321+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||27/29|NM_001366076.2:c.4291+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||26/29|NM_018313.5:c.4132+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||27/29|NM_181042.5:c.4288+3409G>A|||||||||-1||EntrezGene||||||3:g.52592374C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:648:0:0,0:305,343:648,0:0:2,0:37.3:1:36.7:1:1:0:60:161:1:0:0.1	0/1:178:2:1,1:67,109:176,2:0.0112:2,2:48.5:1:37:0:1:1.62:60:4:0.0114:0:1
    1153. 

  1153. 3	52592408	52592408	T	C	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.014	0.531	D	0.999	0.764	D	0.991	0.818	D	0.000	0.843	D	1.000	0.810	D	3.185	0.891	M	-3.55	0.948	D	-2.77	0.587	D	0.89	0.880	0.774	0.941	D	0.874	0.958	D	0.284	0.904	D	1.948	0.295	15.88	0.997	0.800	0.990	0.892	D	c	0.664	0.701	1.000	0.747	0.563	0.310	0	6.06	0.983	7.502	0.803	1.061	0.807	1.000	0.715	1.000	0.888	15.180	0.725	High mobility group box domain	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	132	3	52592408	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=475;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04701;SOR=0;LSEQ=CTCGCTCTCTCTCCTGCTGC;RSEQ=CAGCAACTTTAGCTGCCCGC;CSQ=C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||29/31|NM_001350074.2:c.4396+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||26/29|NM_001350075.2:c.4288+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||29/31|NM_001350076.2:c.4393+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||30/32|NM_001350077.2:c.4387+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||29/31|NM_001350078.2:c.4396+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||28/30|NM_001350079.2:c.4276+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||28/30|NM_001366070.2:c.4396+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|28/31||NM_001366071.2:c.4373A>G|NP_001353000.1:p.Glu1458Gly|4616|4373|1458|E/G|gAg/gGg|||-1||EntrezGene||YES||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||27/29|NM_001366072.2:c.4351+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||27/29|NM_001366073.2:c.4342+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||28/30|NM_001366074.2:c.4339+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||28/30|NM_001366075.2:c.4321+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||27/29|NM_001366076.2:c.4291+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||26/29|NM_018313.5:c.4132+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||,C|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||27/29|NM_181042.5:c.4288+3375A>G|||||||||-1||EntrezGene||||||3:g.52592408T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:475:0:0,0:167,308:475,0:0:2,0:35:1:36.3:1:1:0:60:94:1:0:0.1	0/1:132:2:1,1:35,95:130,2:0.0152:2,2:55.5:1:37:0:0.47259:2.69:60:4:0.0152:0:1
    1154. 

  1154. 3	52597337	52597337	C	G	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon25:c.G4048C:p.A1350P,PBRM1:NM_181042:exon26:c.G4048C:p.A1350P,PBRM1:NM_001350079:exon27:c.G4036C:p.A1346P,PBRM1:NM_001350074:exon28:c.G4156C:p.A1386P,PBRM1:NM_001350076:exon28:c.G4153C:p.A1385P,PBRM1:NM_001350078:exon28:c.G4156C:p.A1386P,PBRM1:NM_001350077:exon29:c.G4147C:p.A1383P	.	.	.	.	.	.	.	.	.	.	.	0.175	0.224	T	0.256	0.296	B	0.099	0.290	B	0.001	0.410	D	0.685	0.810	D	0.345	0.112	N	1.29	0.363	T	-0.82	0.295	N	0.506	0.560	-1.044	0.161	T	0.041	0.174	T	0.010	0.260	T	2.666	0.382	20.6	0.993	0.587	0.360	0.252	N	c	-0.547	-0.419	0.004	0.103	0.707	0.730	0	2.71	0.310	-1.361	0.027	0.935	0.490	0.001	0.137	1.000	0.888	6.546	0.215	High mobility group box domain	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	178	3	52597337	.	C	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=297;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13993;SOR=0;LSEQ=CATGAGGTCCAGCTCACTGG;RSEQ=CAGGGGGGTCTGAAGCTGAG;CSQ=G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|28/32||NM_001350074.2:c.4156G>C|NP_001337003.1:p.Ala1386Pro|4540|4156|1386|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|25/30||NM_001350075.2:c.4048G>C|NP_001337004.1:p.Ala1350Pro|4228|4048|1350|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|28/32||NM_001350076.2:c.4153G>C|NP_001337005.1:p.Ala1385Pro|4538|4153|1385|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|29/33||NM_001350077.2:c.4147G>C|NP_001337006.1:p.Ala1383Pro|4590|4147|1383|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|28/32||NM_001350078.2:c.4156G>C|NP_001337007.1:p.Ala1386Pro|4541|4156|1386|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|27/31||NM_001350079.2:c.4036G>C|NP_001337008.1:p.Ala1346Pro|4421|4036|1346|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|27/31||NM_001366070.2:c.4156G>C|NP_001352999.1:p.Ala1386Pro|4399|4156|1386|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|26/31||NM_001366071.2:c.4111G>C|NP_001353000.1:p.Ala1371Pro|4354|4111|1371|A/P|Gcc/Ccc|||-1||EntrezGene||YES||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|26/30||NM_001366072.2:c.4111G>C|NP_001353001.1:p.Ala1371Pro|4354|4111|1371|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|26/30||NM_001366073.2:c.4102G>C|NP_001353002.1:p.Ala1368Pro|4345|4102|1368|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|27/31||NM_001366074.2:c.4099G>C|NP_001353003.1:p.Ala1367Pro|4484|4099|1367|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|27/31||NM_001366075.2:c.4081G>C|NP_001353004.1:p.Ala1361Pro|4324|4081|1361|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|26/30||NM_001366076.2:c.4051G>C|NP_001353005.1:p.Ala1351Pro|4294|4051|1351|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||25/29|NM_018313.5:c.3930+43G>C|||||||||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|26/30||NM_181042.5:c.4048G>C|NP_851385.1:p.Ala1350Pro|4367|4048|1350|A/P|Gcc/Ccc|||-1||EntrezGene||||||3:g.52597337C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:297:0:0,0:179,118:297,0:0:2,0:34.5:1:36.5:1:1:0:60:147.5:1:0:0.1	0/1:178:2:1,1:99,77:176,2:0.0112:2,2:16:0:37:0:1:1.28387:60:4:0.0116:0:1
    1155. 

  1155. 3	52597434	52597434	G	A	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon25:c.C3951T:p.A1317A,PBRM1:NM_018313:exon25:c.C3876T:p.A1292A,PBRM1:NM_181042:exon26:c.C3951T:p.A1317A,PBRM1:NM_001350079:exon27:c.C3939T:p.A1313A,PBRM1:NM_001350074:exon28:c.C4059T:p.A1353A,PBRM1:NM_001350076:exon28:c.C4056T:p.A1352A,PBRM1:NM_001350078:exon28:c.C4059T:p.A1353A,PBRM1:NM_001350077:exon29:c.C4050T:p.A1350A	0.0008	3.23e-05	0	0	0	0	0	6.665e-05	0	rs148182673	rs148182673	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56289713;OCCURENCE=1(stomach),1(meninges)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU121226125	GACA-JP|1|585|0.0017094	0.25	31	154	3	52597434	.	G	A	31	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=412;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.07368;SOR=0;LSEQ=TCATCTCCACCTTCTAACTC;RSEQ=GCAAATTTAGCTTCTAGCAA;CSQ=A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|28/32||NM_001350074.2:c.4059C>T|NP_001337003.1:p.Ala1353%3D|4443|4059|1353|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|25/30||NM_001350075.2:c.3951C>T|NP_001337004.1:p.Ala1317%3D|4131|3951|1317|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|28/32||NM_001350076.2:c.4056C>T|NP_001337005.1:p.Ala1352%3D|4441|4056|1352|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|29/33||NM_001350077.2:c.4050C>T|NP_001337006.1:p.Ala1350%3D|4493|4050|1350|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|28/32||NM_001350078.2:c.4059C>T|NP_001337007.1:p.Ala1353%3D|4444|4059|1353|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|27/31||NM_001350079.2:c.3939C>T|NP_001337008.1:p.Ala1313%3D|4324|3939|1313|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|27/31||NM_001366070.2:c.4059C>T|NP_001352999.1:p.Ala1353%3D|4302|4059|1353|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|26/31||NM_001366071.2:c.4014C>T|NP_001353000.1:p.Ala1338%3D|4257|4014|1338|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||YES||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|26/30||NM_001366072.2:c.4014C>T|NP_001353001.1:p.Ala1338%3D|4257|4014|1338|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|26/30||NM_001366073.2:c.4005C>T|NP_001353002.1:p.Ala1335%3D|4248|4005|1335|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|27/31||NM_001366074.2:c.4002C>T|NP_001353003.1:p.Ala1334%3D|4387|4002|1334|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|27/31||NM_001366075.2:c.3984C>T|NP_001353004.1:p.Ala1328%3D|4227|3984|1328|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|26/30||NM_001366076.2:c.3954C>T|NP_001353005.1:p.Ala1318%3D|4197|3954|1318|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|25/30||NM_018313.5:c.3876C>T|NP_060783.3:p.Ala1292%3D|4053|3876|1292|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|26/30||NM_181042.5:c.3951C>T|NP_851385.1:p.Ala1317%3D|4270|3951|1317|A|gcC/gcT|rs148182673&COSV56289713||-1||EntrezGene||||||3:g.52597434G>A|9.147e-05|0.0001846|0.0001156|0|5.437e-05|0|0.0001055|0.0004888|0|0.0008|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:412:0:0,0:200,211:411,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:154:2:1,1:62,90:152,2:0.013:2,2:37:1:31:1:1:1.45:60:4:0.0132:0:1
    1156. 

  1156. 3	52597435	52597435	G	A	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon25:c.C3950T:p.A1317V,PBRM1:NM_018313:exon25:c.C3875T:p.A1292V,PBRM1:NM_181042:exon26:c.C3950T:p.A1317V,PBRM1:NM_001350079:exon27:c.C3938T:p.A1313V,PBRM1:NM_001350074:exon28:c.C4058T:p.A1353V,PBRM1:NM_001350076:exon28:c.C4055T:p.A1352V,PBRM1:NM_001350078:exon28:c.C4058T:p.A1353V,PBRM1:NM_001350077:exon29:c.C4049T:p.A1350V	.	.	.	.	.	.	.	.	.	.	.	0.11	0.586	T	0.86	0.670	P	0.453	0.774	P	0.000	0.843	D	1.000	0.810	D	2.045	0.562	M	1.29	0.361	T	-1.59	0.416	N	0.794	0.790	-0.970	0.373	T	0.162	0.498	T	0.024	0.473	T	5.400	0.732	26.0	0.996	0.758	0.995	0.962	D	c	0.552	0.654	1.000	0.747	0.707	0.730	0	5.63	0.861	9.912	0.987	1.048	0.713	1.000	0.715	0.998	0.697	18.212	0.898	.	.	.	ID=COSV105168733;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	154	3	52597435	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=411;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07394;SOR=0;LSEQ=CATCTCCACCTTCTAACTCG;RSEQ=CAAATTTAGCTTCTAGCAAC;CSQ=A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|28/32||NM_001350074.2:c.4058C>T|NP_001337003.1:p.Ala1353Val|4442|4058|1353|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|25/30||NM_001350075.2:c.3950C>T|NP_001337004.1:p.Ala1317Val|4130|3950|1317|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|28/32||NM_001350076.2:c.4055C>T|NP_001337005.1:p.Ala1352Val|4440|4055|1352|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|29/33||NM_001350077.2:c.4049C>T|NP_001337006.1:p.Ala1350Val|4492|4049|1350|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|28/32||NM_001350078.2:c.4058C>T|NP_001337007.1:p.Ala1353Val|4443|4058|1353|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|27/31||NM_001350079.2:c.3938C>T|NP_001337008.1:p.Ala1313Val|4323|3938|1313|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|27/31||NM_001366070.2:c.4058C>T|NP_001352999.1:p.Ala1353Val|4301|4058|1353|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|26/31||NM_001366071.2:c.4013C>T|NP_001353000.1:p.Ala1338Val|4256|4013|1338|A/V|gCc/gTc|||-1||EntrezGene||YES||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|26/30||NM_001366072.2:c.4013C>T|NP_001353001.1:p.Ala1338Val|4256|4013|1338|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|26/30||NM_001366073.2:c.4004C>T|NP_001353002.1:p.Ala1335Val|4247|4004|1335|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|27/31||NM_001366074.2:c.4001C>T|NP_001353003.1:p.Ala1334Val|4386|4001|1334|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|27/31||NM_001366075.2:c.3983C>T|NP_001353004.1:p.Ala1328Val|4226|3983|1328|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|26/30||NM_001366076.2:c.3953C>T|NP_001353005.1:p.Ala1318Val|4196|3953|1318|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|25/30||NM_018313.5:c.3875C>T|NP_060783.3:p.Ala1292Val|4052|3875|1292|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|26/30||NM_181042.5:c.3950C>T|NP_851385.1:p.Ala1317Val|4269|3950|1317|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.52597435G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:411:0:0,0:199,212:411,0:0:2,0:38.2:1:35.6:1:1:0:60:36.364:1:0:0.1	0/1:154:2:1,1:62,90:152,2:0.013:2,2:31:1:37:0:1:1.45:60:4:0.0135:0:1
    1157. 

  1157. 3	52598212	52598212	G	A	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon24:c.C3729T:p.S1243S,PBRM1:NM_018313:exon24:c.C3654T:p.S1218S,PBRM1:NM_181042:exon25:c.C3729T:p.S1243S,PBRM1:NM_001350079:exon26:c.C3717T:p.S1239S,PBRM1:NM_001350074:exon27:c.C3837T:p.S1279S,PBRM1:NM_001350076:exon27:c.C3834T:p.S1278S,PBRM1:NM_001350078:exon27:c.C3837T:p.S1279S,PBRM1:NM_001350077:exon28:c.C3828T:p.S1276S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV105168658;OCCURENCE=2(skin)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	87	3	52598212	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=131;VD=2;AF=0.0153;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.36;SOR=inf;LSEQ=GGTATTTCAGTTGGCCTGCA;RSEQ=GAGAGGAAGTCCTTGAATGA;CSQ=A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|27/32||NM_001350074.2:c.3837C>T|NP_001337003.1:p.Ser1279%3D|4221|3837|1279|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|24/30||NM_001350075.2:c.3729C>T|NP_001337004.1:p.Ser1243%3D|3909|3729|1243|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|27/32||NM_001350076.2:c.3834C>T|NP_001337005.1:p.Ser1278%3D|4219|3834|1278|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|28/33||NM_001350077.2:c.3828C>T|NP_001337006.1:p.Ser1276%3D|4271|3828|1276|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|27/32||NM_001350078.2:c.3837C>T|NP_001337007.1:p.Ser1279%3D|4222|3837|1279|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|26/31||NM_001350079.2:c.3717C>T|NP_001337008.1:p.Ser1239%3D|4102|3717|1239|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|26/31||NM_001366070.2:c.3837C>T|NP_001352999.1:p.Ser1279%3D|4080|3837|1279|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|25/31||NM_001366071.2:c.3792C>T|NP_001353000.1:p.Ser1264%3D|4035|3792|1264|S|tcC/tcT|||-1||EntrezGene||YES||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|25/30||NM_001366072.2:c.3792C>T|NP_001353001.1:p.Ser1264%3D|4035|3792|1264|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|25/30||NM_001366073.2:c.3783C>T|NP_001353002.1:p.Ser1261%3D|4026|3783|1261|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|26/31||NM_001366074.2:c.3780C>T|NP_001353003.1:p.Ser1260%3D|4165|3780|1260|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|26/31||NM_001366075.2:c.3762C>T|NP_001353004.1:p.Ser1254%3D|4005|3762|1254|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|25/30||NM_001366076.2:c.3732C>T|NP_001353005.1:p.Ser1244%3D|3975|3732|1244|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|24/30||NM_018313.5:c.3654C>T|NP_060783.3:p.Ser1218%3D|3831|3654|1218|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|25/30||NM_181042.5:c.3729C>T|NP_851385.1:p.Ser1243%3D|4048|3729|1243|S|tcC/tcT|||-1||EntrezGene||||||3:g.52598212G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:131:2:1,1:63,66:129,2:0.0153:2,2:17.5:1:37:0:1:1.05:60:4:0.0156:0:1	0/0:87:0:0,0:36,51:87,0:0:2,0:39.3:1:36.7:1:1:0:60:174:1:0:0.1
    1158. 

  1158. 3	52610545	52610545	A	T	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	180	3	52610545	.	A	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.51759;SOR=0;LSEQ=ACACGATTAAATAAAAAAGC;RSEQ=CAAATACCTACCGAGAATAC;CSQ=T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||26/31|NM_001350074.2:c.3799+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||23/29|NM_001350075.2:c.3691+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||26/31|NM_001350076.2:c.3796+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||27/32|NM_001350077.2:c.3790+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||26/31|NM_001350078.2:c.3799+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||25/30|NM_001350079.2:c.3679+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||25/30|NM_001366070.2:c.3799+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||24/30|NM_001366071.2:c.3754+12T>A|||||||||-1||EntrezGene||YES||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||24/29|NM_001366072.2:c.3754+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||24/29|NM_001366073.2:c.3745+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||25/30|NM_001366074.2:c.3742+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||25/30|NM_001366075.2:c.3724+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||24/29|NM_001366076.2:c.3694+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||23/29|NM_018313.5:c.3616+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||24/29|NM_181042.5:c.3691+12T>A|||||||||-1||EntrezGene||||||3:g.52610545A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:70:0:0,0:40,30:70,0:0:2,0:34:1:36.3:1:1:0:60:140:1:0:0.6	0/1:180:2:1,1:113,65:178,2:0.0111:2,2:30:1:31:1:1:1.73277:60:4:0.0112:0:1.5
    1159. 

  1159. 3	52610651	52610651	T	A	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon23:c.A3597T:p.P1199P,PBRM1:NM_018313:exon23:c.A3522T:p.P1174P,PBRM1:NM_181042:exon24:c.A3597T:p.P1199P,PBRM1:NM_001350079:exon25:c.A3585T:p.P1195P,PBRM1:NM_001350074:exon26:c.A3705T:p.P1235P,PBRM1:NM_001350076:exon26:c.A3702T:p.P1234P,PBRM1:NM_001350078:exon26:c.A3705T:p.P1235P,PBRM1:NM_001350077:exon27:c.A3696T:p.P1232P	0.54	0.3383	0.1784	0.4868	0.4470	0.4127	0.3580	0.4059	0.3714	rs17264436	rs17264436	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56259420;OCCURENCE=3(haematopoietic_and_lymphoid_tissue),16(soft_tissue),96(meninges)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4125477	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.75	238	219	3	52610651	.	T	A	238	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=80;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGCTCATGCTCTGTTTCTTC;RSEQ=GGGTGAATGAAGATGGGGCC;CSQ=A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|26/32||NM_001350074.2:c.3705A>T|NP_001337003.1:p.Pro1235%3D|4089|3705|1235|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|23/30||NM_001350075.2:c.3597A>T|NP_001337004.1:p.Pro1199%3D|3777|3597|1199|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|26/32||NM_001350076.2:c.3702A>T|NP_001337005.1:p.Pro1234%3D|4087|3702|1234|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|27/33||NM_001350077.2:c.3696A>T|NP_001337006.1:p.Pro1232%3D|4139|3696|1232|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|26/32||NM_001350078.2:c.3705A>T|NP_001337007.1:p.Pro1235%3D|4090|3705|1235|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|25/31||NM_001350079.2:c.3585A>T|NP_001337008.1:p.Pro1195%3D|3970|3585|1195|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|25/31||NM_001366070.2:c.3705A>T|NP_001352999.1:p.Pro1235%3D|3948|3705|1235|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|24/31||NM_001366071.2:c.3660A>T|NP_001353000.1:p.Pro1220%3D|3903|3660|1220|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||YES||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|24/30||NM_001366072.2:c.3660A>T|NP_001353001.1:p.Pro1220%3D|3903|3660|1220|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|24/30||NM_001366073.2:c.3651A>T|NP_001353002.1:p.Pro1217%3D|3894|3651|1217|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|25/31||NM_001366074.2:c.3648A>T|NP_001353003.1:p.Pro1216%3D|4033|3648|1216|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|25/31||NM_001366075.2:c.3630A>T|NP_001353004.1:p.Pro1210%3D|3873|3630|1210|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|24/30||NM_001366076.2:c.3600A>T|NP_001353005.1:p.Pro1200%3D|3843|3600|1200|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|23/30||NM_018313.5:c.3522A>T|NP_060783.3:p.Pro1174%3D|3699|3522|1174|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1,A|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|24/30||NM_181042.5:c.3597A>T|NP_851385.1:p.Pro1199%3D|3916|3597|1199|P|ccA/ccT|rs17264436&COSV56259420||-1||EntrezGene||||||3:g.52610651T>A|0.3831|0.1697|0.5298|0.4494|0.4238|0.4038|0.3991|0.3829|0.2148|0.5298|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:80:80:31,49:0,0:0,80:1:0,2:37.5:1:36.2:1:1:0:60:79:1:0:1.1	0/1:219:93:35,58:55,70:125,93:0.4247:2,2:41.3:1:36.5:1:0.40436:1.30046:60:92:0.4279:0:1.2
    1160. 

  1160. 3	52620436	52620436	C	T	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	89	3	52620436	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=112;VD=2;AF=0.0179;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.30925;SOR=inf;LSEQ=TTCTGTGTGGCTATTATCTG;RSEQ=ATACCTTTTCCAAGTTAAAA;CSQ=T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||24/31|NM_001350074.2:c.3495+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||21/29|NM_001350075.2:c.3387+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||24/31|NM_001350076.2:c.3492+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||25/32|NM_001350077.2:c.3486+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||24/31|NM_001350078.2:c.3495+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||23/30|NM_001350079.2:c.3375+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||23/30|NM_001366070.2:c.3495+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||22/30|NM_001366071.2:c.3450+5G>A|||||||||-1||EntrezGene||YES||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||22/29|NM_001366072.2:c.3450+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||22/29|NM_001366073.2:c.3441+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||23/30|NM_001366074.2:c.3438+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||23/30|NM_001366075.2:c.3420+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||22/29|NM_001366076.2:c.3390+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding||21/29|NM_018313.5:c.3312+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||,T|splice_donor_5th_base_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding||22/29|NM_181042.5:c.3387+5G>A|||||||||-1||EntrezGene||||||3:g.52620436C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:112:2:1,1:89,21:110,2:0.0179:2,2:41:1:31:1:0.35569:4.16385:60:4:0.0187:0:1	0/0:89:0:0,0:72,17:89,0:0:2,0:33.6:1:36.3:1:1:0:60:178:1:0:0.1
    1161. 

  1161. 3	52621527	52621527	C	G	splicing	PBRM1	NM_001350078:exon23:c.3074-1G>C;NM_001350075:exon20:c.2966-1G>C;NM_001350076:exon23:c.3071-1G>C;NM_001350074:exon23:c.3074-1G>C;NM_001350077:exon24:c.3065-1G>C;NM_181042:exon21:c.2966-1G>C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.638	0.378	20.4	0.994	0.621	0.989	0.881	D	c	0.512	0.614	1.000	0.747	0.322	0.047	0	5.92	0.955	7.863	0.853	0.935	0.490	1.000	0.715	0.997	0.653	20.308	0.986	.	.	.	ID=COSV56270893;OCCURENCE=1(urinary_tract)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU4964170	BLCA-US|1|411|0.00243309	0.25	37	123	3	52621527	.	C	G	37	v3;p8	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=58;VD=2;AF=0.0345;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.10147;SOR=inf;LSEQ=GCCATACAACCATTTTTCAC;RSEQ=TCAAAAATGGGGGGTGGGGG;CSQ=G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||22/31|NM_001350074.2:c.3074-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||19/29|NM_001350075.2:c.2966-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||22/31|NM_001350076.2:c.3071-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||23/32|NM_001350077.2:c.3065-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||22/31|NM_001350078.2:c.3074-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||21/30|NM_001350079.2:c.3029-76G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||21/30|NM_001366070.2:c.3074-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||20/30|NM_001366071.2:c.3029-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||YES||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||20/29|NM_001366072.2:c.3029-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||20/29|NM_001366073.2:c.3020-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||21/30|NM_001366074.2:c.3017-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||21/30|NM_001366075.2:c.3074-76G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||20/29|NM_001366076.2:c.2969-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||19/29|NM_018313.5:c.2966-76G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1,G|splice_acceptor_variant|HIGH|PBRM1|55193|Transcript|NM_181042.5|protein_coding||20/29|NM_181042.5:c.2966-1G>C|||||||COSV56270893&COSV56302997||-1||EntrezGene||||||3:g.52621527C>G|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:58:2:1,1:29,27:56,2:0.0345:2,2:7.5:1:37:0:1:1.07272:60:4:0.0377:0:1	0/0:123:0:0,0:51,70:121,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1162. 

  1162. 3	52637486	52637486	C	G	intronic	PBRM1	.	.	.	0.81	0.5977	0.7511	0.6411	0.5728	0.4346	0.4851	0.5542	0.5397	rs2276824	rs2276824	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56271593;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU640061	LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235	0.25	37	9	3	52637486	.	C	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCTAATTATGAGAACA;RSEQ=CTAGAAGACAGTGCATTTTT;CSQ=G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||21/31|NM_001350074.2:c.2887+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||18/29|NM_001350075.2:c.2779+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||21/31|NM_001350076.2:c.2887+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||22/32|NM_001350077.2:c.2878+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||21/31|NM_001350078.2:c.2887+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||20/30|NM_001350079.2:c.2842+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||20/30|NM_001366070.2:c.2887+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||19/30|NM_001366071.2:c.2842+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||YES||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||19/29|NM_001366072.2:c.2842+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||19/29|NM_001366073.2:c.2833+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||20/30|NM_001366074.2:c.2830+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||20/30|NM_001366075.2:c.2887+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||19/29|NM_001366076.2:c.2782+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||18/29|NM_018313.5:c.2779+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||19/29|NM_181042.5:c.2779+51G>C|||||||rs2276824&COSV56271593||-1||EntrezGene||||||3:g.52637486C>G|0.5431|0.7545|0.6516|0.5664|0.4482|0.5349|0.5618|0.5482|0.3135|0.8056|AFR||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:9:2:2,0:7,0:7,2:0.2222:0,0:59.5:1:37:0:1:0:60:4:0.2222:0:1
    1163. 

  1163. 3	52637647	52637647	G	A	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon18:c.C2669T:p.A890V,PBRM1:NM_018313:exon18:c.C2669T:p.A890V,PBRM1:NM_181042:exon19:c.C2669T:p.A890V,PBRM1:NM_001350079:exon20:c.C2732T:p.A911V,PBRM1:NM_001350074:exon21:c.C2777T:p.A926V,PBRM1:NM_001350076:exon21:c.C2777T:p.A926V,PBRM1:NM_001350078:exon21:c.C2777T:p.A926V,PBRM1:NM_001350077:exon22:c.C2768T:p.A923V	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.978	0.818	D	0.000	0.843	D	1	0.810	D	2.395	0.694	M	0.69	0.540	T	-3.9	0.729	D	0.945	0.945	-0.234	0.768	T	0.390	0.744	T	0.024	0.475	T	6.663	0.913	32	0.999	0.991	0.993	0.939	D	c	0.962	0.937	1.000	0.747	0.732	0.924	0	5.57	0.840	9.882	0.985	1.048	0.713	1.000	0.715	0.999	0.750	19.928	0.971	Bromo adjacent homology (BAH) domain;Bromodomain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	63	3	52637647	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=2;AF=0.1818;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02036;SOR=inf;LSEQ=GTTTTGTGGTATAGCTGAGT;RSEQ=CCGGTGAAAGAAGAATCTCT;CSQ=A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|21/32||NM_001350074.2:c.2777C>T|NP_001337003.1:p.Ala926Val|3161|2777|926|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|18/30||NM_001350075.2:c.2669C>T|NP_001337004.1:p.Ala890Val|2849|2669|890|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|21/32||NM_001350076.2:c.2777C>T|NP_001337005.1:p.Ala926Val|3162|2777|926|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|22/33||NM_001350077.2:c.2768C>T|NP_001337006.1:p.Ala923Val|3211|2768|923|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|21/32||NM_001350078.2:c.2777C>T|NP_001337007.1:p.Ala926Val|3162|2777|926|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|20/31||NM_001350079.2:c.2732C>T|NP_001337008.1:p.Ala911Val|3117|2732|911|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|20/31||NM_001366070.2:c.2777C>T|NP_001352999.1:p.Ala926Val|3020|2777|926|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|19/31||NM_001366071.2:c.2732C>T|NP_001353000.1:p.Ala911Val|2975|2732|911|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||YES||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|19/30||NM_001366072.2:c.2732C>T|NP_001353001.1:p.Ala911Val|2975|2732|911|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|19/30||NM_001366073.2:c.2723C>T|NP_001353002.1:p.Ala908Val|2966|2723|908|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|20/31||NM_001366074.2:c.2720C>T|NP_001353003.1:p.Ala907Val|3105|2720|907|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|20/31||NM_001366075.2:c.2777C>T|NP_001353004.1:p.Ala926Val|3020|2777|926|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|19/30||NM_001366076.2:c.2672C>T|NP_001353005.1:p.Ala891Val|2915|2672|891|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|18/30||NM_018313.5:c.2669C>T|NP_060783.3:p.Ala890Val|2846|2669|890|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|19/30||NM_181042.5:c.2669C>T|NP_851385.1:p.Ala890Val|2988|2669|890|A/V|gCa/gTa|COSV56273754||-1||EntrezGene||||||3:g.52637647G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:11:2:1,1:5,4:9,2:0.1818:2,2:25:1:37:0:1:1.22474:60:4:0.1818:0:1	0/0:63:0:0,0:29,34:63,0:0:2,0:38:1:35.6:1:1:0:60:30.5:1:0:0
    1164. 

  1164. 3	52637661	52637661	A	G	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon18:c.T2655C:p.I885I,PBRM1:NM_018313:exon18:c.T2655C:p.I885I,PBRM1:NM_181042:exon19:c.T2655C:p.I885I,PBRM1:NM_001350079:exon20:c.T2718C:p.I906I,PBRM1:NM_001350074:exon21:c.T2763C:p.I921I,PBRM1:NM_001350076:exon21:c.T2763C:p.I921I,PBRM1:NM_001350078:exon21:c.T2763C:p.I921I,PBRM1:NM_001350077:exon22:c.T2754C:p.I918I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	64	3	52637661	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.74639;SOR=0;LSEQ=CTGAGTGCCGGTGAAAGAAG;RSEQ=ATCTCTCCATTTTTGCAGAG;CSQ=G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|21/32||NM_001350074.2:c.2763T>C|NP_001337003.1:p.Ile921%3D|3147|2763|921|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|18/30||NM_001350075.2:c.2655T>C|NP_001337004.1:p.Ile885%3D|2835|2655|885|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|21/32||NM_001350076.2:c.2763T>C|NP_001337005.1:p.Ile921%3D|3148|2763|921|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|22/33||NM_001350077.2:c.2754T>C|NP_001337006.1:p.Ile918%3D|3197|2754|918|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|21/32||NM_001350078.2:c.2763T>C|NP_001337007.1:p.Ile921%3D|3148|2763|921|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|20/31||NM_001350079.2:c.2718T>C|NP_001337008.1:p.Ile906%3D|3103|2718|906|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|20/31||NM_001366070.2:c.2763T>C|NP_001352999.1:p.Ile921%3D|3006|2763|921|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|19/31||NM_001366071.2:c.2718T>C|NP_001353000.1:p.Ile906%3D|2961|2718|906|I|atT/atC|||-1||EntrezGene||YES||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|19/30||NM_001366072.2:c.2718T>C|NP_001353001.1:p.Ile906%3D|2961|2718|906|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|19/30||NM_001366073.2:c.2709T>C|NP_001353002.1:p.Ile903%3D|2952|2709|903|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|20/31||NM_001366074.2:c.2706T>C|NP_001353003.1:p.Ile902%3D|3091|2706|902|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|20/31||NM_001366075.2:c.2763T>C|NP_001353004.1:p.Ile921%3D|3006|2763|921|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|19/30||NM_001366076.2:c.2658T>C|NP_001353005.1:p.Ile886%3D|2901|2658|886|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|18/30||NM_018313.5:c.2655T>C|NP_060783.3:p.Ile885%3D|2832|2655|885|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||,G|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|19/30||NM_181042.5:c.2655T>C|NP_851385.1:p.Ile885%3D|2974|2655|885|I|atT/atC|||-1||EntrezGene||||||3:g.52637661A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:5,5:10,0:0:2,0:33.5:1:35.8:1:1:0:60:20:1:0:0.1	0/1:64:2:1,1:25,37:62,2:0.0312:2,2:60.5:1:37:0:1:1.47:60:4:0.0317:0:1
    1165. 

  1165. 3	52643307	52643307	A	G	intronic	PBRM1	.	.	.	0.57	0.4527	0.5287	0.5359	0.4570	0.4145	0.3649	0.4309	0.4133	rs3733045	rs3733045	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56278425;OCCURENCE=1(large_intestine),2(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU745146	ESAD-UK|1|409|0.00244499,LAML-KR|2|205|0.0097561,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.75	198	77	3	52643307	.	A	G	198	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=13;AF=1;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.00149;SOR=inf;LSEQ=ATAGCACATATCCTCAAAAT;RSEQ=AAAATGGCTTTGAAAACATA;CSQ=G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||20/31|NM_001350074.2:c.2675+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||17/29|NM_001350075.2:c.2567+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||20/31|NM_001350076.2:c.2675+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||21/32|NM_001350077.2:c.2666+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||20/31|NM_001350078.2:c.2675+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||19/30|NM_001350079.2:c.2630+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||19/30|NM_001366070.2:c.2675+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||18/30|NM_001366071.2:c.2630+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||YES||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||18/29|NM_001366072.2:c.2630+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||18/29|NM_001366073.2:c.2621+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||19/30|NM_001366074.2:c.2618+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||19/30|NM_001366075.2:c.2675+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||18/29|NM_001366076.2:c.2570+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||17/29|NM_018313.5:c.2567+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1,G|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||18/29|NM_181042.5:c.2567+22T>C|||||||rs3733045&COSV56278425||-1||EntrezGene||||||3:g.52643307A>G|0.4356|0.5282|0.5652|0.4686|0.4279|0.4133|0.4276|0.4193|0.2773|0.5652|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:13:13:9,4:0,0:0,13:1:0,2:25.7:1:33:1:1:0:60:5.5:1:0:1	1/0:77:44:39,5:26,7:33,44:0.5714:2,2:30.3:1:36.4:1:0.34242:2.08:60:43:0.5658:0:1
    1166. 

  1166. 3	52643398	52643398	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon17:c.G2498A:p.R833H,PBRM1:NM_018313:exon17:c.G2498A:p.R833H,PBRM1:NM_181042:exon18:c.G2498A:p.R833H,PBRM1:NM_001350079:exon19:c.G2561A:p.R854H,PBRM1:NM_001350074:exon20:c.G2606A:p.R869H,PBRM1:NM_001350076:exon20:c.G2606A:p.R869H,PBRM1:NM_001350078:exon20:c.G2606A:p.R869H,PBRM1:NM_001350077:exon21:c.G2597A:p.R866H	0.	3.228e-05	0	0	0	0	0	6.661e-05	0	rs755255835	.	0.208	0.205	T	0.015	0.485	B	0.004	0.354	B	0.000	0.629	D	1.000	0.588	D	2.135	0.597	M	1.55	0.299	T	-2.3	0.527	N	0.631	0.651	-1.056	0.128	T	0.068	0.279	T	0.007	0.184	T	3.270	0.452	22.8	0.999	0.970	0.902	0.510	D	c	-0.000	0.170	1.000	0.747	0.707	0.730	0	5.2	0.716	6.073	0.707	0.935	0.490	1.000	0.715	0.998	0.697	15.273	0.733	Bromodomain	.	.	ID=COSV56276373;OCCURENCE=1(liver)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	MU82427944	LICA-FR|1|252|0.00396825	0.25	37	248	3	52643398	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=116;VD=2;AF=0.0172;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.10096;SOR=inf;LSEQ=ATAAATCAAGCCGACGGTAG;RSEQ=GATTATTTTCAACATTCTTC;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|20/32||NM_001350074.2:c.2606G>A|NP_001337003.1:p.Arg869His|2990|2606|869|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|17/30||NM_001350075.2:c.2498G>A|NP_001337004.1:p.Arg833His|2678|2498|833|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|20/32||NM_001350076.2:c.2606G>A|NP_001337005.1:p.Arg869His|2991|2606|869|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|21/33||NM_001350077.2:c.2597G>A|NP_001337006.1:p.Arg866His|3040|2597|866|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|20/32||NM_001350078.2:c.2606G>A|NP_001337007.1:p.Arg869His|2991|2606|869|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|19/31||NM_001350079.2:c.2561G>A|NP_001337008.1:p.Arg854His|2946|2561|854|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|19/31||NM_001366070.2:c.2606G>A|NP_001352999.1:p.Arg869His|2849|2606|869|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|18/31||NM_001366071.2:c.2561G>A|NP_001353000.1:p.Arg854His|2804|2561|854|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||YES||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|18/30||NM_001366072.2:c.2561G>A|NP_001353001.1:p.Arg854His|2804|2561|854|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|18/30||NM_001366073.2:c.2552G>A|NP_001353002.1:p.Arg851His|2795|2552|851|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|19/31||NM_001366074.2:c.2549G>A|NP_001353003.1:p.Arg850His|2934|2549|850|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|19/31||NM_001366075.2:c.2606G>A|NP_001353004.1:p.Arg869His|2849|2606|869|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|18/30||NM_001366076.2:c.2501G>A|NP_001353005.1:p.Arg834His|2744|2501|834|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|17/30||NM_018313.5:c.2498G>A|NP_060783.3:p.Arg833His|2675|2498|833|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|18/30||NM_181042.5:c.2498G>A|NP_851385.1:p.Arg833His|2817|2498|833|R/H|cGc/cAc|rs755255835&COSV56276373||-1||EntrezGene||||||3:g.52643398C>T|7.958e-06|0|0|0|0|0|1.759e-05|0|0|1.759e-05|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:116:2:1,1:71,43:114,2:0.0172:2,2:28:1:37:0:1:1.64368:60:4:0.0177:0:1	0/0:248:0:0,0:166,82:248,0:0:2,0:37.1:1:35.2:1:1:0:60:23.8:1:0:0.2
    1167. 

  1167. 3	52643685	52643685	T	C	exonic	PBRM1	.	synonymous SNV	PBRM1:NM_001350075:exon17:c.A2211G:p.T737T,PBRM1:NM_018313:exon17:c.A2211G:p.T737T,PBRM1:NM_181042:exon18:c.A2211G:p.T737T,PBRM1:NM_001350079:exon19:c.A2274G:p.T758T,PBRM1:NM_001350074:exon20:c.A2319G:p.T773T,PBRM1:NM_001350076:exon20:c.A2319G:p.T773T,PBRM1:NM_001350078:exon20:c.A2319G:p.T773T,PBRM1:NM_001350077:exon21:c.A2310G:p.T770T	0.54	0.3418	0.1795	0.4881	0.4470	0.4126	0.3603	0.4115	0.3778	rs3755806	rs3755806	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56259469;OCCURENCE=96(meninges),4(haematopoietic_and_lymphoid_tissue),1(urinary_tract),16(soft_tissue),2(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU793407	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,LUSC-KR|3|170|0.0176471,COCA-CN|3|321|0.00934579	0.75	294	244	3	52643685	.	T	C	294	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=285;VD=283;AF=0.993;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=161.883;LSEQ=AAAGACTCCGGCTCATTGTA;RSEQ=GTACAGGCATTATTAAACAT;CSQ=C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|20/32||NM_001350074.2:c.2319A>G|NP_001337003.1:p.Thr773%3D|2703|2319|773|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|17/30||NM_001350075.2:c.2211A>G|NP_001337004.1:p.Thr737%3D|2391|2211|737|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|20/32||NM_001350076.2:c.2319A>G|NP_001337005.1:p.Thr773%3D|2704|2319|773|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|21/33||NM_001350077.2:c.2310A>G|NP_001337006.1:p.Thr770%3D|2753|2310|770|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|20/32||NM_001350078.2:c.2319A>G|NP_001337007.1:p.Thr773%3D|2704|2319|773|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|19/31||NM_001350079.2:c.2274A>G|NP_001337008.1:p.Thr758%3D|2659|2274|758|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|19/31||NM_001366070.2:c.2319A>G|NP_001352999.1:p.Thr773%3D|2562|2319|773|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|18/31||NM_001366071.2:c.2274A>G|NP_001353000.1:p.Thr758%3D|2517|2274|758|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||YES||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|18/30||NM_001366072.2:c.2274A>G|NP_001353001.1:p.Thr758%3D|2517|2274|758|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|18/30||NM_001366073.2:c.2265A>G|NP_001353002.1:p.Thr755%3D|2508|2265|755|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|19/31||NM_001366074.2:c.2262A>G|NP_001353003.1:p.Thr754%3D|2647|2262|754|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|19/31||NM_001366075.2:c.2319A>G|NP_001353004.1:p.Thr773%3D|2562|2319|773|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|18/30||NM_001366076.2:c.2214A>G|NP_001353005.1:p.Thr738%3D|2457|2214|738|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding|17/30||NM_018313.5:c.2211A>G|NP_060783.3:p.Thr737%3D|2388|2211|737|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1,C|synonymous_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding|18/30||NM_181042.5:c.2211A>G|NP_851385.1:p.Thr737%3D|2530|2211|737|T|acA/acG|rs3755806&COSV56259469||-1||EntrezGene||||||3:g.52643685T>C|0.3908|0.1717|0.5335|0.4514|0.4267|0.4055|0.4056|0.3876|0.2404|0.5335|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:285:283:136,147:0,0:0,283:0.993:0,2:35.7:1:36.2:1:1:0:60:93.333:0.9929:0:1.1	0/1:244:113:49,64:53,77:130,113:0.4631:2,2:36.6:1:36.5:1:0.69774:1.11:60:55.5:0.4606:0:1
    1168. 

  1168. 3	52643838	52643838	C	A	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon17:c.G2058T:p.R686S,PBRM1:NM_018313:exon17:c.G2058T:p.R686S,PBRM1:NM_181042:exon18:c.G2058T:p.R686S,PBRM1:NM_001350079:exon19:c.G2121T:p.R707S,PBRM1:NM_001350074:exon20:c.G2166T:p.R722S,PBRM1:NM_001350076:exon20:c.G2166T:p.R722S,PBRM1:NM_001350078:exon20:c.G2166T:p.R722S,PBRM1:NM_001350077:exon21:c.G2157T:p.R719S	.	.	.	.	.	.	.	.	.	.	.	0.003	0.721	D	0.997	0.899	D	0.992	0.850	D	0.000	0.843	D	0.937	0.413	D	1.46	0.370	L	1.55	0.299	T	-3.6	0.698	D	0.806	0.846	-1.042	0.168	T	0.100	0.372	T	0.039	0.584	D	4.654	0.624	24.5	0.982	0.390	0.212	0.211	N	c	-0.078	-0.194	0.031	0.140	0.732	0.924	0	-3.18	0.048	-0.198	0.094	0.077	0.185	0.476	0.265	0.998	0.697	8.749	0.336	Bromodomain;Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	.	.	0.25	37	208	3	52643838	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=174;VD=2;AF=0.0115;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.20683;SOR=inf;LSEQ=AACTCAGATCTAGAGGGAAG;RSEQ=CTCAGAAATATGGCACTGAG;CSQ=A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|20/32||NM_001350074.2:c.2166G>T|NP_001337003.1:p.Arg722Ser|2550|2166|722|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|17/30||NM_001350075.2:c.2058G>T|NP_001337004.1:p.Arg686Ser|2238|2058|686|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|20/32||NM_001350076.2:c.2166G>T|NP_001337005.1:p.Arg722Ser|2551|2166|722|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|21/33||NM_001350077.2:c.2157G>T|NP_001337006.1:p.Arg719Ser|2600|2157|719|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|20/32||NM_001350078.2:c.2166G>T|NP_001337007.1:p.Arg722Ser|2551|2166|722|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|19/31||NM_001350079.2:c.2121G>T|NP_001337008.1:p.Arg707Ser|2506|2121|707|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|19/31||NM_001366070.2:c.2166G>T|NP_001352999.1:p.Arg722Ser|2409|2166|722|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|18/31||NM_001366071.2:c.2121G>T|NP_001353000.1:p.Arg707Ser|2364|2121|707|R/S|agG/agT|||-1||EntrezGene||YES||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|18/30||NM_001366072.2:c.2121G>T|NP_001353001.1:p.Arg707Ser|2364|2121|707|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|18/30||NM_001366073.2:c.2112G>T|NP_001353002.1:p.Arg704Ser|2355|2112|704|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|19/31||NM_001366074.2:c.2109G>T|NP_001353003.1:p.Arg703Ser|2494|2109|703|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|19/31||NM_001366075.2:c.2166G>T|NP_001353004.1:p.Arg722Ser|2409|2166|722|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|18/30||NM_001366076.2:c.2061G>T|NP_001353005.1:p.Arg687Ser|2304|2061|687|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|17/30||NM_018313.5:c.2058G>T|NP_060783.3:p.Arg686Ser|2235|2058|686|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||,A|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|18/30||NM_181042.5:c.2058G>T|NP_851385.1:p.Arg686Ser|2377|2058|686|R/S|agG/agT|||-1||EntrezGene||||||3:g.52643838C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:174:2:1,1:58,114:172,2:0.0115:2,2:45:1:37:0:1:1.96:60:4:0.0116:0:1	0/0:208:0:0,0:101,107:208,0:0:2,0:37.1:1:35.9:1:1:0:60:68.333:1:0:0.1
    1169. 

  1169. 3	52643842	52643842	A	G	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon17:c.T2054C:p.L685P,PBRM1:NM_018313:exon17:c.T2054C:p.L685P,PBRM1:NM_181042:exon18:c.T2054C:p.L685P,PBRM1:NM_001350079:exon19:c.T2117C:p.L706P,PBRM1:NM_001350074:exon20:c.T2162C:p.L721P,PBRM1:NM_001350076:exon20:c.T2162C:p.L721P,PBRM1:NM_001350078:exon20:c.T2162C:p.L721P,PBRM1:NM_001350077:exon21:c.T2153C:p.L718P	.	.	.	.	.	.	.	.	.	.	.	0.005	0.682	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	3.505	0.930	H	1.41	0.334	T	-3.98	0.771	D	0.806	0.840	-0.265	0.760	T	0.295	0.667	T	0.101	0.775	D	5.781	0.790	27.1	0.999	0.982	0.993	0.942	D	c	1.036	0.986	1.000	0.747	0.732	0.924	0	6.17	0.997	9.294	0.951	1.199	0.960	1.000	0.715	0.996	0.625	16.822	0.856	Bromodomain;Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	210	3	52643842	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20079;SOR=inf;LSEQ=CAGATCTAGAGGGAAGCCTC;RSEQ=GAAATATGGCACTGAGGCGG;CSQ=G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|20/32||NM_001350074.2:c.2162T>C|NP_001337003.1:p.Leu721Pro|2546|2162|721|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|17/30||NM_001350075.2:c.2054T>C|NP_001337004.1:p.Leu685Pro|2234|2054|685|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|20/32||NM_001350076.2:c.2162T>C|NP_001337005.1:p.Leu721Pro|2547|2162|721|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|21/33||NM_001350077.2:c.2153T>C|NP_001337006.1:p.Leu718Pro|2596|2153|718|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|20/32||NM_001350078.2:c.2162T>C|NP_001337007.1:p.Leu721Pro|2547|2162|721|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|19/31||NM_001350079.2:c.2117T>C|NP_001337008.1:p.Leu706Pro|2502|2117|706|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|19/31||NM_001366070.2:c.2162T>C|NP_001352999.1:p.Leu721Pro|2405|2162|721|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|18/31||NM_001366071.2:c.2117T>C|NP_001353000.1:p.Leu706Pro|2360|2117|706|L/P|cTg/cCg|||-1||EntrezGene||YES||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|18/30||NM_001366072.2:c.2117T>C|NP_001353001.1:p.Leu706Pro|2360|2117|706|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|18/30||NM_001366073.2:c.2108T>C|NP_001353002.1:p.Leu703Pro|2351|2108|703|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|19/31||NM_001366074.2:c.2105T>C|NP_001353003.1:p.Leu702Pro|2490|2105|702|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|19/31||NM_001366075.2:c.2162T>C|NP_001353004.1:p.Leu721Pro|2405|2162|721|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|18/30||NM_001366076.2:c.2057T>C|NP_001353005.1:p.Leu686Pro|2300|2057|686|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|17/30||NM_018313.5:c.2054T>C|NP_060783.3:p.Leu685Pro|2231|2054|685|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|18/30||NM_181042.5:c.2054T>C|NP_851385.1:p.Leu685Pro|2373|2054|685|L/P|cTg/cCg|||-1||EntrezGene||||||3:g.52643842A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:57,112:169,2:0.0117:2,2:20:1:37:0:1:1.96:60:4:0.0119:0:1	0/0:210:0:0,0:100,110:210,0:0:2,0:36.6:1:36.5:1:1:0:60:104:1:0:0.1
    1170. 

  1170. 3	52651278	52651278	C	A	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon15:c.G1818T:p.Q606H,PBRM1:NM_018313:exon15:c.G1818T:p.Q606H,PBRM1:NM_181042:exon16:c.G1818T:p.Q606H,PBRM1:NM_001350079:exon17:c.G1881T:p.Q627H,PBRM1:NM_001350074:exon18:c.G1926T:p.Q642H,PBRM1:NM_001350076:exon18:c.G1926T:p.Q642H,PBRM1:NM_001350078:exon18:c.G1926T:p.Q642H,PBRM1:NM_001350077:exon19:c.G1917T:p.Q639H	.	.	.	.	.	.	.	.	.	.	.	0.095	0.326	T	0.997	0.715	D	0.923	0.695	D	0.000	0.843	D	1.000	0.588	D	1.795	0.474	L	1.51	0.309	T	-2.98	0.640	D	0.507	0.562	-0.888	0.491	T	0.192	0.545	T	0.025	0.480	T	3.148	0.438	22.6	0.993	0.583	0.988	0.871	D	c	0.712	0.715	1.000	0.500	0.707	0.730	0	5.74	0.900	6.089	0.708	0.852	0.362	1.000	0.715	0.925	0.399	19.919	0.971	Bromodomain;Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	88	3	52651278	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=121;VD=2;AF=0.0165;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.33401;SOR=inf;LSEQ=GGACCGCTGGCCCTCCTTAC;RSEQ=TGGGAGCCCTCCTCATTATA;CSQ=A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|18/32||NM_001350074.2:c.1926G>T|NP_001337003.1:p.Gln642His|2310|1926|642|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|15/30||NM_001350075.2:c.1818G>T|NP_001337004.1:p.Gln606His|1998|1818|606|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|18/32||NM_001350076.2:c.1926G>T|NP_001337005.1:p.Gln642His|2311|1926|642|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|19/33||NM_001350077.2:c.1917G>T|NP_001337006.1:p.Gln639His|2360|1917|639|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|18/32||NM_001350078.2:c.1926G>T|NP_001337007.1:p.Gln642His|2311|1926|642|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|17/31||NM_001350079.2:c.1881G>T|NP_001337008.1:p.Gln627His|2266|1881|627|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|17/31||NM_001366070.2:c.1926G>T|NP_001352999.1:p.Gln642His|2169|1926|642|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|16/31||NM_001366071.2:c.1881G>T|NP_001353000.1:p.Gln627His|2124|1881|627|Q/H|caG/caT|||-1||EntrezGene||YES||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|16/30||NM_001366072.2:c.1881G>T|NP_001353001.1:p.Gln627His|2124|1881|627|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|16/30||NM_001366073.2:c.1872G>T|NP_001353002.1:p.Gln624His|2115|1872|624|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|17/31||NM_001366074.2:c.1869G>T|NP_001353003.1:p.Gln623His|2254|1869|623|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|17/31||NM_001366075.2:c.1926G>T|NP_001353004.1:p.Gln642His|2169|1926|642|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|16/30||NM_001366076.2:c.1821G>T|NP_001353005.1:p.Gln607His|2064|1821|607|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|15/30||NM_018313.5:c.1818G>T|NP_060783.3:p.Gln606His|1995|1818|606|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||,A|missense_variant&splice_region_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|16/30||NM_181042.5:c.1818G>T|NP_851385.1:p.Gln606His|2137|1818|606|Q/H|caG/caT|||-1||EntrezGene||||||3:g.52651278C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:121:2:1,1:69,50:119,2:0.0165:2,2:45:0:37:0:1:1.37625:60:4:0.0167:0:1	0/0:88:0:0,0:56,32:88,0:0:2,0:38.7:1:36.2:1:1:0:60:87:1:0:0.1
    1171. 

  1171. 3	52651298	52651298	A	G	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon15:c.T1798C:p.Y600H,PBRM1:NM_018313:exon15:c.T1798C:p.Y600H,PBRM1:NM_181042:exon16:c.T1798C:p.Y600H,PBRM1:NM_001350079:exon17:c.T1861C:p.Y621H,PBRM1:NM_001350074:exon18:c.T1906C:p.Y636H,PBRM1:NM_001350076:exon18:c.T1906C:p.Y636H,PBRM1:NM_001350078:exon18:c.T1906C:p.Y636H,PBRM1:NM_001350077:exon19:c.T1897C:p.Y633H	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.971	D	0.000	0.843	D	1	0.810	D	4.06	0.972	H	1.03	0.405	T	-4.69	0.800	D	0.761	0.760	0.183	0.856	D	0.430	0.772	T	0.059	0.678	D	5.362	0.726	25.9	0.999	0.941	0.995	0.962	D	c	1.063	0.970	1.000	0.747	0.707	0.730	0	5.74	0.900	9.325	0.960	1.088	0.866	1.000	0.715	0.996	0.625	16.035	0.803	Bromodomain;Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	108	3	52651298	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.31168;SOR=inf;LSEQ=CTGGGAGCCCTCCTCATTAT;RSEQ=GTGCCTGGCATTCCGGAACA;CSQ=G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|18/32||NM_001350074.2:c.1906T>C|NP_001337003.1:p.Tyr636His|2290|1906|636|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|15/30||NM_001350075.2:c.1798T>C|NP_001337004.1:p.Tyr600His|1978|1798|600|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|18/32||NM_001350076.2:c.1906T>C|NP_001337005.1:p.Tyr636His|2291|1906|636|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|19/33||NM_001350077.2:c.1897T>C|NP_001337006.1:p.Tyr633His|2340|1897|633|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|18/32||NM_001350078.2:c.1906T>C|NP_001337007.1:p.Tyr636His|2291|1906|636|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|17/31||NM_001350079.2:c.1861T>C|NP_001337008.1:p.Tyr621His|2246|1861|621|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|17/31||NM_001366070.2:c.1906T>C|NP_001352999.1:p.Tyr636His|2149|1906|636|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|16/31||NM_001366071.2:c.1861T>C|NP_001353000.1:p.Tyr621His|2104|1861|621|Y/H|Tat/Cat|||-1||EntrezGene||YES||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|16/30||NM_001366072.2:c.1861T>C|NP_001353001.1:p.Tyr621His|2104|1861|621|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|16/30||NM_001366073.2:c.1852T>C|NP_001353002.1:p.Tyr618His|2095|1852|618|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|17/31||NM_001366074.2:c.1849T>C|NP_001353003.1:p.Tyr617His|2234|1849|617|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|17/31||NM_001366075.2:c.1906T>C|NP_001353004.1:p.Tyr636His|2149|1906|636|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|16/30||NM_001366076.2:c.1801T>C|NP_001353005.1:p.Tyr601His|2044|1801|601|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|15/30||NM_018313.5:c.1798T>C|NP_060783.3:p.Tyr600His|1975|1798|600|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|16/30||NM_181042.5:c.1798T>C|NP_851385.1:p.Tyr600His|2117|1798|600|Y/H|Tat/Cat|||-1||EntrezGene||||||3:g.52651298A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:73,62:135,2:0.0146:2,2:61.5:1:37:0:1:1.17601:60:4:0.0147:0:1	0/0:108:0:0,0:64,44:108,0:0:2,0:35.2:1:36.1:1:1:0:60:35:1:0:0.1
    1172. 

  1172. 3	52651351	52651351	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon15:c.G1745A:p.G582D,PBRM1:NM_018313:exon15:c.G1745A:p.G582D,PBRM1:NM_181042:exon16:c.G1745A:p.G582D,PBRM1:NM_001350079:exon17:c.G1808A:p.G603D,PBRM1:NM_001350074:exon18:c.G1853A:p.G618D,PBRM1:NM_001350076:exon18:c.G1853A:p.G618D,PBRM1:NM_001350078:exon18:c.G1853A:p.G618D,PBRM1:NM_001350077:exon19:c.G1844A:p.G615D	.	.	.	.	.	.	.	.	.	.	.	0.093	0.393	T	0.041	0.380	B	0.04	0.364	B	0.000	0.491	D	0.998	0.487	D	-0.965	0.012	N	2.31	0.168	T	-0.69	0.316	N	0.341	0.417	-0.867	0.508	T	0.014	0.054	T	0.010	0.265	T	4.659	0.624	24.5	0.998	0.863	0.869	0.460	D	c	-0.331	-0.037	0.063	0.153	0.707	0.730	0	4.93	0.643	1.719	0.374	0.852	0.362	0.995	0.385	0.994	0.587	16.220	0.820	Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	135	3	52651351	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=119;VD=2;AF=0.0168;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.21851;SOR=inf;LSEQ=CTTCTATCATTCCCTCTTCA;RSEQ=CAGCATATTTGTCATTGCGG;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|18/32||NM_001350074.2:c.1853G>A|NP_001337003.1:p.Gly618Asp|2237|1853|618|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|15/30||NM_001350075.2:c.1745G>A|NP_001337004.1:p.Gly582Asp|1925|1745|582|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|18/32||NM_001350076.2:c.1853G>A|NP_001337005.1:p.Gly618Asp|2238|1853|618|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|19/33||NM_001350077.2:c.1844G>A|NP_001337006.1:p.Gly615Asp|2287|1844|615|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|18/32||NM_001350078.2:c.1853G>A|NP_001337007.1:p.Gly618Asp|2238|1853|618|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|17/31||NM_001350079.2:c.1808G>A|NP_001337008.1:p.Gly603Asp|2193|1808|603|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|17/31||NM_001366070.2:c.1853G>A|NP_001352999.1:p.Gly618Asp|2096|1853|618|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|16/31||NM_001366071.2:c.1808G>A|NP_001353000.1:p.Gly603Asp|2051|1808|603|G/D|gGt/gAt|||-1||EntrezGene||YES||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|16/30||NM_001366072.2:c.1808G>A|NP_001353001.1:p.Gly603Asp|2051|1808|603|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|16/30||NM_001366073.2:c.1799G>A|NP_001353002.1:p.Gly600Asp|2042|1799|600|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|17/31||NM_001366074.2:c.1796G>A|NP_001353003.1:p.Gly599Asp|2181|1796|599|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|17/31||NM_001366075.2:c.1853G>A|NP_001353004.1:p.Gly618Asp|2096|1853|618|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|16/30||NM_001366076.2:c.1748G>A|NP_001353005.1:p.Gly583Asp|1991|1748|583|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|15/30||NM_018313.5:c.1745G>A|NP_060783.3:p.Gly582Asp|1922|1745|582|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|16/30||NM_181042.5:c.1745G>A|NP_851385.1:p.Gly582Asp|2064|1745|582|G/D|gGt/gAt|||-1||EntrezGene||||||3:g.52651351C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:119:2:1,1:59,58:117,2:0.0168:2,2:50.5:1:37:0:1:1.0171:60:4:0.0168:0:1	0/0:135:0:0,0:77,58:135,0:0:2,0:37.6:1:36.6:1:1:0:60:270:1:0:0.1
    1173. 

  1173. 3	52658902	52658902	G	T	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	196	3	52658902	.	G	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.57197;SOR=0;LSEQ=GAATGTTTATGCATAAAAAA;RSEQ=GACTGCACACCTGGATAGCC;CSQ=T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||17/31|NM_001350074.2:c.1649+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||14/29|NM_001350075.2:c.1541+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||17/31|NM_001350076.2:c.1649+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||18/32|NM_001350077.2:c.1640+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||17/31|NM_001350078.2:c.1649+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||16/30|NM_001350079.2:c.1604+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||16/30|NM_001366070.2:c.1649+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||15/30|NM_001366071.2:c.1604+2387C>A|||||||||-1||EntrezGene||YES||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||15/29|NM_001366072.2:c.1604+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||15/29|NM_001366073.2:c.1595+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||16/30|NM_001366074.2:c.1592+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||16/30|NM_001366075.2:c.1649+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||15/29|NM_001366076.2:c.1544+11C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||14/29|NM_018313.5:c.1541+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||15/29|NM_181042.5:c.1541+2387C>A|||||||||-1||EntrezGene||||||3:g.52658902G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:63:0:0,0:37,26:63,0:0:2,0:30.8:1:36.2:1:1:0:60:62:1:0:0.2	0/1:196:2:1,1:119,75:194,2:0.0102:2,2:8:1:31:1:1:1.58275:60:4:0.0104:0:1
    1174. 

  1174. 3	52658903	52658903	G	T	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	201	3	52658903	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=63;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.57898;SOR=0;LSEQ=AATGTTTATGCATAAAAAAG;RSEQ=ACTGCACACCTGGATAGCCT;CSQ=T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||17/31|NM_001350074.2:c.1649+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||14/29|NM_001350075.2:c.1541+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||17/31|NM_001350076.2:c.1649+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||18/32|NM_001350077.2:c.1640+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||17/31|NM_001350078.2:c.1649+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||16/30|NM_001350079.2:c.1604+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||16/30|NM_001366070.2:c.1649+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||15/30|NM_001366071.2:c.1604+2386C>A|||||||||-1||EntrezGene||YES||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||15/29|NM_001366072.2:c.1604+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||15/29|NM_001366073.2:c.1595+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||16/30|NM_001366074.2:c.1592+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||16/30|NM_001366075.2:c.1649+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||15/29|NM_001366076.2:c.1544+10C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||14/29|NM_018313.5:c.1541+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||,T|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||15/29|NM_181042.5:c.1541+2386C>A|||||||||-1||EntrezGene||||||3:g.52658903G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:63:0:0,0:37,26:63,0:0:2,0:31.2:1:34.6:1:1:0:60:14.75:1:0:0.2	0/1:201:2:1,1:120,79:199,2:0.01:2,2:24:1:37:0:1:1.5157:60:4:0.0102:0:1
    1175. 

  1175. 3	52658960	52658960	G	A	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	216	3	52658960	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=67;VD=2;AF=0.0299;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.05541;SOR=inf;LSEQ=TCACTGTCATGAGTGTTCCT;RSEQ=GGAAAGCAGAAACAAACATT;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||16/31|NM_001350074.2:c.1605-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||14/29|NM_001350075.2:c.1541+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||16/31|NM_001350076.2:c.1605-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||17/32|NM_001350077.2:c.1596-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||16/31|NM_001350078.2:c.1605-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||16/30|NM_001350079.2:c.1604+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||15/30|NM_001366070.2:c.1605-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||15/30|NM_001366071.2:c.1604+2329C>T|||||||||-1||EntrezGene||YES||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||15/29|NM_001366072.2:c.1604+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||15/29|NM_001366073.2:c.1595+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||16/30|NM_001366074.2:c.1592+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||15/30|NM_001366075.2:c.1605-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||14/29|NM_001366076.2:c.1500-3C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||14/29|NM_018313.5:c.1541+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||15/29|NM_181042.5:c.1541+2329C>T|||||||||-1||EntrezGene||||||3:g.52658960G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:67:2:1,1:31,34:65,2:0.0299:2,2:63:1:37:0:1:1.1:60:4:0.0303:0:1	0/0:216:0:0,0:95,120:215,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1176. 

  1176. 3	52661302	52661302	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon14:c.G1528A:p.A510T,PBRM1:NM_018313:exon14:c.G1528A:p.A510T,PBRM1:NM_181042:exon15:c.G1528A:p.A510T,PBRM1:NM_001350074:exon16:c.G1591A:p.A531T,PBRM1:NM_001350076:exon16:c.G1591A:p.A531T,PBRM1:NM_001350078:exon16:c.G1591A:p.A531T,PBRM1:NM_001350079:exon16:c.G1591A:p.A531T,PBRM1:NM_001350077:exon17:c.G1582A:p.A528T	.	.	.	.	.	.	.	.	.	.	.	0.669	0.071	T	0.001	0.067	B	0.002	0.080	B	0.000	0.629	D	0.999	0.453	D	-0.55	0.024	N	2.2	0.344	T	0.21	0.116	N	0.088	0.238	-1.023	0.228	T	0.038	0.164	T	0.004	0.093	T	4.794	0.643	24.7	0.985	0.416	0.850	0.438	D	c	-0.246	0.040	0.726	0.230	0.707	0.730	0	5.93	0.959	2.831	0.476	0.935	0.490	1.000	0.715	1.000	0.888	13.263	0.594	Bromodomain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	74	256	3	52661302	.	C	T	74	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=94;VD=4;AF=0.0426;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04678;SOR=5.61087;LSEQ=TATATACCTTTTTCTTTTGG;RSEQ=ACTACCAGTATCAGAGGTGG;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|16/32||NM_001350074.2:c.1591G>A|NP_001337003.1:p.Ala531Thr|1975|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|14/30||NM_001350075.2:c.1528G>A|NP_001337004.1:p.Ala510Thr|1708|1528|510|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|16/32||NM_001350076.2:c.1591G>A|NP_001337005.1:p.Ala531Thr|1976|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|17/33||NM_001350077.2:c.1582G>A|NP_001337006.1:p.Ala528Thr|2025|1582|528|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|16/32||NM_001350078.2:c.1591G>A|NP_001337007.1:p.Ala531Thr|1976|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|16/31||NM_001350079.2:c.1591G>A|NP_001337008.1:p.Ala531Thr|1976|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|15/31||NM_001366070.2:c.1591G>A|NP_001352999.1:p.Ala531Thr|1834|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|15/31||NM_001366071.2:c.1591G>A|NP_001353000.1:p.Ala531Thr|1834|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||YES||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|15/30||NM_001366072.2:c.1591G>A|NP_001353001.1:p.Ala531Thr|1834|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|15/30||NM_001366073.2:c.1582G>A|NP_001353002.1:p.Ala528Thr|1825|1582|528|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|16/31||NM_001366074.2:c.1579G>A|NP_001353003.1:p.Ala527Thr|1964|1579|527|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|15/31||NM_001366075.2:c.1591G>A|NP_001353004.1:p.Ala531Thr|1834|1591|531|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|14/30||NM_001366076.2:c.1486G>A|NP_001353005.1:p.Ala496Thr|1729|1486|496|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|14/30||NM_018313.5:c.1528G>A|NP_060783.3:p.Ala510Thr|1705|1528|510|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|15/30||NM_181042.5:c.1528G>A|NP_851385.1:p.Ala510Thr|1847|1528|510|A/T|Gcc/Acc|COSV56305877||-1||EntrezGene||||||3:g.52661302C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:94:4:3,1:52,38:90,4:0.0426:2,2:20.5:1:37:0:0.63916:2.18:60:8:0.043:0:1	0/0:256:2:1,1:137,117:254,2:0.0078:2,2:20:1:37:0:1:1.17021:60:4:0.0081:0:1
    1177. 

  1177. 3	52668729	52668729	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon12:c.G1190A:p.R397Q,PBRM1:NM_018313:exon12:c.G1190A:p.R397Q,PBRM1:NM_181042:exon13:c.G1190A:p.R397Q,PBRM1:NM_001350074:exon14:c.G1253A:p.R418Q,PBRM1:NM_001350076:exon14:c.G1253A:p.R418Q,PBRM1:NM_001350078:exon14:c.G1253A:p.R418Q,PBRM1:NM_001350079:exon14:c.G1253A:p.R418Q,PBRM1:NM_001350077:exon15:c.G1244A:p.R415Q	0.0001	.	.	.	.	.	.	.	.	rs759670972	.	0.249	0.200	T	0.835	0.899	P	0.605	0.807	P	0.000	0.843	D	1.000	0.530	D	1.49	0.374	L	2.16	0.192	T	-1.22	0.437	N	0.791	0.781	-1.115	0.027	T	0.121	0.421	T	0.018	0.398	T	4.337	0.581	24.0	0.999	0.988	0.984	0.826	D	c	0.675	0.707	1.000	0.747	0.707	0.730	0	5.68	0.880	7.568	0.814	0.892	0.403	1.000	0.715	1.000	0.888	19.791	0.964	Bromodomain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	241	3	52668729	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=101;VD=2;AF=0.0198;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0866;SOR=inf;LSEQ=TTAGCTGCCCTTGGTTATTC;RSEQ=GACAACTCCTAACTGTGTCA;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|14/32||NM_001350074.2:c.1253G>A|NP_001337003.1:p.Arg418Gln|1637|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|12/30||NM_001350075.2:c.1190G>A|NP_001337004.1:p.Arg397Gln|1370|1190|397|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|14/32||NM_001350076.2:c.1253G>A|NP_001337005.1:p.Arg418Gln|1638|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|15/33||NM_001350077.2:c.1244G>A|NP_001337006.1:p.Arg415Gln|1687|1244|415|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|14/32||NM_001350078.2:c.1253G>A|NP_001337007.1:p.Arg418Gln|1638|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|14/31||NM_001350079.2:c.1253G>A|NP_001337008.1:p.Arg418Gln|1638|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|13/31||NM_001366070.2:c.1253G>A|NP_001352999.1:p.Arg418Gln|1496|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|13/31||NM_001366071.2:c.1253G>A|NP_001353000.1:p.Arg418Gln|1496|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||YES||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|13/30||NM_001366072.2:c.1253G>A|NP_001353001.1:p.Arg418Gln|1496|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|13/30||NM_001366073.2:c.1244G>A|NP_001353002.1:p.Arg415Gln|1487|1244|415|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|14/31||NM_001366074.2:c.1241G>A|NP_001353003.1:p.Arg414Gln|1626|1241|414|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|13/31||NM_001366075.2:c.1253G>A|NP_001353004.1:p.Arg418Gln|1496|1253|418|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|12/30||NM_001366076.2:c.1148G>A|NP_001353005.1:p.Arg383Gln|1391|1148|383|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|12/30||NM_018313.5:c.1190G>A|NP_060783.3:p.Arg397Gln|1367|1190|397|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|13/30||NM_181042.5:c.1190G>A|NP_851385.1:p.Arg397Gln|1509|1190|397|R/Q|cGg/cAg|rs759670972||-1||EntrezGene||||||3:g.52668729C>T|7.962e-06|0|0|0|0|0|8.811e-06|0|3.267e-05|3.267e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:101:2:1,1:53,46:99,2:0.0198:2,2:46:0:37:0:1:1.15055:60:4:0.0204:0:1	0/0:241:0:0,0:131,110:241,0:0:2,0:35.4:1:35.5:1:1:0:60:39.167:1:0:0.1
    1178. 

  1178. 3	52676024	52676024	T	C	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon11:c.A1033G:p.I345V,PBRM1:NM_018313:exon11:c.A1033G:p.I345V,PBRM1:NM_181042:exon12:c.A1033G:p.I345V,PBRM1:NM_001350074:exon13:c.A1096G:p.I366V,PBRM1:NM_001350076:exon13:c.A1096G:p.I366V,PBRM1:NM_001350078:exon13:c.A1096G:p.I366V,PBRM1:NM_001350079:exon13:c.A1096G:p.I366V,PBRM1:NM_001350077:exon14:c.A1087G:p.I363V	0.	.	.	.	.	.	.	.	.	rs761199482	.	0.355	0.121	T	0.049	0.568	B	0.028	0.551	B	0.000	0.843	D	0.997	0.435	D	0.995	0.252	L	1.43	0.334	T	-0.11	0.105	N	0.162	0.207	-1.104	0.036	T	0.075	0.301	T	0.005	0.133	T	1.028	0.193	10.82	0.987	0.450	0.924	0.553	D	c	-0.137	0.078	0.963	0.286	0.707	0.730	0	5.71	0.890	4.476	0.597	1.056	0.757	1.000	0.715	1.000	0.888	15.989	0.799	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	131	3	52676024	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=116;VD=2;AF=0.0172;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.21955;SOR=inf;LSEQ=ATATTGAAGTGCCATTGTAA;RSEQ=TGCTGATAAACGACCTCCTT;CSQ=C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|13/32||NM_001350074.2:c.1096A>G|NP_001337003.1:p.Ile366Val|1480|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|11/30||NM_001350075.2:c.1033A>G|NP_001337004.1:p.Ile345Val|1213|1033|345|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|13/32||NM_001350076.2:c.1096A>G|NP_001337005.1:p.Ile366Val|1481|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|14/33||NM_001350077.2:c.1087A>G|NP_001337006.1:p.Ile363Val|1530|1087|363|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|13/32||NM_001350078.2:c.1096A>G|NP_001337007.1:p.Ile366Val|1481|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|13/31||NM_001350079.2:c.1096A>G|NP_001337008.1:p.Ile366Val|1481|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|12/31||NM_001366070.2:c.1096A>G|NP_001352999.1:p.Ile366Val|1339|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|12/31||NM_001366071.2:c.1096A>G|NP_001353000.1:p.Ile366Val|1339|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||YES||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|12/30||NM_001366072.2:c.1096A>G|NP_001353001.1:p.Ile366Val|1339|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|12/30||NM_001366073.2:c.1087A>G|NP_001353002.1:p.Ile363Val|1330|1087|363|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|13/31||NM_001366074.2:c.1084A>G|NP_001353003.1:p.Ile362Val|1469|1084|362|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|12/31||NM_001366075.2:c.1096A>G|NP_001353004.1:p.Ile366Val|1339|1096|366|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|11/30||NM_001366076.2:c.991A>G|NP_001353005.1:p.Ile331Val|1234|991|331|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|11/30||NM_018313.5:c.1033A>G|NP_060783.3:p.Ile345Val|1210|1033|345|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||,C|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|12/30||NM_181042.5:c.1033A>G|NP_851385.1:p.Ile345Val|1352|1033|345|I/V|Att/Gtt|rs761199482||-1||EntrezGene||||||3:g.52676024T>C|3.98e-06|0|0|0|0|0|8.804e-06|0|0|8.804e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:116:2:1,1:37,77:114,2:0.0172:2,2:55:0:37:0:0.54978:2.07:60:4:0.0179:0:2.5	0/0:131:0:0,0:66,65:131,0:0:2,0:38.6:1:36:1:1:0:60:262:1:0:0.6
    1179. 

  1179. 3	52676027	52676027	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon11:c.G1030A:p.A344T,PBRM1:NM_018313:exon11:c.G1030A:p.A344T,PBRM1:NM_181042:exon12:c.G1030A:p.A344T,PBRM1:NM_001350074:exon13:c.G1093A:p.A365T,PBRM1:NM_001350076:exon13:c.G1093A:p.A365T,PBRM1:NM_001350078:exon13:c.G1093A:p.A365T,PBRM1:NM_001350079:exon13:c.G1093A:p.A365T,PBRM1:NM_001350077:exon14:c.G1084A:p.A362T	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	0.976	0.564	D	0.6	0.497	P	0.000	0.843	D	1.000	0.486	D	1.75	0.456	L	1.17	0.379	T	-2.67	0.571	D	0.277	0.364	-1.111	0.030	T	0.100	0.373	T	0.009	0.241	T	5.638	0.768	26.6	0.998	0.874	0.946	0.613	D	c	0.329	0.441	0.920	0.266	0.707	0.730	0	5.71	0.890	4.221	0.581	0.931	0.441	1.000	0.715	0.998	0.697	19.863	0.968	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	132	3	52676027	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=115;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.28459;SOR=0;LSEQ=TTGAAGTGCCATTGTAATTG;RSEQ=TGATAAACGACCTCCTTGTA;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|13/32||NM_001350074.2:c.1093G>A|NP_001337003.1:p.Ala365Thr|1477|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|11/30||NM_001350075.2:c.1030G>A|NP_001337004.1:p.Ala344Thr|1210|1030|344|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|13/32||NM_001350076.2:c.1093G>A|NP_001337005.1:p.Ala365Thr|1478|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|14/33||NM_001350077.2:c.1084G>A|NP_001337006.1:p.Ala362Thr|1527|1084|362|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|13/32||NM_001350078.2:c.1093G>A|NP_001337007.1:p.Ala365Thr|1478|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|13/31||NM_001350079.2:c.1093G>A|NP_001337008.1:p.Ala365Thr|1478|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|12/31||NM_001366070.2:c.1093G>A|NP_001352999.1:p.Ala365Thr|1336|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|12/31||NM_001366071.2:c.1093G>A|NP_001353000.1:p.Ala365Thr|1336|1093|365|A/T|Gca/Aca|||-1||EntrezGene||YES||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|12/30||NM_001366072.2:c.1093G>A|NP_001353001.1:p.Ala365Thr|1336|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|12/30||NM_001366073.2:c.1084G>A|NP_001353002.1:p.Ala362Thr|1327|1084|362|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|13/31||NM_001366074.2:c.1081G>A|NP_001353003.1:p.Ala361Thr|1466|1081|361|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|12/31||NM_001366075.2:c.1093G>A|NP_001353004.1:p.Ala365Thr|1336|1093|365|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|11/30||NM_001366076.2:c.988G>A|NP_001353005.1:p.Ala330Thr|1231|988|330|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|11/30||NM_018313.5:c.1030G>A|NP_060783.3:p.Ala344Thr|1207|1030|344|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|12/30||NM_181042.5:c.1030G>A|NP_851385.1:p.Ala344Thr|1349|1030|344|A/T|Gca/Aca|||-1||EntrezGene||||||3:g.52676027C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:115:0:0,0:38,77:115,0:0:2,0:36.7:1:34.2:1:1:0:60:15.429:1:0:0.9	0/1:132:2:1,1:65,65:130,2:0.0152:2,2:29.5:1:37:0:1:1:60:4:0.0163:0:1
    1180. 

  1180. 3	52676065	52676065	C	T	intronic	PBRM1	.	.	.	0.44	0.4080	0.2370	0.5062	0.4847	0.4590	0.4737	0.4721	0.4524	rs11719685	rs11719685	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56260926;OCCURENCE=1(breast),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(kidney)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11667377	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.75	201	107	3	52676065	.	C	T	201	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=62;VD=58;AF=0.9355;SHIFT3=0;MSI=13;MSILEN=1;SSF=0;SOR=26.8798;LSEQ=GTACTGCTCTTTTATTACTA;RSEQ=AAAAAAAAAAAAAGCAATTA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||12/31|NM_001350074.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||10/29|NM_001350075.2:c.996-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||12/31|NM_001350076.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||13/32|NM_001350077.2:c.1050-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||12/31|NM_001350078.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||12/30|NM_001350079.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||11/30|NM_001366070.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||11/30|NM_001366071.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||YES||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||11/29|NM_001366072.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||11/29|NM_001366073.2:c.1050-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||12/30|NM_001366074.2:c.1047-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||11/30|NM_001366075.2:c.1059-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||10/29|NM_001366076.2:c.954-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding||10/29|NM_018313.5:c.996-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1,T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding||11/29|NM_181042.5:c.996-4G>A|||||||rs11719685&COSV56259504&COSV56260926||-1||EntrezGene||||||3:g.52676065C>T|0.3421|0.1986|0.4081|0.3765|0.3635|0.3691|0.3554|0.343|0.2353|0.4395|AMR||0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:62:58:20,38:0,0:0,58:0.9355:0,2:25.8:1:34.4:1:1:0:60:18.333:0.9649:0:1.3	0/1:107:37:14,23:22,22:44,37:0.3458:2,2:39.6:1:34:1:0.36962:1.63271:60:17.5:0.3977:0:1.2
    1181. 

  1181. 3	52682428	52682428	C	T	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon8:c.G745A:p.A249T,PBRM1:NM_018313:exon8:c.G745A:p.A249T,PBRM1:NM_181042:exon9:c.G745A:p.A249T,PBRM1:NM_001350074:exon10:c.G808A:p.A270T,PBRM1:NM_001350076:exon10:c.G808A:p.A270T,PBRM1:NM_001350078:exon10:c.G808A:p.A270T,PBRM1:NM_001350079:exon10:c.G808A:p.A270T,PBRM1:NM_001350077:exon11:c.G799A:p.A267T	.	.	.	.	.	.	.	.	.	.	.	0.135	0.329	T	0.002	0.194	B	0.015	0.247	B	0.000	0.843	D	0.999	0.467	D	1.095	0.275	L	1.58	0.291	T	-1.15	0.354	N	0.221	0.315	-1.078	0.078	T	0.076	0.306	T	0.010	0.252	T	5.082	0.685	25.3	0.999	0.938	0.937	0.588	D	c	-0.044	0.114	0.970	0.291	0.732	0.924	0	4.8	0.610	4.503	0.599	0.935	0.490	1.000	0.715	1.000	0.888	10.631	0.445	Bromodomain|Bromodomain, conserved site	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	31	164	3	52682428	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=19;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.80262;SOR=0;LSEQ=GAGGAGATCTATATCTTTGG;RSEQ=CATTGCATGAATACTTTTGT;CSQ=T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|10/32||NM_001350074.2:c.808G>A|NP_001337003.1:p.Ala270Thr|1192|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|8/30||NM_001350075.2:c.745G>A|NP_001337004.1:p.Ala249Thr|925|745|249|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|10/32||NM_001350076.2:c.808G>A|NP_001337005.1:p.Ala270Thr|1193|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|11/33||NM_001350077.2:c.799G>A|NP_001337006.1:p.Ala267Thr|1242|799|267|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|10/32||NM_001350078.2:c.808G>A|NP_001337007.1:p.Ala270Thr|1193|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|10/31||NM_001350079.2:c.808G>A|NP_001337008.1:p.Ala270Thr|1193|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|9/31||NM_001366070.2:c.808G>A|NP_001352999.1:p.Ala270Thr|1051|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|9/31||NM_001366071.2:c.808G>A|NP_001353000.1:p.Ala270Thr|1051|808|270|A/T|Gcc/Acc|||-1||EntrezGene||YES||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|9/30||NM_001366072.2:c.808G>A|NP_001353001.1:p.Ala270Thr|1051|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|9/30||NM_001366073.2:c.799G>A|NP_001353002.1:p.Ala267Thr|1042|799|267|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|10/31||NM_001366074.2:c.796G>A|NP_001353003.1:p.Ala266Thr|1181|796|266|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|9/31||NM_001366075.2:c.808G>A|NP_001353004.1:p.Ala270Thr|1051|808|270|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|9/30||NM_001366076.2:c.799G>A|NP_001353005.1:p.Ala267Thr|1042|799|267|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|8/30||NM_018313.5:c.745G>A|NP_060783.3:p.Ala249Thr|922|745|249|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||,T|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|9/30||NM_181042.5:c.745G>A|NP_851385.1:p.Ala249Thr|1064|745|249|A/T|Gcc/Acc|||-1||EntrezGene||||||3:g.52682428C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:19:0:0,0:9,10:19,0:0:2,0:39.6:1:37:0:1:0:60:38:1:0:0.1	0/1:164:2:1,1:74,88:162,2:0.0122:2,2:22:1:31:1:1:1.19:60:4:0.0122:0:1
    1182. 

  1182. 3	52685840	52685840	A	C	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	171	3	52685840	.	A	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=32;VD=0;AF=0;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.70892;SOR=0;LSEQ=GATATTGCTGGAAGACAAAA;RSEQ=ACCAGGCATGCTCAATAAGT;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||8/31|NM_001350074.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||6/29|NM_001350075.2:c.646-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||8/31|NM_001350076.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||9/32|NM_001350077.2:c.700-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||8/31|NM_001350078.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||8/30|NM_001350079.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||7/30|NM_001366070.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||7/30|NM_001366071.2:c.709-14T>G|||||||||-1||EntrezGene||YES||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||7/29|NM_001366072.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||7/29|NM_001366073.2:c.700-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||8/30|NM_001366074.2:c.697-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||7/30|NM_001366075.2:c.709-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||7/29|NM_001366076.2:c.700-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding||6/29|NM_018313.5:c.646-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding||7/29|NM_181042.5:c.646-14T>G|||||||||-1||EntrezGene||||||3:g.52685840A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:32:0:0,0:16,16:32,0:0:2,0:38.3:1:34.6:1:1:0:60:15:1:0:0.1	0/1:171:2:1,1:77,92:169,2:0.0117:2,2:37.5:1:37:0:1:1.19:60:4:0.0118:0:1
    1183. 

  1183. 3	52692252	52692252	A	G	exonic	PBRM1	.	nonsynonymous SNV	PBRM1:NM_001350075:exon6:c.T608C:p.L203P,PBRM1:NM_018313:exon6:c.T608C:p.L203P,PBRM1:NM_181042:exon7:c.T608C:p.L203P,PBRM1:NM_001350074:exon8:c.T671C:p.L224P,PBRM1:NM_001350076:exon8:c.T671C:p.L224P,PBRM1:NM_001350078:exon8:c.T671C:p.L224P,PBRM1:NM_001350079:exon8:c.T671C:p.L224P,PBRM1:NM_001350077:exon9:c.T662C:p.L221P	.	.	.	.	.	.	.	.	.	.	.	0.328	0.178	T	0.998	0.715	D	0.956	0.850	D	0.000	0.843	D	1	0.810	D	-0.28	0.037	N	1.7	0.269	T	-2.69	0.598	D	0.514	0.853	-1.062	0.113	T	0.104	0.383	T	0.038	0.580	D	4.978	0.670	25.1	0.999	0.934	0.990	0.897	D	c	0.593	0.623	1.000	0.517	0.707	0.730	0	5.21	0.719	8.947	0.927	1.088	0.866	1.000	0.715	0.989	0.536	15.148	0.722	Bromodomain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	175	3	52692252	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.2946;SOR=0;LSEQ=TCTGAAAAAGTTCGCTAATG;RSEQ=GACGTCCTGATGGATTTGTA;CSQ=G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350074.2|protein_coding|8/32||NM_001350074.2:c.671T>C|NP_001337003.1:p.Leu224Pro|1055|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350075.2|protein_coding|6/30||NM_001350075.2:c.608T>C|NP_001337004.1:p.Leu203Pro|788|608|203|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350076.2|protein_coding|8/32||NM_001350076.2:c.671T>C|NP_001337005.1:p.Leu224Pro|1056|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350077.2|protein_coding|9/33||NM_001350077.2:c.662T>C|NP_001337006.1:p.Leu221Pro|1105|662|221|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350078.2|protein_coding|8/32||NM_001350078.2:c.671T>C|NP_001337007.1:p.Leu224Pro|1056|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001350079.2|protein_coding|8/31||NM_001350079.2:c.671T>C|NP_001337008.1:p.Leu224Pro|1056|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366070.2|protein_coding|7/31||NM_001366070.2:c.671T>C|NP_001352999.1:p.Leu224Pro|914|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366071.2|protein_coding|7/31||NM_001366071.2:c.671T>C|NP_001353000.1:p.Leu224Pro|914|671|224|L/P|cTc/cCc|||-1||EntrezGene||YES||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366072.2|protein_coding|7/30||NM_001366072.2:c.671T>C|NP_001353001.1:p.Leu224Pro|914|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366073.2|protein_coding|7/30||NM_001366073.2:c.662T>C|NP_001353002.1:p.Leu221Pro|905|662|221|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366074.2|protein_coding|8/31||NM_001366074.2:c.659T>C|NP_001353003.1:p.Leu220Pro|1044|659|220|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366075.2|protein_coding|7/31||NM_001366075.2:c.671T>C|NP_001353004.1:p.Leu224Pro|914|671|224|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_001366076.2|protein_coding|7/30||NM_001366076.2:c.662T>C|NP_001353005.1:p.Leu221Pro|905|662|221|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_018313.5|protein_coding|6/30||NM_018313.5:c.608T>C|NP_060783.3:p.Leu203Pro|785|608|203|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||,G|missense_variant|MODERATE|PBRM1|55193|Transcript|NM_181042.5|protein_coding|7/30||NM_181042.5:c.608T>C|NP_851385.1:p.Leu203Pro|927|608|203|L/P|cTc/cCc|||-1||EntrezGene||||||3:g.52692252A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:147:0:0,0:70,77:147,0:0:2,0:43.5:1:36.5:1:1:0:60:294:1:0:0.2	0/1:175:2:1,1:103,70:173,2:0.0114:2,2:64:0:37:0:1:1.46807:60:4:0.0118:0:1
    1184. 

  1184. 3	52696310	52696310	-	A	intronic	PBRM1	.	.	.	0.13	0.0011	0.0005	0.005	0	0	0.0118	0.0007	0	rs781206124	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112262819	BTCA-SG|2|71|0.028169	0.5	102	78	3	52696310	.	G	GA	102	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=138;VD=6;AF=0.0435;SHIFT3=11;MSI=12;MSILEN=1;SSF=0.39867;SOR=1.72327;LSEQ=TGGCTGTATGTTAGCAAAGA;RSEQ=AAAAAAAAAAACACTTTAGT;CSQ=A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||6/31|NM_001350074.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||4/29|NM_001350075.2:c.385-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||6/31|NM_001350076.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||7/32|NM_001350077.2:c.439-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||6/31|NM_001350078.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||6/30|NM_001350079.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||5/30|NM_001366070.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||5/30|NM_001366071.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||YES||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||5/29|NM_001366072.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||5/29|NM_001366073.2:c.439-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||6/30|NM_001366074.2:c.436-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||5/30|NM_001366075.2:c.448-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||5/29|NM_001366076.2:c.439-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||4/29|NM_018313.5:c.385-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||5/29|NM_181042.5:c.385-19dup|||||||rs758227657||-1||EntrezGene||||||3:g.52696321dup|0.109|0.08368|0.1511|0.1566|0.1272|0.09876|0.09126|0.1264|0.1509|0.1566|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:138:6:1,5:26,77:103,6:0.0435:2,2:32:1:39.5:0:1:1.68125:64:12:0.069:0:1.4	0/1:78:2:1,1:26,42:68,2:0.0256:2,2:42.1:1:39.5:0:1:1.6:64:4:0.0377:0:1.1
    1185. 

  1185. 3	52712512	52712512	T	C	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	199	3	52712512	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1160;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02135;SOR=0;LSEQ=TGTACTGATGTGCTTCGAAC;RSEQ=CACCTTCGCTTTGGTGCCCT;CSQ=C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||5/31|NM_001350074.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||3/29|NM_001350075.2:c.236+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||5/31|NM_001350076.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||6/32|NM_001350077.2:c.290+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||5/31|NM_001350078.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||5/30|NM_001350079.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||4/30|NM_001366070.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||4/30|NM_001366071.2:c.299+4A>G|||||||||-1||EntrezGene||YES||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||4/29|NM_001366072.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||4/29|NM_001366073.2:c.290+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||5/30|NM_001366074.2:c.287+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||4/30|NM_001366075.2:c.299+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||4/29|NM_001366076.2:c.290+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_018313.5|protein_coding||3/29|NM_018313.5:c.236+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|PBRM1|55193|Transcript|NM_181042.5|protein_coding||4/29|NM_181042.5:c.236+4A>G|||||||||-1||EntrezGene||||||3:g.52712512T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1160:0:0,0:588,572:1160,0:0:2,0:41.1:1:36.5:1:1:0:60:95.667:1:0:0.1	0/1:199:2:1,1:105,92:197,2:0.0101:2,2:33:0:37:0:1:1.14054:60:4:0.0102:0:1
    1186. 

  1186. 3	52713775	52713775	T	A	intronic	PBRM1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	68	3	52713775	.	T	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=41;VD=2;AF=0.0488;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.13931;SOR=inf;LSEQ=ATCAGCCATGTTCTTACATT;RSEQ=AAATAGACTCTGTCACCAAG;CSQ=A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350074.2|protein_coding||3/31|NM_001350074.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350075.2|protein_coding||1/29|NM_001350075.2:c.-15-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350076.2|protein_coding||3/31|NM_001350076.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350077.2|protein_coding||4/32|NM_001350077.2:c.40-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350078.2|protein_coding||3/31|NM_001350078.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001350079.2|protein_coding||3/30|NM_001350079.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366070.2|protein_coding||2/30|NM_001366070.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366071.2|protein_coding||2/30|NM_001366071.2:c.49-33A>T|||||||||-1||EntrezGene||YES||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366072.2|protein_coding||2/29|NM_001366072.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366073.2|protein_coding||2/29|NM_001366073.2:c.40-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366074.2|protein_coding||3/30|NM_001366074.2:c.40-36A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366075.2|protein_coding||2/30|NM_001366075.2:c.49-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_001366076.2|protein_coding||2/29|NM_001366076.2:c.40-33A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_018313.5|protein_coding||1/29|NM_018313.5:c.-12-36A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||,A|intron_variant|MODIFIER|PBRM1|55193|Transcript|NM_181042.5|protein_coding||2/29|NM_181042.5:c.-12-36A>T|||||||||-1||EntrezGene||||||3:g.52713775T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:41:2:1,1:11,28:39,2:0.0488:2,2:5:0:37:0:0.50488:2.48:60:4:0.0488:0:2	0/0:68:0:0,0:16,52:68,0:0:2,0:40.3:1:36.4:1:1:0:60:67:1:0:0.2
    1187. 

  1187. 3	69812920	69812920	G	T	intronic	MITF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	115	3	69812920	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=176;VD=2;AF=0.0114;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.36497;SOR=inf;LSEQ=TGTCCTCTCCTTTTGCTTCT;RSEQ=ACCTAAGTAAAAGCTAATGG;CSQ=T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||1/9|NM_001184967.2:c.-53+77G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||1/9|NM_001354604.2:c.104+24068G>T|||||||||1||EntrezGene||YES||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||1/9|NM_001354605.2:c.104+24068G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||1/9|NM_001354606.2:c.104+24068G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||1/10|NM_001354607.2:c.-77+24068G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||1/10|NM_001354608.2:c.-92+24068G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding|||||||||||42|1||EntrezGene||||||3:g.69812920G>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||1/9|NM_198159.3:c.104+24068G>T|||||||||1||EntrezGene||||||3:g.69812920G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:176:2:1,1:96,78:174,2:0.0114:2,2:20:0:37:0:1:1.2293:60:4:0.0114:0:1	0/0:115:0:0,0:78,37:115,0:0:2,0:38.5:1:36.1:1:1:0:60:56.5:1:0:0
    1188. 

  1188. 3	69813111	69813111	C	A	intronic	MITF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	194	3	69813111	.	C	A	44	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.55394;SOR=0;LSEQ=AAGGTAATACAGATGATAAC;RSEQ=AAAGTACCTCAGTTTACAGG;CSQ=A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||1/9|NM_001184967.2:c.-53+268C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||1/9|NM_001354604.2:c.104+24259C>A|||||||||1||EntrezGene||YES||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||1/9|NM_001354605.2:c.104+24259C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||1/9|NM_001354606.2:c.104+24259C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||1/10|NM_001354607.2:c.-77+24259C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||1/10|NM_001354608.2:c.-92+24259C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding||1/9|NM_006722.3:c.101+18C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||1/9|NM_198159.3:c.104+24259C>A|||||||||1||EntrezGene||||||3:g.69813111C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:12,30:42,0:0:2,0:26.7:1:36.4:1:1:0:60:84:1:0:0	0/1:194:3:2,1:71,120:191,3:0.0155:2,2:6.3:1:28.3:1:0.55767:3.36:60:2:0.0105:0:3.3
    1189. 

  1189. 3	69915458	69915458	T	C	exonic	MITF	.	nonsynonymous SNV	MITF:NM_198177:exon1:c.T17C:p.V6A	.	.	.	.	.	.	.	.	.	.	.	0.164	0.258	T	0.017	0.163	B	0.023	0.188	B	.	.	.	1	0.810	D	.	.	.	2.62	0.253	T	0.29	0.080	N	0.197	0.241	-1.063	0.111	T	0.041	0.175	T	0.008	0.226	T	1.678	0.263	14.28	0.976	0.343	0.886	0.484	D	c	-0.047	0.192	1.000	0.747	0.487	0.133	0	5.93	0.959	5.747	0.681	1.061	0.807	1.000	0.715	1.000	0.888	16.05	0.805	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	175	3	69915458	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=744;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03609;SOR=0;LSEQ=AAAGATGGAGGCGCTTAGAG;RSEQ=TCAGATGTTCATGCCATGCT;CSQ=C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||1/9|NM_001184967.2:c.-52-12827T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||1/9|NM_001354604.2:c.105-12827T>C|||||||||1||EntrezGene||YES||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||1/9|NM_001354605.2:c.105-12830T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||1/9|NM_001354606.2:c.105-12830T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||2/10|NM_001354607.2:c.54-12827T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||2/10|NM_001354608.2:c.-52-12827T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding||1/9|NM_006722.3:c.102-12827T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||1/9|NM_198159.3:c.105-12827T>C|||||||||1||EntrezGene||||||3:g.69915458T>C||||||||||||||,C|missense_variant|MODERATE|MITF|4286|Transcript|NM_198177.3|protein_coding|1/10||NM_198177.3:c.17T>C|NP_937820.1:p.Val6Ala|84|17|6|V/A|gTt/gCt|||1||EntrezGene||||||3:g.69915458T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:744:0:0,0:288,455:743,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:175:2:1,1:82,91:173,2:0.0114:2,2:53.5:1:37:0:1:1.11:60:4:0.0119:0:1
    1190. 

  1190. 3	69985788	69985788	G	A	UTR5	MITF	NM_000248:c.-86G>A;NM_001184968:c.-86G>A;NM_198158:c.-86G>A;NM_198178:c.-86G>A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	93	3	69985788	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.78352;SOR=0;LSEQ=ATAGTACCTTCTCTTTGCCA;RSEQ=TCCATCTTCAAATTGGAATT;CSQ=A|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_000248.4|protein_coding|1/9||NM_000248.4:c.-86G>A||46|||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||2/9|NM_001184967.2:c.199-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_001184968.2|protein_coding|1/3||NM_001184968.2:c.-86G>A||46|||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||2/9|NM_001354604.2:c.355-1185G>A|||||||||1||EntrezGene||YES||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||2/9|NM_001354605.2:c.352-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||2/9|NM_001354606.2:c.352-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||3/10|NM_001354607.2:c.304-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||3/10|NM_001354608.2:c.199-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding||2/9|NM_006722.3:c.352-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_198158.3|protein_coding|1/9||NM_198158.3:c.-86G>A||46|||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||2/9|NM_198159.3:c.355-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198177.3|protein_coding||2/9|NM_198177.3:c.307-1185G>A|||||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_198178.3|protein_coding|1/9||NM_198178.3:c.-86G>A||46|||||||1||EntrezGene||||||3:g.69985788G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:6,6:12,0:0:2,0:32:1:37:0:1:0:60:24:1:0:0	0/1:93:2:1,1:57,34:91,2:0.0215:2,2:66:1:37:0:1:1.66671:60:4:0.022:0:1
    1191. 

  1191. 3	69985857	69985857	C	T	UTR5	MITF	NM_000248:c.-17C>T;NM_001184968:c.-17C>T;NM_198158:c.-17C>T;NM_198178:c.-17C>T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	119	3	69985857	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.82454;SOR=0;LSEQ=CGTCTCTCACTGGATTGGTG;RSEQ=CACCTAAAACATTGTTATGC;CSQ=T|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_000248.4|protein_coding|1/9||NM_000248.4:c.-17C>T||115|||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||2/9|NM_001184967.2:c.199-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_001184968.2|protein_coding|1/3||NM_001184968.2:c.-17C>T||115|||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||2/9|NM_001354604.2:c.355-1116C>T|||||||||1||EntrezGene||YES||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||2/9|NM_001354605.2:c.352-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||2/9|NM_001354606.2:c.352-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||3/10|NM_001354607.2:c.304-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||3/10|NM_001354608.2:c.199-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding||2/9|NM_006722.3:c.352-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_198158.3|protein_coding|1/9||NM_198158.3:c.-17C>T||115|||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||2/9|NM_198159.3:c.355-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198177.3|protein_coding||2/9|NM_198177.3:c.307-1116C>T|||||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||,T|5_prime_UTR_variant|MODIFIER|MITF|4286|Transcript|NM_198178.3|protein_coding|1/9||NM_198178.3:c.-17C>T||115|||||||1||EntrezGene||||||3:g.69985857C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:5,7:12,0:0:2,0:40.6:1:36:1:1:0:60:24:1:0:0	0/1:119:2:1,1:53,64:117,2:0.0168:2,2:30:1:37:0:1:1.21:60:4:0.0172:0:1
    1192. 

  1192. 3	70000964	70000964	G	A	exonic	MITF	.	synonymous SNV	MITF:NM_000248:exon6:c.G561A:p.A187A	0.0023	6.459e-05	0.0002	0	0	0	0	0	0	rs778126895	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58834747;OCCURENCE=1(liver)	748510	Tietz_syndrome|Waardenburg_syndrome_type_2A|not_provided	MONDO:MONDO:0007077,MedGen:C0391816,OMIM:103500,Orphanet:ORPHA42665|MONDO:MONDO:0008671,MedGen:C1860339,OMIM:193510|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	MU85043977	LICA-CN|1|402|0.00248756	0.25	154	244	3	70000964	.	G	A	154	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=18;AF=0.6;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=ACTTCATTCACGTGCACAGC;RSEQ=TGTATTTTTCCCACAGAGTC;CSQ=A|splice_region_variant&synonymous_variant|LOW|MITF|4286|Transcript|NM_000248.4|protein_coding|6/9||NM_000248.4:c.561G>A|NP_000239.1:p.Ala187%3D|692|561|187|A|gcG/gcA|rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001184967.2|protein_coding||6/9|NM_001184967.2:c.725-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_region_variant&synonymous_variant|LOW|MITF|4286|Transcript|NM_001354604.2|protein_coding|7/10||NM_001354604.2:c.882G>A|NP_001341533.1:p.Ala294%3D|1016|882|294|A|gcG/gcA|rs778126895&COSV58834747||1||EntrezGene||YES||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_region_variant&synonymous_variant|LOW|MITF|4286|Transcript|NM_001354605.2|protein_coding|7/10||NM_001354605.2:c.879G>A|NP_001341534.1:p.Ala293%3D|1013|879|293|A|gcG/gcA|rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354606.2|protein_coding||6/9|NM_001354606.2:c.878-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354607.2|protein_coding||7/10|NM_001354607.2:c.830-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354608.2|protein_coding||7/10|NM_001354608.2:c.725-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_006722.3|protein_coding||6/9|NM_006722.3:c.878-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198158.3|protein_coding||5/8|NM_198158.3:c.560-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198159.3|protein_coding||6/9|NM_198159.3:c.881-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198177.3|protein_coding||6/9|NM_198177.3:c.833-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198178.3|protein_coding||5/8|NM_198178.3:c.392-17G>A|||||||rs778126895&COSV58834747||1||EntrezGene||||||3:g.70000964G>A|0.0001915|0.0005539|0.0001449|0|0.001804|0|8.835e-06|0|0|0.001804|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:30:18:10,8:5,6:11,18:0.6:2,2:46.7:1:37:0:0.71038:1.48:60:36:0.6207:0:1	0/0:244:0:0,0:140,104:244,0:0:2,0:39.2:1:36.2:1:1:0:60:80.333:1:0:0.1
    1193. 

  1193. 3	70000990	70000990	C	T	exonic	MITF	.	nonsynonymous SNV	MITF:NM_000248:exon6:c.C587T:p.A196V,MITF:NM_198158:exon6:c.C569T:p.A190V,MITF:NM_198178:exon6:c.C401T:p.A134V,MITF:NM_001184967:exon7:c.C734T:p.A245V,MITF:NM_006722:exon7:c.C887T:p.A296V,MITF:NM_198159:exon7:c.C890T:p.A297V,MITF:NM_198177:exon7:c.C842T:p.A281V	.	.	.	.	.	.	.	.	.	.	.	0.241	0.218	T	0.303	0.309	B	0.085	0.385	B	0.000	0.843	D	1.000	0.588	D	0.95	0.239	L	2.67	0.245	T	-2.0	0.465	N	0.128	0.192	-1.076	0.082	T	0.054	0.230	T	0.022	0.447	T	3.224	0.447	22.7	0.994	0.640	0.909	0.521	D	c	0.023	0.227	1.000	0.747	0.554	0.246	0	5.82	0.927	2.932	0.484	0.935	0.490	0.994	0.380	1.000	0.888	20.104	0.979	MiT/TFE transcription factors, N-terminal	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	262	3	70000990	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=31;VD=2;AF=0.0645;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01087;SOR=inf;LSEQ=TTTTCCCACAGAGTCTGAAG;RSEQ=AAGAGCACTGGCCAAAGAGA;CSQ=T|missense_variant|MODERATE|MITF|4286|Transcript|NM_000248.4|protein_coding|6/9||NM_000248.4:c.587C>T|NP_000239.1:p.Ala196Val|718|587|196|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001184967.2|protein_coding|7/10||NM_001184967.2:c.734C>T|NP_001171896.1:p.Ala245Val|975|734|245|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354604.2|protein_coding|7/10||NM_001354604.2:c.908C>T|NP_001341533.1:p.Ala303Val|1042|908|303|A/V|gCa/gTa|||1||EntrezGene||YES||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354605.2|protein_coding|7/10||NM_001354605.2:c.905C>T|NP_001341534.1:p.Ala302Val|1039|905|302|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354606.2|protein_coding|7/10||NM_001354606.2:c.887C>T|NP_001341535.1:p.Ala296Val|1021|887|296|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354607.2|protein_coding|8/11||NM_001354607.2:c.839C>T|NP_001341536.1:p.Ala280Val|1153|839|280|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354608.2|protein_coding|8/11||NM_001354608.2:c.734C>T|NP_001341537.1:p.Ala245Val|1063|734|245|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_006722.3|protein_coding|7/10||NM_006722.3:c.887C>T|NP_006713.1:p.Ala296Val|918|887|296|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_198158.3|protein_coding|6/9||NM_198158.3:c.569C>T|NP_937801.1:p.Ala190Val|700|569|190|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_198159.3|protein_coding|7/10||NM_198159.3:c.890C>T|NP_937802.1:p.Ala297Val|1024|890|297|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_198177.3|protein_coding|7/10||NM_198177.3:c.842C>T|NP_937820.1:p.Ala281Val|909|842|281|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||,T|missense_variant|MODERATE|MITF|4286|Transcript|NM_198178.3|protein_coding|6/9||NM_198178.3:c.401C>T|NP_937821.2:p.Ala134Val|532|401|134|A/V|gCa/gTa|||1||EntrezGene||||||3:g.70000990C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:31:2:1,1:14,15:29,2:0.0645:2,2:61.5:1:31:1:1:1.07:60:4:0.0645:0:1	0/0:262:0:0,0:130,132:262,0:0:2,0:37.7:1:36:1:1:0:60:51.4:1:0:0.1
    1194. 

  1194. 3	70008384	70008384	A	G	intronic	MITF	.	.	.	0.0005	6.456e-05	0.0002	0	0	0	0	0	0	rs367622311	rs367622311	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	134	3	70008384	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=212;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.1493;SOR=0;LSEQ=TTGAATTTTCATTGAGCCTC;RSEQ=AATCCTAAAAATATCTGTTT;CSQ=G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_000248.4|protein_coding||7/8|NM_000248.4:c.711-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001184967.2|protein_coding||8/9|NM_001184967.2:c.858-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354604.2|protein_coding||8/9|NM_001354604.2:c.1032-40A>G|||||||rs367622311||1||EntrezGene||YES||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354605.2|protein_coding||8/9|NM_001354605.2:c.1029-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354606.2|protein_coding||8/9|NM_001354606.2:c.1011-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354607.2|protein_coding||9/10|NM_001354607.2:c.963-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_001354608.2|protein_coding||9/10|NM_001354608.2:c.858-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_006722.3|protein_coding||8/9|NM_006722.3:c.1011-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198158.3|protein_coding||7/8|NM_198158.3:c.693-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198159.3|protein_coding||8/9|NM_198159.3:c.1014-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198177.3|protein_coding||8/9|NM_198177.3:c.966-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||,G|intron_variant|MODIFIER|MITF|4286|Transcript|NM_198178.3|protein_coding||7/8|NM_198178.3:c.525-40A>G|||||||rs367622311||1||EntrezGene||||||3:g.70008384A>G|1.619e-05|0.0001888|0|0|0|0|9.009e-06|0|0|0.0004539|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:212:0:0,0:173,39:212,0:0:2,0:27.5:1:36.1:1:1:0:60:52:1:0:0.1	0/1:134:2:1,1:97,35:132,2:0.0149:2,2:63:1:37:0:0.46661:2.74672:60:4:0.0152:0:2
    1195. 

  1195. 3	70013987	70013987	T	A	intronic	MITF	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	159	3	70013987	.	T	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=259;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14413;SOR=0;LSEQ=TTTCAGTGTTTTATCTTTAC;RSEQ=CTTATTATAGGAACTTGAAA;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_000248.4|protein_coding||8/8|NM_000248.4:c.859-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001184967.2|protein_coding||9/9|NM_001184967.2:c.1006-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354604.2|protein_coding||9/9|NM_001354604.2:c.1180-11T>A|||||||||1||EntrezGene||YES||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354605.2|protein_coding||9/9|NM_001354605.2:c.1177-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354606.2|protein_coding||9/9|NM_001354606.2:c.1159-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354607.2|protein_coding||10/10|NM_001354607.2:c.1111-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_001354608.2|protein_coding||10/10|NM_001354608.2:c.1006-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_006722.3|protein_coding||9/9|NM_006722.3:c.1159-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198158.3|protein_coding||8/8|NM_198158.3:c.841-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198159.3|protein_coding||9/9|NM_198159.3:c.1162-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198177.3|protein_coding||9/9|NM_198177.3:c.1114-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|MITF|4286|Transcript|NM_198178.3|protein_coding||8/8|NM_198178.3:c.673-11T>A|||||||||1||EntrezGene||||||3:g.70013987T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:259:0:0,0:201,58:259,0:0:2,0:26.3:1:36.2:1:1:0:60:63.75:1:0:0.1	0/1:159:2:1,1:123,34:157,2:0.0126:2,2:37:1:37:0:0.39288:3.57976:60:4:0.0127:0:1
    1196. 

  1196. 3	70014009	70014009	G	A	exonic	MITF	.	nonsynonymous SNV	MITF:NM_000248:exon9:c.G870A:p.M290I,MITF:NM_198158:exon9:c.G852A:p.M284I,MITF:NM_198178:exon9:c.G684A:p.M228I,MITF:NM_001184967:exon10:c.G1017A:p.M339I,MITF:NM_006722:exon10:c.G1170A:p.M390I,MITF:NM_198159:exon10:c.G1173A:p.M391I,MITF:NM_198177:exon10:c.G1125A:p.M375I	.	.	.	.	.	.	.	.	.	.	.	0.602	0.077	T	0.043	0.202	B	0.048	0.328	B	0.000	0.843	N	1	0.810	D	1.165	0.299	L	-0.0	0.626	T	-1.38	0.342	N	0.26	0.320	-0.908	0.472	T	0.182	0.529	T	0.021	0.437	T	2.723	0.388	20.9	0.955	0.265	0.977	0.761	D	c	-0.073	0.123	0.909	0.263	0.554	0.246	0	5.0	0.661	4.544	0.602	1.048	0.713	1.000	0.715	1.000	0.888	15.084	0.717	MiT/TFE transcription factors, C-terminal;Myc-type, basic helix-loop-helix (bHLH) domain	.	.	ID=COSV100096658;OCCURENCE=1(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129750070	UCEC-US|1|531|0.00188324	0.25	37	195	3	70014009	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=502;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.07798;SOR=0;LSEQ=TTATTATAGGAACTTGAAAT;RSEQ=CAGGCTCGAGCTCATGGACT;CSQ=A|missense_variant|MODERATE|MITF|4286|Transcript|NM_000248.4|protein_coding|9/9||NM_000248.4:c.870G>A|NP_000239.1:p.Met290Ile|1001|870|290|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001184967.2|protein_coding|10/10||NM_001184967.2:c.1017G>A|NP_001171896.1:p.Met339Ile|1258|1017|339|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354604.2|protein_coding|10/10||NM_001354604.2:c.1191G>A|NP_001341533.1:p.Met397Ile|1325|1191|397|M/I|atG/atA|COSV100096658||1||EntrezGene||YES||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354605.2|protein_coding|10/10||NM_001354605.2:c.1188G>A|NP_001341534.1:p.Met396Ile|1322|1188|396|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354606.2|protein_coding|10/10||NM_001354606.2:c.1170G>A|NP_001341535.1:p.Met390Ile|1304|1170|390|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354607.2|protein_coding|11/11||NM_001354607.2:c.1122G>A|NP_001341536.1:p.Met374Ile|1436|1122|374|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_001354608.2|protein_coding|11/11||NM_001354608.2:c.1017G>A|NP_001341537.1:p.Met339Ile|1346|1017|339|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_006722.3|protein_coding|10/10||NM_006722.3:c.1170G>A|NP_006713.1:p.Met390Ile|1201|1170|390|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_198158.3|protein_coding|9/9||NM_198158.3:c.852G>A|NP_937801.1:p.Met284Ile|983|852|284|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_198159.3|protein_coding|10/10||NM_198159.3:c.1173G>A|NP_937802.1:p.Met391Ile|1307|1173|391|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_198177.3|protein_coding|10/10||NM_198177.3:c.1125G>A|NP_937820.1:p.Met375Ile|1192|1125|375|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1,A|missense_variant|MODERATE|MITF|4286|Transcript|NM_198178.3|protein_coding|9/9||NM_198178.3:c.684G>A|NP_937821.2:p.Met228Ile|815|684|228|M/I|atG/atA|COSV100096658||1||EntrezGene||||||3:g.70014009G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:502:0:0,0:374,128:502,0:0:2,0:26.1:1:36.4:1:1:0:60:99.4:1:0:0.1	0/1:195:2:1,1:148,45:193,2:0.0103:2,2:42:1:37:0:0.41708:3.26389:60:4:0.0106:0:1
    1197. 

  1197. 3	71008434	71008434	A	G	exonic	FOXP1	.	synonymous SNV	FOXP1:NM_001244813:exon15:c.T1698C:p.D566D,FOXP1:NM_001349344:exon15:c.T1695C:p.D565D,FOXP1:NM_001244812:exon16:c.T1770C:p.D590D,FOXP1:NM_001244815:exon16:c.T2004C:p.D668D,FOXP1:NM_001349337:exon16:c.T2001C:p.D667D,FOXP1:NM_001349342:exon16:c.T1698C:p.D566D,FOXP1:NM_001349343:exon16:c.T1695C:p.D565D,FOXP1:NM_001244814:exon17:c.T1998C:p.D666D,FOXP1:NM_001244816:exon20:c.T1998C:p.D666D,FOXP1:NM_001349340:exon20:c.T1998C:p.D666D,FOXP1:NM_001244808:exon21:c.T1995C:p.D665D,FOXP1:NM_001244810:exon21:c.T2046C:p.D682D,FOXP1:NM_001349338:exon21:c.T1998C:p.D666D,FOXP1:NM_001349339:exon21:c.T1998C:p.D666D,FOXP1:NM_001349341:exon21:c.T1995C:p.D665D,FOXP1:NM_032682:exon21:c.T1998C:p.D666D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	190	3	71008434	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1444;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.01346;SOR=0;LSEQ=TTTACTGGTTCATCTTCGTA;RSEQ=TCTCTGTCATGGTCAAAATC;CSQ=G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|21/21||NM_001244808.3:c.1995T>C|NP_001231737.1:p.Asp665%3D|2599|1995|665|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|21/21||NM_001244810.2:c.2046T>C|NP_001231739.1:p.Asp682%3D|2561|2046|682|D|gaT/gaC|||-1||EntrezGene||YES||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|16/16||NM_001244812.3:c.1770T>C|NP_001231741.1:p.Asp590%3D|1935|1770|590|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|15/15||NM_001244813.3:c.1698T>C|NP_001231742.1:p.Asp566%3D|1817|1698|566|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|17/17||NM_001244814.3:c.1998T>C|NP_001231743.1:p.Asp666%3D|2233|1998|666|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|16/16||NM_001244815.2:c.1698T>C|NP_001231744.2:p.Asp566%3D|1907|1698|566|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|20/20||NM_001244816.2:c.1998T>C|NP_001231745.1:p.Asp666%3D|2429|1998|666|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|16/16||NM_001349337.2:c.1695T>C|NP_001336266.2:p.Asp565%3D|1904|1695|565|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|21/21||NM_001349338.3:c.1998T>C|NP_001336267.1:p.Asp666%3D|2602|1998|666|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|20/20||NM_001349340.3:c.1998T>C|NP_001336269.1:p.Asp666%3D|2507|1998|666|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|21/21||NM_001349341.3:c.1995T>C|NP_001336270.1:p.Asp665%3D|2599|1995|665|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|16/16||NM_001349342.3:c.1698T>C|NP_001336271.1:p.Asp566%3D|1925|1698|566|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|16/16||NM_001349343.3:c.1695T>C|NP_001336272.1:p.Asp565%3D|1922|1695|565|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|15/15||NM_001349344.3:c.1695T>C|NP_001336273.1:p.Asp565%3D|1814|1695|565|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|16/16||NM_001370548.1:c.1695T>C|NP_001357477.1:p.Asp565%3D|1904|1695|565|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|synonymous_variant|LOW|FOXP1|27086|Transcript|NM_032682.6|protein_coding|21/21||NM_032682.6:c.1998T>C|NP_116071.2:p.Asp666%3D|2513|1998|666|D|gaT/gaC|||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA|20/20||NR_146142.3:n.2514T>C||2514|||||||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA|20/20||NR_146143.3:n.2511T>C||2511|||||||-1||EntrezGene||||||3:g.71008434A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1444:0:0,0:837,606:1443,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:190:2:1,1:118,70:188,2:0.0105:2,2:48.5:1:37:0:1:1.6808:60:4:0.0107:0:1
    1198. 

  1198. 3	71008547	71008547	A	G	intronic	FOXP1	.	.	.	0.015	0.0012	0	0	0	0.0105	0.0032	0.0004	0.0031	rs187666567	rs187666567	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	134554	History_of_neurodevelopmental_disorder|not_specified|not_provided	MedGen:C2711754|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	242	217	3	71008547	.	A	G	242	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1498;VD=0;AF=0;SHIFT3=0;MSI=6;MSILEN=1;SSF=0;SOR=0;LSEQ=GACGTGTACAGGATGCCTGG;RSEQ=AAAAATATGCAGAGGTTCAG;CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||20/20|NM_001244808.3:c.1887-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||20/20|NM_001244810.2:c.1938-5T>C|||||||rs187666567||-1||EntrezGene||YES||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||15/15|NM_001244812.3:c.1662-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||14/14|NM_001244813.3:c.1590-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||16/16|NM_001244814.3:c.1890-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||15/15|NM_001244815.2:c.1590-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||19/19|NM_001244816.2:c.1890-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||15/15|NM_001349337.2:c.1587-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||20/20|NM_001349338.3:c.1890-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||19/19|NM_001349340.3:c.1890-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||20/20|NM_001349341.3:c.1887-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||15/15|NM_001349342.3:c.1590-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||15/15|NM_001349343.3:c.1587-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||14/14|NM_001349344.3:c.1587-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||15/15|NM_001370548.1:c.1587-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_032682.6|protein_coding||20/20|NM_032682.6:c.1890-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||19/19|NR_146142.3:n.2406-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||19/19|NR_146143.3:n.2403-5T>C|||||||rs187666567||-1||EntrezGene||||||3:g.71008547A>G|0.001389|0|0|0|0.01023|0.004158|0.0005283|0.001467|6.533e-05|0.0149|EAS|likely_benign&benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1498:0:0,0:657,837:1494,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:217:116:51,65:50,51:101,116:0.5346:2,2:36.8:1:35.4:1:0.49527:1.24822:60:22.2:0.5236:0:2.1
    1199. 

  1199. 3	71008557	71008557	C	A	intronic	FOXP1	.	.	.	0.076	0.0337	0.0692	0.0477	0.0067	0.0956	0.0304	0.0076	0.0215	rs7639736	rs7639736	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU18274297	COCA-CN|2|321|0.00623053	0.25	239	206	3	71008557	.	C	A	239	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1427;VD=1;AF=0.0007;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=0.0007;LSEQ=GGATGCCTGGAAAAAATATG;RSEQ=AGAGGTTCAGTGAGGGTACT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||20/20|NM_001244808.3:c.1887-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||20/20|NM_001244810.2:c.1938-15G>T|||||||rs7639736||-1||EntrezGene||YES||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||15/15|NM_001244812.3:c.1662-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||14/14|NM_001244813.3:c.1590-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||16/16|NM_001244814.3:c.1890-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||15/15|NM_001244815.2:c.1590-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||19/19|NM_001244816.2:c.1890-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||15/15|NM_001349337.2:c.1587-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||20/20|NM_001349338.3:c.1890-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||19/19|NM_001349340.3:c.1890-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||20/20|NM_001349341.3:c.1887-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||15/15|NM_001349342.3:c.1590-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||15/15|NM_001349343.3:c.1587-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||14/14|NM_001349344.3:c.1587-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||15/15|NM_001370548.1:c.1587-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_032682.6|protein_coding||20/20|NM_032682.6:c.1890-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||19/19|NR_146142.3:n.2406-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||,A|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||19/19|NR_146143.3:n.2403-15G>T|||||||rs7639736||-1||EntrezGene||||||3:g.71008557C>A|0.02851|0.07268|0.06306|0.005659|0.072|0.03309|0.007823|0.02482|0.02166|0.0764|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1427:1:1,0:611,815:1426,1:0.0007:2,0:19:0:11:0:0.42887:0:60:0:0:0:2	1/0:206:104:45,59:47,54:101,104:0.5049:2,2:38.1:1:35.8:1:0.67492:1.14041:60:51:0.505:0:2.1
    1200. 

  1200. 3	71015021	71015021	G	T	intronic	FOXP1	.	.	.	1.	0.9489	0.9831	0.9535	0.9139	1	0.9476	0.9238	0.9559	rs7638391	rs7638391	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV59535400;OCCURENCE=1(bone)	102122	not_specified	MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81765255	COCA-CN|5|321|0.0155763	1	327	187	3	71015021	.	G	T	327	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=750;VD=748;AF=0.9973;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.48759;SOR=2.00903;LSEQ=GGGTCAGATAGCAAAGACCT;RSEQ=TTGGGTGGACAATACTCACA;CSQ=T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||20/20|NM_001244808.3:c.1886+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||20/20|NM_001244810.2:c.1937+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||YES||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||15/15|NM_001244812.3:c.1661+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||14/14|NM_001244813.3:c.1589+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||16/16|NM_001244814.3:c.1889+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||15/15|NM_001244815.2:c.1589+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||19/19|NM_001244816.2:c.1889+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||15/15|NM_001349337.2:c.1586+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||20/20|NM_001349338.3:c.1889+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||19/19|NM_001349340.3:c.1889+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||20/20|NM_001349341.3:c.1886+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||15/15|NM_001349342.3:c.1589+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||15/15|NM_001349343.3:c.1586+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||14/14|NM_001349344.3:c.1586+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||15/15|NM_001370548.1:c.1586+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_032682.6|protein_coding||20/20|NM_032682.6:c.1889+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||19/19|NR_146142.3:n.2405+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||19/19|NR_146143.3:n.2402+20C>A|||||||rs7638391&COSV59535400||-1||EntrezGene||||||3:g.71015021G>T|0.9452|0.9867|0.9634|0.9146|0.9999|0.9442|0.9209|0.9396|0.9722|1|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:750:748:468,280:0,0:0,748:0.9973:0,2:40.7:1:34.3:1:1:0:60:15.261:0.9972:0:1.1	1/1:187:186:124,62:0,0:0,186:0.9947:0,2:37.3:1:33.8:1:1:0:60:12.286:1:0:1.1
    1201. 

  1201. 3	71021128	71021128	-	A	intronic	FOXP1	.	.	.	0.17	0.0019	0.0009	0.0043	0.0038	0	0.0062	0.0018	0.0037	rs368010894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112255919	BTCA-SG|3|71|0.0422535	0.5	265	271	3	71021128	.	G	GA	265	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=2029;VD=150;AF=0.0739;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.46999;SOR=1.05878;LSEQ=GCAAAGCCAAAGCAACAGCA;RSEQ=AAAAAAAAAACAAAAGCAAG;CSQ=A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||18/20|NM_001244808.3:c.1649+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||18/20|NM_001244810.2:c.1700+33dup|||||||rs368010894||-1||EntrezGene||YES||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||13/15|NM_001244812.3:c.1424+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||12/14|NM_001244813.3:c.1352+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||14/16|NM_001244814.3:c.1652+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||13/15|NM_001244815.2:c.1352+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||17/19|NM_001244816.2:c.1652+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||13/15|NM_001349337.2:c.1349+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||18/20|NM_001349338.3:c.1652+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||17/19|NM_001349340.3:c.1652+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||18/20|NM_001349341.3:c.1649+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||13/15|NM_001349342.3:c.1352+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||13/15|NM_001349343.3:c.1349+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||12/14|NM_001349344.3:c.1349+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||13/15|NM_001370548.1:c.1349+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_032682.6|protein_coding||18/20|NM_032682.6:c.1652+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||17/19|NR_146142.3:n.2168+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||17/19|NR_146143.3:n.2165+577dup|||||||rs368010894||-1||EntrezGene||||||3:g.71021138dup|0.2667|0.2483|0.2946|0.2621|0.2984|0.2929|0.2446|0.2706|0.3041|0.3041|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2029:150:90,60:943,587:1530,150:0.0739:2,2:42:1:36.7:1:0.72532:1.07094:60.2:300:0.0993:0:0.3	0/1:271:19:13,5:144,77:221,19:0.0701:2,2:35:1:37.2:1:0.6156:1.39:60.3:38:0.0888:0.0148:0.2
    1202. 

  1202. 3	71021723	71021723	C	A	exonic	FOXP1	.	nonsynonymous SNV	FOXP1:NM_001244813:exon12:c.G1335T:p.R445S,FOXP1:NM_001349344:exon12:c.G1332T:p.R444S,FOXP1:NM_001244812:exon13:c.G1407T:p.R469S,FOXP1:NM_001244815:exon13:c.G1641T:p.R547S,FOXP1:NM_001349337:exon13:c.G1638T:p.R546S,FOXP1:NM_001349342:exon13:c.G1335T:p.R445S,FOXP1:NM_001349343:exon13:c.G1332T:p.R444S,FOXP1:NM_001244814:exon14:c.G1635T:p.R545S,FOXP1:NM_001244816:exon17:c.G1635T:p.R545S,FOXP1:NM_001349340:exon17:c.G1635T:p.R545S,FOXP1:NM_001244808:exon18:c.G1632T:p.R544S,FOXP1:NM_001349338:exon18:c.G1635T:p.R545S,FOXP1:NM_001349339:exon18:c.G1635T:p.R545S,FOXP1:NM_001349341:exon18:c.G1632T:p.R544S,FOXP1:NM_032682:exon18:c.G1635T:p.R545S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	3.55	0.934	H	-3.66	0.952	D	-5.01	0.835	D	0.813	0.821	1.019	0.975	D	0.920	0.974	D	0.375	0.929	D	6.699	0.916	32	0.998	0.894	0.979	0.781	D	c	0.952	0.910	1.000	0.747	0.672	0.522	0	5.87	0.942	5.053	0.639	0.935	0.490	1.000	0.715	1.000	0.888	13.749	0.622	Fork head domain|Winged helix-turn-helix DNA-binding domain;Winged helix-turn-helix DNA-binding domain	.	.	ID=COSV59549354;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	MU131471581	LUAD-US|1|516|0.00193798	0.25	37	186	3	71021723	.	C	A	37	v3;f0.01;pSTD;q22.5;SN1.5;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1402;VD=1;AF=0.0007;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.03779;SOR=0.06589;LSEQ=TACCCACTGATCTTTTGTGG;RSEQ=CTTCGTTTTTGGAATTCTAC;CSQ=A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|18/21||NM_001244808.3:c.1632G>T|NP_001231737.1:p.Arg544Ser|2236|1632|544|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||17/20|NM_001244810.2:c.1531-392G>T|||||||COSV59549354||-1||EntrezGene||YES||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|13/16||NM_001244812.3:c.1407G>T|NP_001231741.1:p.Arg469Ser|1572|1407|469|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|12/15||NM_001244813.3:c.1335G>T|NP_001231742.1:p.Arg445Ser|1454|1335|445|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|14/17||NM_001244814.3:c.1635G>T|NP_001231743.1:p.Arg545Ser|1870|1635|545|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|13/16||NM_001244815.2:c.1335G>T|NP_001231744.2:p.Arg445Ser|1544|1335|445|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|17/20||NM_001244816.2:c.1635G>T|NP_001231745.1:p.Arg545Ser|2066|1635|545|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|13/16||NM_001349337.2:c.1332G>T|NP_001336266.2:p.Arg444Ser|1541|1332|444|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|18/21||NM_001349338.3:c.1635G>T|NP_001336267.1:p.Arg545Ser|2239|1635|545|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|17/20||NM_001349340.3:c.1635G>T|NP_001336269.1:p.Arg545Ser|2144|1635|545|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|18/21||NM_001349341.3:c.1632G>T|NP_001336270.1:p.Arg544Ser|2236|1632|544|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|13/16||NM_001349342.3:c.1335G>T|NP_001336271.1:p.Arg445Ser|1562|1335|445|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|13/16||NM_001349343.3:c.1332G>T|NP_001336272.1:p.Arg444Ser|1559|1332|444|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|12/15||NM_001349344.3:c.1332G>T|NP_001336273.1:p.Arg444Ser|1451|1332|444|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|13/16||NM_001370548.1:c.1332G>T|NP_001357477.1:p.Arg444Ser|1541|1332|444|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|18/21||NM_032682.6:c.1635G>T|NP_116071.2:p.Arg545Ser|2150|1635|545|R/S|agG/agT|COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA|17/20||NR_146142.3:n.2151G>T||2151|||||COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA|17/20||NR_146143.3:n.2148G>T||2148|||||COSV59549354||-1||EntrezGene||||||3:g.71021723C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1402:1:1,0:635,766:1401,1:0.0007:2,0:12:0:11:0:0.45364:0:60:0:0:0:7	0/1:186:2:1,1:101,83:184,2:0.0108:2,2:30.5:1:37:0:1:1.21557:60:4:0.0109:0:1
    1203. 

  1203. 3	71026791	71026791	T	C	intronic	FOXP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	68	3	71026791	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.55629;SOR=0;LSEQ=CATATACTGTGTTATTTACT;RSEQ=ACCTGCCTAATTAAAGATGC;CSQ=C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||16/20|NM_001244808.3:c.1425+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||16/20|NM_001244810.2:c.1428+3A>G|||||||||-1||EntrezGene||YES||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||11/15|NM_001244812.3:c.1200+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||10/14|NM_001244813.3:c.1128+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||12/16|NM_001244814.3:c.1428+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||11/15|NM_001244815.2:c.1128+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||15/19|NM_001244816.2:c.1428+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||11/15|NM_001349337.2:c.1125+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||16/20|NM_001349338.3:c.1428+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||15/19|NM_001349340.3:c.1428+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||16/20|NM_001349341.3:c.1425+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||11/15|NM_001349342.3:c.1128+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||11/15|NM_001349343.3:c.1125+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||10/14|NM_001349344.3:c.1125+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||11/15|NM_001370548.1:c.1125+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant|LOW|FOXP1|27086|Transcript|NM_032682.6|protein_coding||16/20|NM_032682.6:c.1428+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||15/19|NR_146142.3:n.1944+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||,C|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||15/19|NR_146143.3:n.1941+3A>G|||||||||-1||EntrezGene||||||3:g.71026791T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:19,4:23,0:0:2,0:30.9:1:37:0:1:0:60:46:1:0:0.3	0/1:68:2:1,1:40,26:66,2:0.0294:2,2:12.5:1:37:0:1:1.52841:60:4:0.0308:0:1
    1204. 

  1204. 3	71026864	71026864	G	A	exonic	FOXP1	.	nonsynonymous SNV	FOXP1:NM_001244813:exon10:c.C1058T:p.A353V,FOXP1:NM_001349344:exon10:c.C1055T:p.A352V,FOXP1:NM_001244812:exon11:c.C1130T:p.A377V,FOXP1:NM_001244815:exon11:c.C1364T:p.A455V,FOXP1:NM_001349337:exon11:c.C1361T:p.A454V,FOXP1:NM_001349342:exon11:c.C1058T:p.A353V,FOXP1:NM_001349343:exon11:c.C1055T:p.A352V,FOXP1:NM_001244814:exon12:c.C1358T:p.A453V,FOXP1:NM_001244816:exon15:c.C1358T:p.A453V,FOXP1:NM_001349340:exon15:c.C1358T:p.A453V,FOXP1:NM_001244808:exon16:c.C1355T:p.A452V,FOXP1:NM_001244810:exon16:c.C1358T:p.A453V,FOXP1:NM_001349338:exon16:c.C1358T:p.A453V,FOXP1:NM_001349339:exon16:c.C1358T:p.A453V,FOXP1:NM_001349341:exon16:c.C1355T:p.A452V,FOXP1:NM_032682:exon16:c.C1358T:p.A453V	.	.	.	.	.	.	.	.	.	.	.	0.13	0.294	T	0.196	0.338	B	0.053	0.243	B	0.000	0.629	D	1.000	0.524	D	1.32	0.331	L	-2.61	0.906	D	-2.3	0.513	N	0.069	0.175	-0.029	0.817	T	0.581	0.849	D	0.022	0.448	T	3.146	0.438	22.6	0.984	0.406	0.953	0.638	D	c	0.177	0.376	1.000	0.747	0.732	0.924	0	6.17	0.997	5.115	0.643	1.048	0.713	1.000	0.715	1.000	0.888	20.879	0.999	Winged helix-turn-helix DNA-binding domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	107	3	71026864	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=92;VD=2;AF=0.0217;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.21248;SOR=inf;LSEQ=TATAAAATTCTTGGTTCTGC;RSEQ=CAATATCTGCTGAATAAGAA;CSQ=A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|16/21||NM_001244808.3:c.1355C>T|NP_001231737.1:p.Ala452Val|1959|1355|452|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|16/21||NM_001244810.2:c.1358C>T|NP_001231739.1:p.Ala453Val|1873|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||YES||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|11/16||NM_001244812.3:c.1130C>T|NP_001231741.1:p.Ala377Val|1295|1130|377|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|10/15||NM_001244813.3:c.1058C>T|NP_001231742.1:p.Ala353Val|1177|1058|353|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|12/17||NM_001244814.3:c.1358C>T|NP_001231743.1:p.Ala453Val|1593|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|11/16||NM_001244815.2:c.1058C>T|NP_001231744.2:p.Ala353Val|1267|1058|353|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|15/20||NM_001244816.2:c.1358C>T|NP_001231745.1:p.Ala453Val|1789|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|11/16||NM_001349337.2:c.1055C>T|NP_001336266.2:p.Ala352Val|1264|1055|352|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|16/21||NM_001349338.3:c.1358C>T|NP_001336267.1:p.Ala453Val|1962|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|15/20||NM_001349340.3:c.1358C>T|NP_001336269.1:p.Ala453Val|1867|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|16/21||NM_001349341.3:c.1355C>T|NP_001336270.1:p.Ala452Val|1959|1355|452|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|11/16||NM_001349342.3:c.1058C>T|NP_001336271.1:p.Ala353Val|1285|1058|353|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|11/16||NM_001349343.3:c.1055C>T|NP_001336272.1:p.Ala352Val|1282|1055|352|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|10/15||NM_001349344.3:c.1055C>T|NP_001336273.1:p.Ala352Val|1174|1055|352|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|11/16||NM_001370548.1:c.1055C>T|NP_001357477.1:p.Ala352Val|1264|1055|352|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|16/21||NM_032682.6:c.1358C>T|NP_116071.2:p.Ala453Val|1873|1358|453|A/V|gCg/gTg|rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA|15/20||NR_146142.3:n.1874C>T||1874|||||rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||,A|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA|15/20||NR_146143.3:n.1871C>T||1871|||||rs1251323482||-1||EntrezGene||||||3:g.71026864G>A|3.978e-06|0|0|0|0|0|8.797e-06|0|0|8.797e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:92:2:1,1:68,22:90,2:0.0217:2,2:38:1:37:0:0.43956:3.04503:60:4:0.022:0:1	0/0:107:0:0,0:71,36:107,0:0:2,0:37.1:1:35.7:1:1:0:60:34.667:1:0:0.2
    1205. 

  1205. 3	71050172	71050172	G	T	exonic	FOXP1	.	nonsynonymous SNV	FOXP1:NM_001244813:exon7:c.C713A:p.T238K,FOXP1:NM_001349344:exon7:c.C710A:p.T237K,FOXP1:NM_001244812:exon8:c.C785A:p.T262K,FOXP1:NM_001244815:exon8:c.C1019A:p.T340K,FOXP1:NM_001349337:exon8:c.C1016A:p.T339K,FOXP1:NM_001349342:exon8:c.C713A:p.T238K,FOXP1:NM_001349343:exon8:c.C710A:p.T237K,FOXP1:NM_001244814:exon9:c.C1013A:p.T338K,FOXP1:NM_001244816:exon12:c.C1013A:p.T338K,FOXP1:NM_001349340:exon12:c.C1013A:p.T338K,FOXP1:NM_001244808:exon13:c.C1013A:p.T338K,FOXP1:NM_001244810:exon13:c.C1013A:p.T338K,FOXP1:NM_001349338:exon13:c.C1013A:p.T338K,FOXP1:NM_001349339:exon13:c.C1013A:p.T338K,FOXP1:NM_001349341:exon13:c.C1010A:p.T337K,FOXP1:NM_032682:exon13:c.C1013A:p.T338K	.	.	.	.	.	.	.	.	.	.	.	0.022	0.486	D	0.999	0.899	D	0.968	0.832	D	0.000	0.843	D	1	0.810	D	2.835	0.828	M	1.36	0.344	T	-5.43	0.853	D	0.868	0.855	-0.713	0.598	T	0.230	0.596	T	0.027	0.497	D	6.861	0.929	33	0.995	0.678	0.993	0.937	D	c	0.812	0.841	1.0	0.983	0.732	0.924	0	5.73	0.897	9.998	0.993	0.953	0.551	1.000	0.715	1.000	0.888	19.904	0.970	FOXP, coiled-coil domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	245	3	71050172	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=147;VD=2;AF=0.0136;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.14003;SOR=inf;LSEQ=TTTGTACTCTACATTGGGCT;RSEQ=TACTTCTATCGTCCAGCGCA;CSQ=T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|13/21||NM_001244808.3:c.1013C>A|NP_001231737.1:p.Thr338Lys|1617|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|13/21||NM_001244810.2:c.1013C>A|NP_001231739.1:p.Thr338Lys|1528|1013|338|T/K|aCa/aAa|||-1||EntrezGene||YES||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|8/16||NM_001244812.3:c.785C>A|NP_001231741.1:p.Thr262Lys|950|785|262|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|7/15||NM_001244813.3:c.713C>A|NP_001231742.1:p.Thr238Lys|832|713|238|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|9/17||NM_001244814.3:c.1013C>A|NP_001231743.1:p.Thr338Lys|1248|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|8/16||NM_001244815.2:c.713C>A|NP_001231744.2:p.Thr238Lys|922|713|238|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|12/20||NM_001244816.2:c.1013C>A|NP_001231745.1:p.Thr338Lys|1444|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|8/16||NM_001349337.2:c.710C>A|NP_001336266.2:p.Thr237Lys|919|710|237|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|13/21||NM_001349338.3:c.1013C>A|NP_001336267.1:p.Thr338Lys|1617|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|12/20||NM_001349340.3:c.1013C>A|NP_001336269.1:p.Thr338Lys|1522|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|13/21||NM_001349341.3:c.1010C>A|NP_001336270.1:p.Thr337Lys|1614|1010|337|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|8/16||NM_001349342.3:c.713C>A|NP_001336271.1:p.Thr238Lys|940|713|238|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|8/16||NM_001349343.3:c.710C>A|NP_001336272.1:p.Thr237Lys|937|710|237|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|7/15||NM_001349344.3:c.710C>A|NP_001336273.1:p.Thr237Lys|829|710|237|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|8/16||NM_001370548.1:c.713C>A|NP_001357477.1:p.Thr238Lys|922|713|238|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|13/21||NM_032682.6:c.1013C>A|NP_116071.2:p.Thr338Lys|1528|1013|338|T/K|aCa/aAa|||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||12/19|NR_146142.3:n.1579-12944C>A|||||||||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||12/19|NR_146143.3:n.1576-12944C>A|||||||||-1||EntrezGene||||||3:g.71050172G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:147:2:1,1:79,66:145,2:0.0136:2,2:49:0:37:0:1:1.1955:60:4:0.0137:0:1	0/0:245:0:0,0:108,137:245,0:0:2,0:40.9:1:36.6:1:1:0:60:121.5:1:0:0
    1206. 

  1206. 3	71050185	71050185	C	A	exonic	FOXP1	.	nonsynonymous SNV	FOXP1:NM_001244813:exon7:c.G700T:p.D234Y,FOXP1:NM_001349344:exon7:c.G697T:p.D233Y,FOXP1:NM_001244812:exon8:c.G772T:p.D258Y,FOXP1:NM_001244815:exon8:c.G1006T:p.D336Y,FOXP1:NM_001349337:exon8:c.G1003T:p.D335Y,FOXP1:NM_001349342:exon8:c.G700T:p.D234Y,FOXP1:NM_001349343:exon8:c.G697T:p.D233Y,FOXP1:NM_001244814:exon9:c.G1000T:p.D334Y,FOXP1:NM_001244816:exon12:c.G1000T:p.D334Y,FOXP1:NM_001349340:exon12:c.G1000T:p.D334Y,FOXP1:NM_001244808:exon13:c.G1000T:p.D334Y,FOXP1:NM_001244810:exon13:c.G1000T:p.D334Y,FOXP1:NM_001349338:exon13:c.G1000T:p.D334Y,FOXP1:NM_001349339:exon13:c.G1000T:p.D334Y,FOXP1:NM_001349341:exon13:c.G997T:p.D333Y,FOXP1:NM_032682:exon13:c.G1000T:p.D334Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.996	0.916	D	0.000	0.843	D	1	0.810	D	2.85	0.831	M	0.86	0.468	T	-8.12	0.967	D	0.97	0.976	-0.291	0.752	T	0.360	0.722	T	0.050	0.640	D	7.206	0.945	34	0.996	0.727	0.988	0.868	D	c	0.930	0.900	1.0	0.983	0.732	0.924	0	5.73	0.897	7.902	0.860	0.852	0.362	1.000	0.715	1.000	0.888	19.904	0.970	FOXP, coiled-coil domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	31	238	3	71050185	.	C	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=140;VD=2;AF=0.0143;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13656;SOR=inf;LSEQ=TTGGGCTGTACTTCTATCGT;RSEQ=CAGCGCATGCTCACTGTTGA;CSQ=A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|13/21||NM_001244808.3:c.1000G>T|NP_001231737.1:p.Asp334Tyr|1604|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|13/21||NM_001244810.2:c.1000G>T|NP_001231739.1:p.Asp334Tyr|1515|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||YES||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|8/16||NM_001244812.3:c.772G>T|NP_001231741.1:p.Asp258Tyr|937|772|258|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|7/15||NM_001244813.3:c.700G>T|NP_001231742.1:p.Asp234Tyr|819|700|234|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|9/17||NM_001244814.3:c.1000G>T|NP_001231743.1:p.Asp334Tyr|1235|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|8/16||NM_001244815.2:c.700G>T|NP_001231744.2:p.Asp234Tyr|909|700|234|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|12/20||NM_001244816.2:c.1000G>T|NP_001231745.1:p.Asp334Tyr|1431|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|8/16||NM_001349337.2:c.697G>T|NP_001336266.2:p.Asp233Tyr|906|697|233|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|13/21||NM_001349338.3:c.1000G>T|NP_001336267.1:p.Asp334Tyr|1604|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|12/20||NM_001349340.3:c.1000G>T|NP_001336269.1:p.Asp334Tyr|1509|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|13/21||NM_001349341.3:c.997G>T|NP_001336270.1:p.Asp333Tyr|1601|997|333|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|8/16||NM_001349342.3:c.700G>T|NP_001336271.1:p.Asp234Tyr|927|700|234|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|8/16||NM_001349343.3:c.697G>T|NP_001336272.1:p.Asp233Tyr|924|697|233|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|7/15||NM_001349344.3:c.697G>T|NP_001336273.1:p.Asp233Tyr|816|697|233|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|8/16||NM_001370548.1:c.700G>T|NP_001357477.1:p.Asp234Tyr|909|700|234|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|13/21||NM_032682.6:c.1000G>T|NP_116071.2:p.Asp334Tyr|1515|1000|334|D/Y|Gac/Tac|COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||12/19|NR_146142.3:n.1579-12957G>T|||||||COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1,A|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||12/19|NR_146143.3:n.1576-12957G>T|||||||COSV59546438||-1||EntrezGene||||||3:g.71050185C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:140:2:1,1:73,65:138,2:0.0143:2,2:52.5:1:31:1:1:1.12214:60:4:0.0146:0:1	0/0:238:0:0,0:100,138:238,0:0:2,0:41.9:1:36.5:1:1:0:60:118:1:0:0
    1207. 

  1207. 3	71101737	71101737	A	G	exonic	FOXP1	.	nonsynonymous SNV	FOXP1:NM_001244813:exon3:c.T161C:p.L54S,FOXP1:NM_001349344:exon3:c.T158C:p.L53S,FOXP1:NM_001244815:exon4:c.T467C:p.L156S,FOXP1:NM_001349337:exon4:c.T464C:p.L155S,FOXP1:NM_001349342:exon4:c.T161C:p.L54S,FOXP1:NM_001349343:exon4:c.T158C:p.L53S,FOXP1:NM_001244814:exon5:c.T461C:p.L154S,FOXP1:NM_001244816:exon8:c.T461C:p.L154S,FOXP1:NM_001349340:exon8:c.T461C:p.L154S,FOXP1:NM_001244808:exon9:c.T461C:p.L154S,FOXP1:NM_001244810:exon9:c.T461C:p.L154S,FOXP1:NM_001349338:exon9:c.T461C:p.L154S,FOXP1:NM_001349339:exon9:c.T461C:p.L154S,FOXP1:NM_001349341:exon9:c.T458C:p.L153S,FOXP1:NM_032682:exon9:c.T461C:p.L154S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.764	D	0.994	0.807	D	0.000	0.559	D	1.000	0.810	D	3.07	0.873	M	1.24	0.386	T	-3.96	0.861	D	0.743	0.739	-0.524	0.678	T	0.272	0.644	T	0.052	0.651	D	5.445	0.739	26.1	0.999	0.940	0.963	0.681	D	c	0.857	0.846	1.0	0.983	0.757	0.989	0	5.92	0.955	8.366	0.899	1.199	0.960	1.000	0.715	1.000	0.888	16.363	0.830	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	.	.	0.25	37	199	3	71101737	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=615;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.05954;SOR=0;LSEQ=GTTGTAAAAGTTGAAGCTGC;RSEQ=ACTGTTCCTGTTGTTTTTTA;CSQ=G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|9/21||NM_001244808.3:c.461T>C|NP_001231737.1:p.Leu154Ser|1065|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|9/21||NM_001244810.2:c.461T>C|NP_001231739.1:p.Leu154Ser|976|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||YES||||3:g.71101737A>G|||||||||||||1|1,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||4/15|NM_001244812.3:c.283-5491T>C|||||||COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244813.3|protein_coding|3/15||NM_001244813.3:c.161T>C|NP_001231742.1:p.Leu54Ser|280|161|54|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|5/17||NM_001244814.3:c.461T>C|NP_001231743.1:p.Leu154Ser|696|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244815.2|protein_coding|4/16||NM_001244815.2:c.161T>C|NP_001231744.2:p.Leu54Ser|370|161|54|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|8/20||NM_001244816.2:c.461T>C|NP_001231745.1:p.Leu154Ser|892|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349337.2|protein_coding|4/16||NM_001349337.2:c.158T>C|NP_001336266.2:p.Leu53Ser|367|158|53|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|9/21||NM_001349338.3:c.461T>C|NP_001336267.1:p.Leu154Ser|1065|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|8/20||NM_001349340.3:c.461T>C|NP_001336269.1:p.Leu154Ser|970|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|9/21||NM_001349341.3:c.458T>C|NP_001336270.1:p.Leu153Ser|1062|458|153|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349342.3|protein_coding|4/16||NM_001349342.3:c.161T>C|NP_001336271.1:p.Leu54Ser|388|161|54|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349343.3|protein_coding|4/16||NM_001349343.3:c.158T>C|NP_001336272.1:p.Leu53Ser|385|158|53|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001349344.3|protein_coding|3/15||NM_001349344.3:c.158T>C|NP_001336273.1:p.Leu53Ser|277|158|53|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_001370548.1|protein_coding|4/16||NM_001370548.1:c.161T>C|NP_001357477.1:p.Leu54Ser|370|161|54|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|missense_variant|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|9/21||NM_032682.6:c.461T>C|NP_116071.2:p.Leu154Ser|976|461|154|L/S|tTg/tCg|COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA|9/20||NR_146142.3:n.1065T>C||1065|||||COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1,G|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA|9/20||NR_146143.3:n.1062T>C||1062|||||COSV59547759||-1||EntrezGene||||||3:g.71101737A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:615:0:0,0:304,311:615,0:0:2,0:38.9:1:36.6:1:1:0:60:306.5:1:0:0.1	0/1:199:2:1,1:101,95:196,2:0.0101:2,2:57:1:37:0:1:1.06286:60:4:0.0101:0:1
    1208. 

  1208. 3	71102957	71102957	A	G	intronic	FOXP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	184	3	71102957	.	A	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=925;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.0274;SOR=0;LSEQ=TGAAGGATAAATAGGAAGCC;RSEQ=GGAAATCAGAAGCACGCAGC;CSQ=G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||7/20|NM_001244808.3:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||7/20|NM_001244810.2:c.283-33T>C|||||||||-1||EntrezGene||YES||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||4/15|NM_001244812.3:c.283-6711T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244813.3|protein_coding||1/14|NM_001244813.3:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||3/16|NM_001244814.3:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244815.2|protein_coding||2/15|NM_001244815.2:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||6/19|NM_001244816.2:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349337.2|protein_coding||2/15|NM_001349337.2:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||7/20|NM_001349338.3:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||6/19|NM_001349340.3:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||7/20|NM_001349341.3:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349342.3|protein_coding||2/15|NM_001349342.3:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349343.3|protein_coding||2/15|NM_001349343.3:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349344.3|protein_coding||1/14|NM_001349344.3:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001370548.1|protein_coding||2/15|NM_001370548.1:c.-18-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_032682.6|protein_coding||7/20|NM_032682.6:c.283-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||7/19|NR_146142.3:n.887-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||7/19|NR_146143.3:n.887-33T>C|||||||||-1||EntrezGene||||||3:g.71102957A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:925:0:0,0:297,627:924,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:184:2:1,1:63,118:181,2:0.0109:2,2:27:0:37:0:1:1.87:60:4:0.0109:0:1
    1209. 

  1209. 3	71247025	71247025	G	-	intronic	FOXP1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	73	145	3	71247024	.	TG	T	73	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=316;VD=4;AF=0.0127;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.21945;SOR=inf;LSEQ=TTATTTTTGCATGAAAGCAG;RSEQ=GGAACCATTTCTCCAAAGAA;CSQ=-|downstream_gene_variant|MODIFIER|FOXP1|27086|Transcript|NM_001012505.2|protein_coding|||||||||||8|-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244808.3|protein_coding||6/20|NM_001244808.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244810.2|protein_coding||6/20|NM_001244810.2:c.180+328del|||||||||-1||EntrezGene||YES||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244812.3|protein_coding||3/15|NM_001244812.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244814.3|protein_coding||2/16|NM_001244814.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001244816.2|protein_coding||5/19|NM_001244816.2:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349338.3|protein_coding||6/20|NM_001349338.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349340.3|protein_coding||5/19|NM_001349340.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_001349341.3|protein_coding||6/20|NM_001349341.3:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant|MODIFIER|FOXP1|27086|Transcript|NM_032682.6|protein_coding||6/20|NM_032682.6:c.180+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA||6/19|NR_146142.3:n.784+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA||6/19|NR_146143.3:n.784+328del|||||||||-1||EntrezGene||||||3:g.71247027del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:316:4:4,0:241,71:312,4:0.0127:2,0:15.8:1:36.5:1:0.57829:0:60:8:0.0128:0.0095:0	0/0:145:0:0,0:107,38:145,0:0:2,0:37:1:36.5:1:1:0:60:71.5:1:0:0.2
    1210. 

  1210. 3	71247357	71247359	TGC	-	exonic	FOXP1	.	nonframeshift deletion	FOXP1:NM_001244814:exon2:c.174_176del:p.Q60del,FOXP1:NM_001244812:exon3:c.174_176del:p.Q60del,FOXP1:NM_001244816:exon5:c.174_176del:p.Q60del,FOXP1:NM_001349340:exon5:c.174_176del:p.Q60del,FOXP1:NM_001012505:exon6:c.174_176del:p.Q60del,FOXP1:NM_001244808:exon6:c.174_176del:p.Q60del,FOXP1:NM_001244810:exon6:c.174_176del:p.Q60del,FOXP1:NM_001349338:exon6:c.174_176del:p.Q60del,FOXP1:NM_001349339:exon6:c.174_176del:p.Q60del,FOXP1:NM_001349341:exon6:c.174_176del:p.Q60del,FOXP1:NM_032682:exon6:c.174_176del:p.Q60del	.	.	.	.	.	.	.	.	.	rs370638902	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	102	98	3	71247356	.	TTGC	T	102	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=673;VD=7;AF=0.0104;SHIFT3=11;MSI=4;MSILEN=3;SSF=0.38458;SOR=inf;LSEQ=ACTCCAAAGCCCAGTACCTG;RSEQ=TGCTGCTGCTGGGCGTGGGC;CSQ=-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001012505.2|protein_coding|6/7||NM_001012505.2:c.174_176del|NP_001012523.1:p.Gln60del|689-691|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001244808.3|protein_coding|6/21||NM_001244808.3:c.174_176del|NP_001231737.1:p.Gln60del|778-780|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001244810.2|protein_coding|6/21||NM_001244810.2:c.174_176del|NP_001231739.1:p.Gln60del|689-691|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||YES||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001244812.3|protein_coding|3/16||NM_001244812.3:c.174_176del|NP_001231741.1:p.Gln60del|339-341|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001244814.3|protein_coding|2/17||NM_001244814.3:c.174_176del|NP_001231743.1:p.Gln60del|409-411|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001244816.2|protein_coding|5/20||NM_001244816.2:c.174_176del|NP_001231745.1:p.Gln60del|605-607|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001349338.3|protein_coding|6/21||NM_001349338.3:c.174_176del|NP_001336267.1:p.Gln60del|778-780|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001349340.3|protein_coding|5/20||NM_001349340.3:c.174_176del|NP_001336269.1:p.Gln60del|683-685|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_001349341.3|protein_coding|6/21||NM_001349341.3:c.174_176del|NP_001336270.1:p.Gln60del|778-780|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|inframe_deletion|MODERATE|FOXP1|27086|Transcript|NM_032682.6|protein_coding|6/21||NM_032682.6:c.174_176del|NP_116071.2:p.Gln60del|689-691|174-176|58-59|QQ/Q|caGCAa/caa|rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146142.3|misc_RNA|6/20||NR_146142.3:n.778_780del||778-780|||||rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||,-|non_coding_transcript_exon_variant|MODIFIER|FOXP1|27086|Transcript|NR_146143.3|misc_RNA|6/20||NR_146143.3:n.778_780del||778-780|||||rs370638902||-1||EntrezGene||||||3:g.71247368_71247370del|7.988e-06|0|0|0|0|4.705e-05|8.826e-06|0|0|4.705e-05|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:673:7:4,3:287,379:666,7:0.0104:2,2:33.6:1:36.4:1:0.47308:1.76:60:14:0.0105:0.003:0.4	0/0:98:0:0,0:51,47:98,0:0:2,0:42.9:1:36.6:1:1:0:60:97:1:0:0.1
    1211. 

  1211. 3	72495777	72495777	C	G	upstream	RYBP	dist=3	.	.	1.	0.9785	0.9394	0.9964	0.9967	0.9279	0.9997	0.9994	0.9928	rs13066407	rs13066407	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81765277	COCA-CN|5|321|0.0155763	0.5	44	0	3	72495777	.	C	G	44	d5	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTGTCTTTTTGGCCTTC;RSEQ=GAGGAGTGGAGAGTGGGGGA;CSQ=G|upstream_gene_variant|MODIFIER|RYBP|23429|Transcript|NM_012234.6|protein_coding||||||||||rs13066407|3|-1|cds_start_NF|EntrezGene||YES||||3:g.72495777C>G|0.9903|0.9349|0.9974|0.9999|0.9326|1|0.9994|0.9962|0.9991|1|EAS&EUR&SAS&gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:3:3:1,2:0,0:0,3:1:0,2:58.7:1:28.3:1:1:0:60:2:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1212. 

  1212. 3	89259011	89259011	G	-	exonic	EPHA3	.	frameshift deletion	EPHA3:NM_005233:exon3:c.155delG:p.E53Kfs*30,EPHA3:NM_182644:exon3:c.155delG:p.E53Kfs*30	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	177	3	89259010	.	TG	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=78;VD=2;AF=0.0256;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.09273;SOR=inf;LSEQ=GTTTCTCTTTGATTCTTCAG;RSEQ=GGAAGAGATCAGTGGTGTGG;CSQ=-|frameshift_variant&splice_region_variant|HIGH|EPHA3|2042|Transcript|NM_005233.6|protein_coding|3/17||NM_005233.6:c.157del|NP_005224.2:p.Glu53LysfsTer30|283|155|52|W/X|tGg/tg|COSV60719833&COSV60725206||1||EntrezGene||YES|||2|3:g.89259013del|||||||||||||1&1|1&1,-|frameshift_variant&splice_region_variant|HIGH|EPHA3|2042|Transcript|NM_182644.3|protein_coding|3/7||NM_182644.3:c.157del|NP_872585.1:p.Glu53LysfsTer30|283|155|52|W/X|tGg/tg|COSV60719833&COSV60725206||1||EntrezGene|||||2|3:g.89259013del|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:78:2:1,1:59,17:76,2:0.0256:2,2:17.5:1:37:0:0.41059:3.40118:60:4:0.0263:0:0	0/0:177:0:0,0:129,48:177,0:0:2,0:33.4:1:36.6:1:1:0:60:176:1:0:0.1
    1213. 

  1213. 3	89259682	89259682	C	A	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	184	3	89259682	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=2;AF=0.0244;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.09423;SOR=inf;LSEQ=TGTGCCAAGGTAAGAGCCTT;RSEQ=TCTATTTTTCTTTGAGCAAT;CSQ=A|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||3/16|NM_005233.6:c.814+12C>A|||||||||1||EntrezGene||YES||||3:g.89259682C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_182644.3|protein_coding||3/6|NM_182644.3:c.814+12C>A|||||||||1||EntrezGene||||||3:g.89259682C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:82:2:1,1:19,61:80,2:0.0244:2,2:30:0:37:0:0.43059:3.15:60:4:0.025:0:1	0/0:184:0:0,0:66,118:184,0:0:2,0:27:0:11:0:1:0:60:0:0:0:1
    1214. 

  1214. 3	89391238	89391238	C	A	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon5:c.C1304A:p.A435D,EPHA3:NM_182644:exon5:c.C1304A:p.A435D	.	.	.	.	.	.	.	.	.	rs571620668	.	0.078	0.341	T	0.999	0.899	D	0.996	0.832	D	0.000	0.843	D	1	0.810	D	2.145	0.603	M	0.57	0.544	T	-4.12	0.753	D	0.912	0.902	-0.367	0.731	T	0.376	0.734	T	0.045	0.621	D	5.118	0.690	25.4	0.997	0.805	0.991	0.906	D	c	0.874	0.847	1.000	0.747	0.487	0.133	0	5.53	0.825	6.137	0.713	0.935	0.490	1.000	0.715	0.998	0.697	19.841	0.967	Fibronectin type III|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	274	3	89391238	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=226;VD=3;AF=0.0133;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09167;SOR=inf;LSEQ=CAGCATCACAACTAATCAGG;RSEQ=TGGTGAGTACATACTAGATG;CSQ=A|missense_variant&splice_region_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|5/17||NM_005233.6:c.1304C>A|NP_005224.2:p.Ala435Asp|1432|1304|435|A/D|gCt/gAt|rs571620668||1||EntrezGene||YES||||3:g.89391238C>A|4.055e-06|0|0|0|0|0|9.085e-06|0|0|9.085e-06|gnomAD_NFE|||,A|missense_variant&splice_region_variant|MODERATE|EPHA3|2042|Transcript|NM_182644.3|protein_coding|5/7||NM_182644.3:c.1304C>A|NP_872585.1:p.Ala435Asp|1432|1304|435|A/D|gCt/gAt|rs571620668||1||EntrezGene||||||3:g.89391238C>A|4.055e-06|0|0|0|0|0|9.085e-06|0|0|9.085e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:226:3:2,1:71,152:223,3:0.0133:2,2:28.7:1:28.3:1:0.24456:4.25:60:2:0.009:0:1.3	0/0:274:0:0,0:89,185:274,0:0:2,0:37.7:1:36.4:1:1:0:60:53.8:1:0:0.1
    1215. 

  1215. 3	89391246	89391246	T	A	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	256	3	89391246	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=195;VD=2;AF=0.0103;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1864;SOR=inf;LSEQ=CAACTAATCAGGCTGGTGAG;RSEQ=ACATACTAGATGCTTCTTAC;CSQ=A|splice_donor_region_variant&intron_variant|LOW|EPHA3|2042|Transcript|NM_005233.6|protein_coding||5/16|NM_005233.6:c.1306+6T>A|||||||||1||EntrezGene||YES||||3:g.89391246T>A||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|EPHA3|2042|Transcript|NM_182644.3|protein_coding||5/6|NM_182644.3:c.1306+6T>A|||||||||1||EntrezGene||||||3:g.89391246T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:195:2:1,1:61,132:193,2:0.0103:2,2:56.5:1:37:0:0.53592:2.15:60:4:0.0103:0:2.5	0/0:256:0:0,0:76,180:256,0:0:2,0:37.7:1:36.9:1:1:0:60:255:1:0:0.1
    1216. 

  1216. 3	89448623	89448623	T	A	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon7:c.T1587A:p.S529R,EPHA3:NM_182644:exon7:c.T1587A:p.S529R	.	.	.	.	.	.	.	.	.	.	.	0.111	0.329	T	0.112	0.377	B	0.022	0.447	B	0.000	0.843	D	0.997	0.439	D	1.485	0.373	L	0.61	0.535	T	-1.46	0.358	N	0.832	0.820	-0.772	0.568	T	0.146	0.471	T	0.030	0.529	D	-0.049	0.089	2.137	0.730	0.098	0.104	0.158	N	c	-1.031	-1.182	0.003	0.099	0.487	0.133	0	-7.91	0.010	-0.912	0.041	-0.507	0.051	0.008	0.178	0.966	0.452	18.505	0.908	Fibronectin type III|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	74	239	3	89448623	.	T	A	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=204;VD=4;AF=0.0196;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.04425;SOR=inf;LSEQ=AAGTTTGAGTTTGAAACTAG;RSEQ=CCAGACTGTATGTATTATTT;CSQ=A|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|7/17||NM_005233.6:c.1587T>A|NP_005224.2:p.Ser529Arg|1715|1587|529|S/R|agT/agA|||1||EntrezGene||YES||||3:g.89448623T>A||||||||||||||,A|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_182644.3|protein_coding|7/7||NM_182644.3:c.1587T>A|NP_872585.1:p.Ser529Arg|1715|1587|529|S/R|agT/agA|||1||EntrezGene||||||3:g.89448623T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:204:4:2,2:85,115:200,4:0.0196:2,2:11:1:37:0:1:1.35:60:8:0.0197:0:1	0/0:239:0:0,0:91,148:239,0:0:2,0:39.8:1:36:1:1:0:60:478:1:0:0.1
    1217. 

  1217. 3	89448681	89448681	A	G	UTR3	EPHA3	NM_182644:c.*25A>G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	130	3	89448681	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=68;VD=2;AF=0.0294;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1168;SOR=inf;LSEQ=GGGGGCAGGGATCTTGCAAA;RSEQ=GATGTCTGATCGTTTATTCT;CSQ=G|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||7/16|NM_005233.6:c.1594+51A>G|||||||||1||EntrezGene||YES||||3:g.89448681A>G||||||||||||||,G|3_prime_UTR_variant|MODIFIER|EPHA3|2042|Transcript|NM_182644.3|protein_coding|7/7||NM_182644.3:c.*25A>G||1773|||||||1||EntrezGene||||||3:g.89448681A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:68:2:1,1:15,51:66,2:0.0294:2,2:12:0:37:0:0.41791:3.32:60:4:0.0294:0:1	0/0:130:0:0,0:36,94:130,0:0:2,0:34:1:36.4:1:1:0:60:129:1:0:0.1
    1218. 

  1218. 3	89456411	89456411	C	A	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	144	3	89456411	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.56476;SOR=0;LSEQ=TTCTTATTTTTTCTCTTCAA;RSEQ=CTCACAGCTTTCTCCATCTC;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|EPHA3|2042|Transcript|NM_005233.6|protein_coding||7/16|NM_005233.6:c.1595-8C>A|||||||||1||EntrezGene||YES||||3:g.89456411C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:21,9:30,0:0:2,0:35.1:1:36.1:1:1:0:60:29:1:0:0.3	0/1:144:3:1,2:87,54:141,3:0.0208:2,2:42.7:1:28.3:1:0.56013:3.19547:60:2:0.0144:0:2
    1219. 

  1219. 3	89456463	89456463	A	G	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon8:c.A1639G:p.I547V	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.001	0.067	B	0.0	0.013	B	0.000	0.843	N	1.000	0.548	D	0.565	0.153	N	3.02	0.090	T	0.45	0.032	N	0.213	0.313	-0.952	0.406	T	0.013	0.053	T	0.011	0.283	T	-0.359	0.064	0.485	0.282	0.014	0.920	0.544	D	c	-0.348	-0.168	0.001	0.077	0.487	0.133	0	4.74	0.596	4.218	0.581	1.088	0.866	1.000	0.715	0.388	0.252	9.796	0.397	Ephrin receptor, transmembrane domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	201	3	89456463	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=54;VD=2;AF=0.037;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.04419;SOR=inf;LSEQ=GCCAAGTGGTCATGATCGCC;RSEQ=TTTCAGCGGCAGTAGCAATT;CSQ=G|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|8/17||NM_005233.6:c.1639A>G|NP_005224.2:p.Ile547Val|1767|1639|547|I/V|Att/Gtt|||1||EntrezGene||YES||||3:g.89456463A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:54:2:1,1:29,23:52,2:0.037:2,2:34.5:1:37:0:1:1.25542:60:4:0.0385:0:1	0/0:201:0:0,0:100,101:201,0:0:2,0:38.3:1:36.2:1:1:0:60:39.2:1:0:0.3
    1220. 

  1220. 3	89456510	89456510	T	G	exonic	EPHA3	.	synonymous SNV	EPHA3:NM_005233:exon8:c.T1686G:p.V562V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	191	3	89456510	.	T	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=48;VD=2;AF=0.0417;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.03966;SOR=inf;LSEQ=CTCACTGTTGTCATCTATGT;RSEQ=TTGATTGGGAGGTGAGTTCA;CSQ=G|synonymous_variant|LOW|EPHA3|2042|Transcript|NM_005233.6|protein_coding|8/17||NM_005233.6:c.1686T>G|NP_005224.2:p.Val562%3D|1814|1686|562|V|gtT/gtG|||1||EntrezGene||YES||||3:g.89456510T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:48:2:1,1:22,24:46,2:0.0417:2,2:51:0:37:0:1:1.09:60:4:0.0435:0:1	0/0:191:0:0,0:81,110:191,0:0:2,0:40.9:1:34.7:1:1:0:60:16.364:1:0:0.4
    1221. 

  1221. 3	89456528	89456528	T	C	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	175	3	89456528	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=45;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.632;SOR=0;LSEQ=GTTTTGATTGGGAGGTGAGT;RSEQ=CACAGTCTGTTTCACTATTC;CSQ=C|splice_region_variant&intron_variant|LOW|EPHA3|2042|Transcript|NM_005233.6|protein_coding||8/16|NM_005233.6:c.1697+7T>C|||||||rs1156248364||1||EntrezGene||YES||||3:g.89456528T>C|3.995e-06|0|2.916e-05|0|0|0|0|0|0|2.916e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:45:0:0,0:19,26:45,0:0:2,0:42.3:1:36.7:1:1:0:60:90:1:0:0.3	0/1:175:2:1,1:69,104:173,2:0.0114:2,2:48.5:1:37:0:1:1.5:60:4:0.0114:0:1
    1222. 

  1222. 3	89457302	89457302	T	C	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	186	3	89457302	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=26;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.76925;SOR=0;LSEQ=GTAAGTTTCTAAACTTGGCT;RSEQ=TTTGTTTTGCTTCACCGTTT;CSQ=C|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||9/16|NM_005233.6:c.1762+21T>C|||||||||1||EntrezGene||YES||||3:g.89457302T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:26:0:0,0:12,14:26,0:0:2,0:37.7:1:36.1:1:1:0:60:52:1:0:0	0/1:186:2:1,1:73,111:184,2:0.0108:2,2:41:1:37:0:1:1.52:60:4:0.0109:0:1
    1223. 

  1223. 3	89462239	89462242	TTGT	-	intronic	EPHA3	.	.	.	0.086	0.0688	0.0201	0.0719	0.1192	0.0665	0.0925	0.0899	0.0798	rs71836049	rs71836049	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	230	145	3	89462238	.	ATTGT	A	230	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=10;VD=0;AF=0;SHIFT3=4;MSI=3;MSILEN=1;SSF=0.00044;SOR=0;LSEQ=GCCATAAAATTTGATCTATA;RSEQ=TTGTACAAATCTAGCTACAA;CSQ=-|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||9/16|NM_005233.6:c.1763-48_1763-45del|||||||rs71836049||1||EntrezGene||YES||||3:g.89462243_89462246del||||||||||0.0855|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:8,2:10,0:0:2,0:29.4:1:37:0:1:0:60:20:1:0:0.1	1/0:145:81:61,20:48,16:64,81:0.5586:2,2:30.4:1:36.3:1:1:1.02:60:80:0.5594:0.069:0.1
    1224. 

  1224. 3	89462464	89462464	G	A	intronic	EPHA3	.	.	.	0.1	0.0678	0.0198	0.0719	0.1192	0.0675	0.0927	0.0880	0.0784	rs77327554	rs77327554	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	247	219	3	89462464	.	G	A	247	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=16;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TAGTACTGTATGTGAATCAC;RSEQ=ATTGCTCAGTCTCTGAAACC;CSQ=A|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||10/16|NM_005233.6:c.1888+48G>A|||||||rs77327554&COSV60719595||1||EntrezGene||YES||||3:g.89462464G>A|0.07532|0.01826|0.04653|0.1246|0.07395|0.09497|0.08713|0.08658|0.06304|0.1246|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:16:0:0,0:6,10:16,0:0:2,0:36.2:1:35.4:1:1:0:60:15:1:0:0.1	1/0:219:111:33,78:36,71:107,111:0.5068:2,2:35.9:1:36.5:1:0.56255:1.19746:60:110:0.5069:0:1
    1225. 

  1225. 3	89468453	89468453	C	A	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon11:c.C1987A:p.Q663K	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.987	0.600	D	0.967	0.699	D	0.000	0.843	D	1	0.810	D	0.63	0.160	N	-1.61	0.823	D	-3.53	0.685	D	0.814	0.802	0.025	0.828	D	0.574	0.846	D	0.149	0.831	D	5.779	0.790	27.1	0.995	0.658	0.984	0.826	D	c	0.511	0.529	1.000	0.747	0.487	0.133	0	5.71	0.890	7.905	0.864	0.935	0.490	1.000	0.715	0.830	0.347	19.849	0.967	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	281	3	89468453	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37874;SOR=0;LSEQ=AAGTTGGCTACACAGAAAAG;RSEQ=AGAGGAGAGACTTCCTGGGA;CSQ=A|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|11/17||NM_005233.6:c.1987C>A|NP_005224.2:p.Gln663Lys|2115|1987|663|Q/K|Cag/Aag|||1||EntrezGene||YES||||3:g.89468453C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:107:0:0,0:55,52:107,0:0:2,0:36:1:35.9:1:1:0:60:25.75:1:0:0.1	0/1:281:3:2,1:147,131:278,3:0.0107:2,2:33:1:28.3:1:1:1.78:60:2:0.0073:0:2.7
    1226. 

  1226. 3	89468564	89468564	T	C	intronic	EPHA3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	165	3	89468564	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.60494;SOR=0;LSEQ=AGTAAAGTAGTCATAAGACC;RSEQ=GTGTTTCCGTATGTTGAGCA;CSQ=C|intron_variant|MODIFIER|EPHA3|2042|Transcript|NM_005233.6|protein_coding||11/16|NM_005233.6:c.2074+24T>C|||||||||1||EntrezGene||YES||||3:g.89468564T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:47:0:0,0:16,31:47,0:0:2,0:36.2:1:36.7:1:1:0:60:94:1:0:0	0/1:165:2:1,1:42,121:163,2:0.0121:2,2:47.5:1:37:0:0.45447:2.86:60:4:0.0122:0:1
    1227. 

  1227. 3	89498499	89498499	C	G	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon14:c.C2471G:p.P824R	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	3.72	0.949	H	-2.35	0.881	D	-8.32	0.970	D	0.982	0.991	1.046	0.980	D	0.896	0.966	D	0.388	0.931	D	4.502	0.603	24.3	0.999	0.948	0.984	0.825	D	c	0.990	0.902	1.000	0.747	0.554	0.246	0	5.34	0.759	7.860	0.853	0.935	0.490	1.000	0.715	0.991	0.552	19.070	0.931	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	373	3	89498499	.	C	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=85;VD=2;AF=0.0235;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.03411;SOR=inf;LSEQ=GATGTCTTATGGAGAGAGAC;RSEQ=ATACTGGGAGATGTCCAATC;CSQ=G|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|14/17||NM_005233.6:c.2471C>G|NP_005224.2:p.Pro824Arg|2599|2471|824|P/R|cCa/cGa|||1||EntrezGene||YES||||3:g.89498499C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:85:2:1,1:41,41:82,2:0.0235:2,2:10.5:1:37:0:1:1:60:4:0.0238:0:1	0/0:373:0:0,0:150,221:371,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1228. 

  1228. 3	89521664	89521664	G	A	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon16:c.G2741A:p.R914H	0.1	0.0684	0.0201	0.0730	0.1192	0.0587	0.0927	0.0900	0.0796	rs17801309	rs17801309	0.584	0.236	T	0.009	0.139	B	0.005	0.104	B	0.002	0.368	N	0.996	0.230	P	1.465	0.370	L	-1.82	0.841	D	-0.43	0.144	N	0.058	0.041	-0.887	0.492	T	0.024	0.103	T	.	.	.	3.120	0.435	22.6	0.990	0.507	0.893	0.495	D	c	-0.305	-0.133	0.000	0.012	0.554	0.246	0	2.91	0.328	1.489	0.349	-0.285	0.084	1.000	0.715	0.783	0.331	8.808	0.339	Protein kinase-like domain|Sterile alpha motif domain|Sterile alpha motif/pointed domain	.	.	ID=COSV60697068;OCCURENCE=1(large_intestine),2(skin)	.	.	.	.	.	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU150961	COCA-CN|1|321|0.00311526	0.25	263	332	3	89521664	.	G	A	263	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=620;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGGATATCACTACCTTCC;RSEQ=CACAACAGGTGACTGGCTTA;CSQ=A|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|16/17||NM_005233.6:c.2741G>A|NP_005224.2:p.Arg914His|2869|2741|914|R/H|cGc/cAc|rs17801309&COSV60697068&COSV60719602||1||EntrezGene||YES||||3:g.89521664G>A|0.07601|0.01834|0.04803|0.1194|0.07354|0.09471|0.08851|0.08809|0.06337|0.1194|gnomAD_ASJ||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:620:0:0,0:264,355:619,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:332:152:78,74:95,85:180,152:0.4578:2,2:36.3:1:36.3:1:0.82588:1.06013:60:304:0.4606:0:1.9
    1229. 

  1229. 3	89521693	89521693	T	C	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon16:c.T2770C:p.W924R	0.67	0.4612	0.6298	0.3681	0.3477	0.1942	0.5043	0.3919	0.4255	rs35124509	rs35124509	0.229	0.183	T	0.0	0.026	B	0.0	0.013	B	0.000	0.843	N	1.000	0.588	P	-2.3	0.001	N	-1.73	0.833	D	3.9	0.001	N	0.052	0.034	-0.915	0.463	T	0.000	0.000	T	.	.	.	2.291	0.336	18.10	0.939	0.233	0.151	0.186	N	c	-0.724	-0.444	0.000	0.029	0.554	0.246	0	3.84	0.433	1.978	0.400	-2.025	0.005	0.997	0.399	0.230	0.224	9.572	0.384	Sterile alpha motif domain|Sterile alpha motif/pointed domain	.	.	ID=COSV60708046;OCCURENCE=2(haematopoietic_and_lymphoid_tissue),1(skin),2(lung)	.	.	.	.	.	Benign	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	MU11759109	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579	0.25	256	343	3	89521693	.	T	C	256	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=507;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGACTGGCTTAATGGTGTC;RSEQ=GGACAGCACACTGCAAGGAA;CSQ=C|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|16/17||NM_005233.6:c.2770T>C|NP_005224.2:p.Trp924Arg|2898|2770|924|W/R|Tgg/Cgg|rs35124509&COSV60708046||1||EntrezGene||YES||||3:g.89521693T>C|0.3701|0.6364|0.3166|0.3472|0.2049|0.4953|0.3894|0.3947|0.2306|0.674|AFR||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:507:0:0,0:191,316:507,0:0:2,0:38.6:1:36.5:1:1:0:60:100.4:1:0:0.1	0/1:343:150:71,79:87,106:193,150:0.4373:2,2:37.2:1:35.5:1:0.74335:1.09:60:29:0.4328:0:1.9
    1230. 

  1230. 3	89521766	89521766	C	T	exonic	EPHA3	.	nonsynonymous SNV	EPHA3:NM_005233:exon16:c.C2843T:p.T948I	.	.	.	.	.	.	.	.	.	.	.	0.794	0.032	T	0.379	0.325	B	0.081	0.275	B	0.000	0.843	D	1.000	0.810	D	0.905	0.233	L	-1.86	0.844	D	-0.09	0.084	N	0.36	0.421	-0.494	0.689	T	0.342	0.708	T	0.038	0.579	D	2.877	0.406	21.7	0.791	0.122	0.949	0.625	D	c	0.061	0.250	0.782	0.238	0.554	0.246	0	5.61	0.853	3.783	0.549	0.852	0.362	1.000	0.715	1.000	0.888	12.923	0.575	Sterile alpha motif domain|Sterile alpha motif/pointed domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	239	3	89521766	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=2;AF=0.0152;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.12597;SOR=inf;LSEQ=CACAATAGCCAAGATTTCCA;RSEQ=AGAGTAAGAAAAAAAAATTC;CSQ=T|missense_variant|MODERATE|EPHA3|2042|Transcript|NM_005233.6|protein_coding|16/17||NM_005233.6:c.2843C>T|NP_005224.2:p.Thr948Ile|2971|2843|948|T/I|aCa/aTa|||1||EntrezGene||YES||||3:g.89521766C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:132:2:0,2:38,92:130,2:0.0152:2,0:16.5:1:37:0:1:0:60:4:0.0156:0:1	0/0:239:0:0,0:80,159:239,0:0:2,0:38.5:1:35.8:1:1:0:60:46.8:1:0:0.6
    1231. 

  1231. 3	89521774	89521774	-	A	intronic	EPHA3	.	.	.	0.0012	3.348e-05	0	0.0012	0	0	0	0	0	rs752119882	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112271885	BTCA-SG|1|71|0.0140845	0.25	39	213	3	89521774	.	G	GA	39	v3	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=100;VD=2;AF=0.02;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.24024;SOR=4.30417;LSEQ=CCAAGATTTCCACAGAGTAA;RSEQ=AAAAAAAAATTCATTAAGAA;CSQ=A|splice_donor_region_variant&intron_variant|LOW|EPHA3|2042|Transcript|NM_005233.6|protein_coding||16/16|NM_005233.6:c.2846+14dup|||||||rs752119882||1||EntrezGene||YES||||3:g.89521783dup|0.0003407|0.0001396|0.00059|0.0005196|0.0005101|0.0002028|0.0002915|0.0002067|0.0003729|0.0007273|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:100:2:1,1:24,70:94,2:0.02:2,2:39.5:1:39:0:0.45504:2.88:63.2:4:0.022:0:0	0/0:213:1:0,1:62,140:202,1:0.0047:2,0:34.8:0:39:0:1:0:63.2:2:0.0052:0:3.2
    1232. 

  1232. 3	119585415	119585415	-	A	intronic	GSK3B	.	.	.	0.0033	0.0003	0.0001	0	0	0	0.0003	0.0004	0	rs760867763	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114016268	COCA-CN|1|321|0.00311526	0.25	64	246	3	119585415	.	G	GA	64	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=9;VD=0;AF=0;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.86537;SOR=0;LSEQ=GACCTGCCCTGAAATTTTGG;RSEQ=AAAAAAAAATTAAGTACATA;CSQ=A|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_001146156.2|protein_coding||8/10|NM_001146156.2:c.910-2964dup|||||||rs539666737||-1||EntrezGene||||||3:g.119585424dup|0.0005806|0.0005427|0.0009888|0.000321|0.000743|9.413e-05|0.0006411|0.0007427|0.0002682|0.001641|AA|||,A|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_001354596.2|protein_coding||8/9|NM_001354596.2:c.910-2964dup|||||||rs539666737||-1||EntrezGene||||||3:g.119585424dup|0.0005806|0.0005427|0.0009888|0.000321|0.000743|9.413e-05|0.0006411|0.0007427|0.0002682|0.001641|AA|||,A|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_002093.4|protein_coding||9/11|NM_002093.4:c.948+21dup|||||||rs539666737||-1||EntrezGene||YES||||3:g.119585424dup|0.0005806|0.0005427|0.0009888|0.000321|0.000743|9.413e-05|0.0006411|0.0007427|0.0002682|0.001641|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:6,3:9,0:0:2,0:39.7:1:37:0:1:0:60:18:1:0:0	0/1:246:4:2,2:133,97:230,4:0.0163:2,2:62.1:1:32.1:1:1:1.36924:63.2:3:0.0133:0:0
    1233. 

  1233. 3	119642235	119642235	A	G	exonic	GSK3B	.	synonymous SNV	GSK3B:NM_001146156:exon4:c.T462C:p.P154P,GSK3B:NM_002093:exon4:c.T462C:p.P154P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	119	3	119642235	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=CATACCTTGACATAAATCAC;RSEQ=GGGAGCGTCTGTTTGGCTCG;CSQ=G|synonymous_variant|LOW|GSK3B|2932|Transcript|NM_001146156.2|protein_coding|4/11||NM_001146156.2:c.462T>C|NP_001139628.1:p.Pro154%3D|1475|462|154|P|ccT/ccC|||-1||EntrezGene||||||3:g.119642235A>G||||||||||||||,G|synonymous_variant|LOW|GSK3B|2932|Transcript|NM_001354596.2|protein_coding|4/10||NM_001354596.2:c.462T>C|NP_001341525.1:p.Pro154%3D|1475|462|154|P|ccT/ccC|||-1||EntrezGene||||||3:g.119642235A>G||||||||||||||,G|synonymous_variant|LOW|GSK3B|2932|Transcript|NM_002093.4|protein_coding|4/12||NM_002093.4:c.462T>C|NP_002084.2:p.Pro154%3D|1475|462|154|P|ccT/ccC|||-1||EntrezGene||YES||||3:g.119642235A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:119:2:1,1:69,48:117,2:0.0168:2,2:30:0:37:0:1:1.433:60:4:0.0172:0:1
    1234. 

  1234. 3	119642270	119642270	C	A	exonic	GSK3B	.	nonsynonymous SNV	GSK3B:NM_001146156:exon4:c.G427T:p.A143S,GSK3B:NM_002093:exon4:c.G427T:p.A143S	0.	.	.	.	.	.	.	.	.	rs200380044	rs200380044	0.385	0.112	T	0.012	0.182	B	0.146	0.323	B	0.000	0.843	D	1	0.810	D	0.455	0.128	N	-0.15	0.652	T	-2.68	0.572	D	0.671	0.695	-0.952	0.406	T	0.157	0.490	T	0.028	0.509	D	2.801	0.398	21.4	0.988	0.454	0.982	0.806	D	c	-0.106	0.092	1.000	0.747	0.732	0.924	0	4.49	0.540	7.568	0.814	0.935	0.490	1.000	0.715	1.000	0.888	17.386	0.872	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	117	3	119642270	.	C	A	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCGACTATAGTGTCTGG;RSEQ=AACTCTGTATACTGTTTCCG;CSQ=A|missense_variant|MODERATE|GSK3B|2932|Transcript|NM_001146156.2|protein_coding|4/11||NM_001146156.2:c.427G>T|NP_001139628.1:p.Ala143Ser|1440|427|143|A/S|Gcc/Tcc|rs200380044||-1||EntrezGene||||||3:g.119642270C>A|4.04e-06|0|0|0|0|0|8.94e-06|0|0|8.94e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|GSK3B|2932|Transcript|NM_001354596.2|protein_coding|4/10||NM_001354596.2:c.427G>T|NP_001341525.1:p.Ala143Ser|1440|427|143|A/S|Gcc/Tcc|rs200380044||-1||EntrezGene||||||3:g.119642270C>A|4.04e-06|0|0|0|0|0|8.94e-06|0|0|8.94e-06|gnomAD_NFE|||,A|missense_variant|MODERATE|GSK3B|2932|Transcript|NM_002093.4|protein_coding|4/12||NM_002093.4:c.427G>T|NP_002084.2:p.Ala143Ser|1440|427|143|A/S|Gcc/Tcc|rs200380044||-1||EntrezGene||YES||||3:g.119642270C>A|4.04e-06|0|0|0|0|0|8.94e-06|0|0|8.94e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:117:2:1,1:59,56:115,2:0.0171:2,2:53:1:37:0:1:1.05312:60:4:0.0174:0:1
    1235. 

  1235. 3	119721107	119721107	T	G	intronic	GSK3B	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	107	3	119721107	.	T	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=173;VD=2;AF=0.0116;SHIFT3=1;MSI=9;MSILEN=1;SSF=0.3809;SOR=inf;LSEQ=CTAAAGGAAGAAAGGAAATT;RSEQ=TTTTTTCACGAGAACTGTAA;CSQ=G|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_001146156.2|protein_coding||1/10|NM_001146156.2:c.89-21A>C|||||||||-1||EntrezGene||||||3:g.119721107T>G||||||||||||||,G|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_001354596.2|protein_coding||1/9|NM_001354596.2:c.89-21A>C|||||||||-1||EntrezGene||||||3:g.119721107T>G||||||||||||||,G|intron_variant|MODIFIER|GSK3B|2932|Transcript|NM_002093.4|protein_coding||1/11|NM_002093.4:c.89-21A>C|||||||||-1||EntrezGene||YES||||3:g.119721107T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:173:2:1,1:56,115:171,2:0.0116:2,2:37.5:1:37:0:0.55169:2.04:60:4:0.0117:0:1	0/0:107:0:0,0:32,75:107,0:0:2,0:44.2:1:36.3:1:1:0:60:214:1:0:0.4
    1236. 

  1236. 3	128200838	128200838	C	-	intronic	GATA2	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs777474510	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	124	3	128200837	.	AC	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1016;VD=0;AF=0;SHIFT3=5;MSI=6;MSILEN=1;SSF=0.01175;SOR=0;LSEQ=GGACTCCCACGCCCACCTCG;RSEQ=CCCCCTCCCTGACCCTCGCT;CSQ=-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_001145661.2|protein_coding||5/6|NM_001145661.2:c.1018-51del|||||||rs777474510||-1||EntrezGene||YES||||3:g.128200843del|2.96e-05|0|8.826e-05|0|0|6.019e-05|0|0|9.971e-05|9.971e-05|gnomAD_SAS|||,-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_001145662.1|protein_coding||4/5|NM_001145662.1:c.1018-93del|||||||rs777474510||-1||EntrezGene||||||3:g.128200843del|2.96e-05|0|8.826e-05|0|0|6.019e-05|0|0|9.971e-05|9.971e-05|gnomAD_SAS|||,-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_032638.5|protein_coding||4/5|NM_032638.5:c.1018-51del|||||||rs777474510||-1||EntrezGene||||||3:g.128200843del|2.96e-05|0|8.826e-05|0|0|6.019e-05|0|0|9.971e-05|9.971e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1016:0:0,0:287,729:1016,0:0:2,0:36.5:1:36.2:1:1:0:60:52.474:1:0:0.2	0/1:124:2:1,1:36,86:122,2:0.0161:2,2:38.5:1:37:1:0.50944:2.37:60:4:0.0164:0.0081:0.5
    1237. 

  1237. 3	128202878	128202878	C	-	intronic	GATA2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	90	3	128202877	.	GC	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=714;VD=0;AF=0;SHIFT3=1;MSI=5;MSILEN=1;SSF=0.01241;SOR=0;LSEQ=GAACAGGGAGAGACACGGGG;RSEQ=CTGCTTAACCGGCAAGTTCT;CSQ=-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_001145661.2|protein_coding||4/6|NM_001145661.2:c.872-30del|||||||||-1||EntrezGene||YES||||3:g.128202879del||||||||||||||,-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_001145662.1|protein_coding||3/5|NM_001145662.1:c.872-30del|||||||||-1||EntrezGene||||||3:g.128202879del||||||||||||||,-|intron_variant|MODIFIER|GATA2|2624|Transcript|NM_032638.5|protein_coding||3/5|NM_032638.5:c.872-30del|||||||||-1||EntrezGene||||||3:g.128202879del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:714:0:0,0:302,412:714,0:0:2,0:36.2:1:36.6:1:1:0:60:177.5:1:0:0.2	0/1:90:2:1,1:44,44:88,2:0.0222:2,2:25:1:37:1:1:1:60:4:0.0222:0.0111:0
    1238. 

  1238. 3	128204784	128204784	C	T	exonic	GATA2	.	synonymous SNV	GATA2:NM_001145662:exon3:c.G657A:p.E219E,GATA2:NM_032638:exon3:c.G657A:p.E219E,GATA2:NM_001145661:exon4:c.G657A:p.E219E	0.0002	3.233e-05	0	0	0	0	0	6.675e-05	0	rs138688940	rs138688940	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	452073	Lymphedema,_primary,_with_myelodysplasia|Dendritic_cell,_monocyte,_B_lymphocyte,_and_natural_killer_lymphocyte_deficiency	MONDO:MONDO:0013540,MedGen:C3279664,OMIM:614038,Orphanet:ORPHA3226|MONDO:MONDO:0013607,MedGen:C3280030,OMIM:614172,Orphanet:ORPHA228423	criteria_provided,_single_submitter	Likely_benign	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	184	3	128204784	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2189;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.00598;SOR=0;LSEQ=CCACTTTCCATCTTCATGCT;RSEQ=TCCGTCAGTGACACCTGGTA;CSQ=T|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145661.2|protein_coding|4/7||NM_001145661.2:c.657G>A|NP_001139133.1:p.Glu219%3D|1092|657|219|E|gaG/gaA|rs138688940&COSV100350963||-1||EntrezGene||YES||||3:g.128204784C>T|7.963e-05|6.157e-05|0|0|0|0|0.0001586|0.0001632|0|0.0001632|gnomAD_OTH|likely_benign|0&1|1&1,T|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145662.1|protein_coding|3/6||NM_001145662.1:c.657G>A|NP_001139134.1:p.Glu219%3D|913|657|219|E|gaG/gaA|rs138688940&COSV100350963||-1||EntrezGene||||||3:g.128204784C>T|7.963e-05|6.157e-05|0|0|0|0|0.0001586|0.0001632|0|0.0001632|gnomAD_OTH|likely_benign|0&1|1&1,T|synonymous_variant|LOW|GATA2|2624|Transcript|NM_032638.5|protein_coding|3/6||NM_032638.5:c.657G>A|NP_116027.2:p.Glu219%3D|1005|657|219|E|gaG/gaA|rs138688940&COSV100350963||-1||EntrezGene||||||3:g.128204784C>T|7.963e-05|6.157e-05|0|0|0|0|0.0001586|0.0001632|0|0.0001632|gnomAD_OTH|likely_benign|0&1|1&1,T|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA||||||||||rs138688940&COSV100350963|3262|1||EntrezGene||YES||||3:g.128204784C>T|7.963e-05|6.157e-05|0|0|0|0|0.0001586|0.0001632|0|0.0001632|gnomAD_OTH|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2189:0:0,0:981,1208:2189,0:0:2,0:36.3:1:36.7:1:1:0:60:311.714:1:0:0.1	0/1:184:2:1,1:68,114:182,2:0.0109:2,2:61:1:31:1:1:1.67:60:4:0.0111:0:1
    1239. 

  1239. 3	128204786	128204786	C	A	exonic	GATA2	.	stopgain	GATA2:NM_001145662:exon3:c.G655T:p.E219X,GATA2:NM_032638:exon3:c.G655T:p.E219X,GATA2:NM_001145661:exon4:c.G655T:p.E219X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.003	0.355	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.623	0.976	37	0.998	0.844	0.994	0.951	D	c	1.004	0.811	1.000	0.747	0.628	0.401	0	4.01	0.457	7.419	0.792	0.736	0.307	1.000	0.715	0.942	0.416	10.690	0.449	.	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	182	3	128204786	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2171;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.00595;SOR=0;LSEQ=ACTTTCCATCTTCATGCTCT;RSEQ=CGTCAGTGACACCTGGTACT;CSQ=A|stop_gained|HIGH|GATA2|2624|Transcript|NM_001145661.2|protein_coding|4/7||NM_001145661.2:c.655G>T|NP_001139133.1:p.Glu219Ter|1090|655|219|E/*|Gag/Tag|||-1||EntrezGene||YES||||3:g.128204786C>A||||||||||||||,A|stop_gained|HIGH|GATA2|2624|Transcript|NM_001145662.1|protein_coding|3/6||NM_001145662.1:c.655G>T|NP_001139134.1:p.Glu219Ter|911|655|219|E/*|Gag/Tag|||-1||EntrezGene||||||3:g.128204786C>A||||||||||||||,A|stop_gained|HIGH|GATA2|2624|Transcript|NM_032638.5|protein_coding|3/6||NM_032638.5:c.655G>T|NP_116027.2:p.Glu219Ter|1003|655|219|E/*|Gag/Tag|||-1||EntrezGene||||||3:g.128204786C>A||||||||||||||,A|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA|||||||||||3260|1||EntrezGene||YES||||3:g.128204786C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2171:0:0,0:975,1196:2171,0:0:2,0:36.2:1:36.6:1:1:0:60:240.222:1:0:0.1	0/1:182:2:1,1:67,113:180,2:0.011:2,2:51.5:1:37:0:1:1.68:60:4:0.0112:0:2
    1240. 

  1240. 3	128204818	128204818	T	C	exonic	GATA2	.	nonsynonymous SNV	GATA2:NM_001145662:exon3:c.A623G:p.K208R,GATA2:NM_032638:exon3:c.A623G:p.K208R,GATA2:NM_001145661:exon4:c.A623G:p.K208R	.	.	.	.	.	.	.	.	.	.	.	0.078	0.339	T	0.705	0.400	P	0.359	0.413	B	0.000	0.843	D	1.000	0.588	D	1.83	0.482	L	-4.34	0.973	D	-0.96	0.279	N	0.345	0.465	0.863	0.952	D	0.878	0.960	D	0.529	0.956	D	3.249	0.450	22.8	0.998	0.878	0.989	0.886	D	c	0.187	0.184	1.000	0.747	0.628	0.401	0	4.01	0.457	7.478	0.799	0.831	0.339	1.000	0.715	0.994	0.587	12.743	0.565	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	146	3	128204818	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1689;VD=0;AF=0;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.00629;SOR=0;LSEQ=CCTGGTACTTGACGCCGTCC;RSEQ=TGTCCTCTCCTCGGGCTGCA;CSQ=C|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145661.2|protein_coding|4/7||NM_001145661.2:c.623A>G|NP_001139133.1:p.Lys208Arg|1058|623|208|K/R|aAg/aGg|||-1||EntrezGene||YES||||3:g.128204818T>C||||||||||||||,C|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145662.1|protein_coding|3/6||NM_001145662.1:c.623A>G|NP_001139134.1:p.Lys208Arg|879|623|208|K/R|aAg/aGg|||-1||EntrezGene||||||3:g.128204818T>C||||||||||||||,C|missense_variant|MODERATE|GATA2|2624|Transcript|NM_032638.5|protein_coding|3/6||NM_032638.5:c.623A>G|NP_116027.2:p.Lys208Arg|971|623|208|K/R|aAg/aGg|||-1||EntrezGene||||||3:g.128204818T>C||||||||||||||,C|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA|||||||||||3228|1||EntrezGene||YES||||3:g.128204818T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1689:0:0,0:775,914:1689,0:0:2,0:37.5:1:35.9:1:1:0:60:53.484:1:0:0.2	0/1:146:2:1,1:63,81:144,2:0.0137:2,2:37:1:37:0:1:1.28:60:4:0.0141:0:1
    1241. 

  1241. 3	128204951	128204951	C	T	exonic	GATA2	.	nonsynonymous SNV	GATA2:NM_001145662:exon3:c.G490A:p.A164T,GATA2:NM_032638:exon3:c.G490A:p.A164T,GATA2:NM_001145661:exon4:c.G490A:p.A164T	0.38	0.1800	0.1769	0.2524	0.2185	0.3781	0.1862	0.1533	0.1933	rs2335052	rs2335052	0.403	0.104	T	0.013	0.154	B	0.025	0.193	B	0.004	0.337	N	0.729	0.298	P	0	0.065	N	-4.32	0.972	D	-0.53	0.164	N	0.117	0.129	-1.065	0.107	T	0.000	0.000	T	.	.	.	1.482	0.240	13.22	0.990	0.494	0.910	0.525	D	c	-0.614	-0.459	1.000	0.489	0.543	0.218	0	1.83	0.242	0.635	0.241	0.739	0.307	0.716	0.285	0.999	0.750	9.555	0.383	.	.	.	ID=COSV62003051;OCCURENCE=1(breast),1(large_intestine),13(soft_tissue),2(lung),33(upper_aerodigestive_tract)	138206	Lymphedema,_primary,_with_myelodysplasia|not_specified	MONDO:MONDO:0013540,MedGen:C3279664,OMIM:614038,Orphanet:ORPHA3226|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU83133	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|2|170|0.0117647,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.5	295	101	3	128204951	.	C	T	295	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=692;VD=348;AF=0.5029;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.06301;SOR=1.42046;LSEQ=AAGGTGGGAGCCAGAGTGGG;RSEQ=TGCTGTAGGGGTGAGGGAGG;CSQ=T|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145661.2|protein_coding|4/7||NM_001145661.2:c.490G>A|NP_001139133.1:p.Ala164Thr|925|490|164|A/T|Gcc/Acc|rs2335052&CM066570&COSV62003051||-1||EntrezGene||YES||||3:g.128204951C>T|0.1983|0.1802|0.2735|0.2295|0.3787|0.1775|0.1542|0.1885|0.1824|0.3787|gnomAD_EAS|benign|0&0&1|1&1&1,T|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145662.1|protein_coding|3/6||NM_001145662.1:c.490G>A|NP_001139134.1:p.Ala164Thr|746|490|164|A/T|Gcc/Acc|rs2335052&CM066570&COSV62003051||-1||EntrezGene||||||3:g.128204951C>T|0.1983|0.1802|0.2735|0.2295|0.3787|0.1775|0.1542|0.1885|0.1824|0.3787|gnomAD_EAS|benign|0&0&1|1&1&1,T|missense_variant|MODERATE|GATA2|2624|Transcript|NM_032638.5|protein_coding|3/6||NM_032638.5:c.490G>A|NP_116027.2:p.Ala164Thr|838|490|164|A/T|Gcc/Acc|rs2335052&CM066570&COSV62003051||-1||EntrezGene||||||3:g.128204951C>T|0.1983|0.1802|0.2735|0.2295|0.3787|0.1775|0.1542|0.1885|0.1824|0.3787|gnomAD_EAS|benign|0&0&1|1&1&1,T|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA||||||||||rs2335052&CM066570&COSV62003051|3095|1||EntrezGene||YES||||3:g.128204951C>T|0.1983|0.1802|0.2735|0.2295|0.3787|0.1775|0.1542|0.1885|0.1824|0.3787|gnomAD_EAS|benign|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:692:348:201,147:199,144:343,348:0.5029:2,2:34.6:1:35:1:1:1.01066:60:28:0.4956:0:1.8	0/1:101:42:25,17:36,23:59,42:0.4158:2,2:38:1:36.1:1:1:1.06369:60:84:0.4242:0:2.4
    1242. 

  1242. 3	128205062	128205062	G	A	exonic	GATA2	.	nonsynonymous SNV	GATA2:NM_001145662:exon3:c.C379T:p.H127Y,GATA2:NM_032638:exon3:c.C379T:p.H127Y,GATA2:NM_001145661:exon4:c.C379T:p.H127Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.989	0.715	D	0.979	0.728	D	0.000	0.843	D	1	0.810	D	2.485	0.726	M	-4.65	0.979	D	-3.41	0.804	D	0.65	0.664	1.077	0.988	D	0.951	0.984	D	0.635	0.969	D	5.340	0.723	25.8	0.997	0.785	0.992	0.932	D	c	0.673	0.605	1.000	0.747	0.598	0.340	0	4.17	0.481	9.238	0.944	0.814	0.334	1.000	0.715	0.988	0.529	16.238	0.821	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	173	3	128205062	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1553;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00999;SOR=0;LSEQ=GCCTCCAGCAGCTGAGGGGT;RSEQ=CAGTGGCGTCTTGGAGAAGG;CSQ=A|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145661.2|protein_coding|4/7||NM_001145661.2:c.379C>T|NP_001139133.1:p.His127Tyr|814|379|127|H/Y|Cac/Tac|rs1163426216||-1||EntrezGene||YES||||3:g.128205062G>A|6.177e-06|0.0001094|0|0|0|0|0|0|0|0.0001094|gnomAD_AFR|||,A|missense_variant|MODERATE|GATA2|2624|Transcript|NM_001145662.1|protein_coding|3/6||NM_001145662.1:c.379C>T|NP_001139134.1:p.His127Tyr|635|379|127|H/Y|Cac/Tac|rs1163426216||-1||EntrezGene||||||3:g.128205062G>A|6.177e-06|0.0001094|0|0|0|0|0|0|0|0.0001094|gnomAD_AFR|||,A|missense_variant|MODERATE|GATA2|2624|Transcript|NM_032638.5|protein_coding|3/6||NM_032638.5:c.379C>T|NP_116027.2:p.His127Tyr|727|379|127|H/Y|Cac/Tac|rs1163426216||-1||EntrezGene||||||3:g.128205062G>A|6.177e-06|0.0001094|0|0|0|0|0|0|0|0.0001094|gnomAD_AFR|||,A|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA||||||||||rs1163426216|2984|1||EntrezGene||YES||||3:g.128205062G>A|6.177e-06|0.0001094|0|0|0|0|0|0|0|0.0001094|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1553:0:0,0:889,663:1552,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:173:2:1,1:99,72:171,2:0.0116:2,2:68.5:1:37:0:1:1.37241:60:4:0.0118:0:1
    1243. 

  1243. 3	128205821	128205821	A	G	exonic	GATA2	.	synonymous SNV	GATA2:NM_001145662:exon2:c.T54C:p.N18N,GATA2:NM_032638:exon2:c.T54C:p.N18N,GATA2:NM_001145661:exon3:c.T54C:p.N18N	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	150	3	128205821	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1013;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01654;SOR=0;LSEQ=TGTGAGTCGGGGTGCTGCGC;RSEQ=TTCAGCACGGCCGGGTGCGC;CSQ=G|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145661.2|protein_coding|3/7||NM_001145661.2:c.54T>C|NP_001139133.1:p.Asn18%3D|489|54|18|N|aaT/aaC|||-1||EntrezGene||YES||||3:g.128205821A>G||||||||||||||,G|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145662.1|protein_coding|2/6||NM_001145662.1:c.54T>C|NP_001139134.1:p.Asn18%3D|310|54|18|N|aaT/aaC|||-1||EntrezGene||||||3:g.128205821A>G||||||||||||||,G|synonymous_variant|LOW|GATA2|2624|Transcript|NM_032638.5|protein_coding|2/6||NM_032638.5:c.54T>C|NP_116027.2:p.Asn18%3D|402|54|18|N|aaT/aaC|||-1||EntrezGene||||||3:g.128205821A>G||||||||||||||,G|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA|||||||||||2225|1||EntrezGene||YES||||3:g.128205821A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1013:0:0,0:408,605:1013,0:0:2,0:37.6:1:36.3:1:1:0:60:91.091:1:0:0.7	0/1:150:2:1,1:53,95:148,2:0.0133:2,2:17:1:37:0:1:1.79:60:4:0.0134:0:1.5
    1244. 

  1244. 3	128205860	128205860	G	C	exonic	GATA2	.	synonymous SNV	GATA2:NM_001145662:exon2:c.C15G:p.P5P,GATA2:NM_032638:exon2:c.C15G:p.P5P,GATA2:NM_001145661:exon3:c.C15G:p.P5P	0.82	0.6532	0.7816	0.7236	0.7318	0.7293	0.5255	0.5987	0.5903	rs1573858	rs1573858	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV62003056;OCCURENCE=4(large_intestine),1(prostate),1(lung),1(thyroid)	250906	Lymphedema,_primary,_with_myelodysplasia|not_specified	MONDO:MONDO:0013540,MedGen:C3279664,OMIM:614038,Orphanet:ORPHA3226|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU77941	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.75	343	101	3	128205860	.	G	C	343	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=657;VD=653;AF=0.9939;SHIFT3=1;MSI=3;MSILEN=1;SSF=0;SOR=157.732;LSEQ=GCCATCCAGCGCGGCTGCTC;RSEQ=GGCGCCACCTCCATGGCCGG;CSQ=C|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145661.2|protein_coding|3/7||NM_001145661.2:c.15C>G|NP_001139133.1:p.Pro5%3D|450|15|5|P|ccC/ccG|rs1573858&COSV62003056||-1||EntrezGene||YES||||3:g.128205860G>C|0.6647|0.7858|0.7091|0.7516|0.7091|0.5328|0.6381|0.6781|0.6731|0.8222|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|GATA2|2624|Transcript|NM_001145662.1|protein_coding|2/6||NM_001145662.1:c.15C>G|NP_001139134.1:p.Pro5%3D|271|15|5|P|ccC/ccG|rs1573858&COSV62003056||-1||EntrezGene||||||3:g.128205860G>C|0.6647|0.7858|0.7091|0.7516|0.7091|0.5328|0.6381|0.6781|0.6731|0.8222|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|GATA2|2624|Transcript|NM_032638.5|protein_coding|2/6||NM_032638.5:c.15C>G|NP_116027.2:p.Pro5%3D|363|15|5|P|ccC/ccG|rs1573858&COSV62003056||-1||EntrezGene||||||3:g.128205860G>C|0.6647|0.7858|0.7091|0.7516|0.7091|0.5328|0.6381|0.6781|0.6731|0.8222|AFR|benign|0&1|1&1,C|upstream_gene_variant|MODIFIER|GATA2-AS1|101927167|Transcript|NR_125398.1|lncRNA||||||||||rs1573858&COSV62003056|2186|1||EntrezGene||YES||||3:g.128205860G>C|0.6647|0.7858|0.7091|0.7516|0.7091|0.5328|0.6381|0.6781|0.6731|0.8222|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:657:653:225,428:0,0:0,653:0.9939:0,2:34.5:1:36.7:1:1:0:60:216.667:0.9954:0:1.1	1/0:101:51:13,38:15,35:50,51:0.505:2,2:33.3:1:36.8:1:0.6611:1.24994:60:102:0.505:0:1.1
    1245. 

  1245. 3	134514482	134514482	G	T	exonic	EPHB1	.	synonymous SNV	EPHB1:NM_004441:exon1:c.G9T:p.L3L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	134	3	134514482	.	G	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1272;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00902;SOR=0;LSEQ=CGTCGGCCGGCGATGGCCCT;RSEQ=GATTATCTACTACTGCTCCT;CSQ=T|synonymous_variant|LOW|EPHB1|2047|Transcript|NM_004441.5|protein_coding|1/16||NM_004441.5:c.9G>T|NP_004432.1:p.Leu3%3D|381|9|3|L|ctG/ctT|COSV67662032||1||EntrezGene||YES||||3:g.134514482G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1272:0:0,0:710,561:1271,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:134:2:1,1:77,55:132,2:0.0149:2,2:61.5:1:37:0:1:1.3964:60:4:0.015:0:1
    1246. 

  1246. 3	134644636	134644636	G	T	intronic	EPHB1	.	.	.	0.83	0.5447	0.7779	0.3642	0.5530	0.5087	0.4106	0.4589	0.4734	rs635721	rs635721	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67662125;OCCURENCE=1(breast),1(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU740134	COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	1	327	168	3	134644636	.	G	T	327	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=682;VD=676;AF=0.9912;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.5829;SOR=0.67493;LSEQ=CTCATTGTTTTTGTTTATTC;RSEQ=TTTTTTCTTTTTAATCTACA;CSQ=T|intron_variant|MODIFIER|EPHB1|2047|Transcript|NM_004441.5|protein_coding||1/15|NM_004441.5:c.59-22G>T|||||||rs635721&COSV67662125||1||EntrezGene||YES||||3:g.134644636G>T|0.4845|0.7905|0.3074|0.5592|0.4983|0.4124|0.4658|0.4815|0.6345|0.829|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:682:676:420,256:0,0:0,676:0.9912:0,2:28.8:1:34.8:1:1:0:60:55.333:0.994:0:1.1	1/1:168:167:108,59:0,0:0,167:0.994:0,2:36.4:1:35.7:1:1:0:60:40.75:1:0:1.2
    1247. 

  1247. 3	134670524	134670524	C	T	exonic	EPHB1	.	synonymous SNV	EPHB1:NM_004441:exon3:c.C435T:p.S145S	0.64	0.4687	0.6072	0.5359	0.5430	0.1963	0.3564	0.4412	0.4284	rs7644369	rs7644369	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67660842;OCCURENCE=1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(lung),1(thyroid)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU150981	LICA-CN|1|402|0.00248756,LAML-KR|1|205|0.00487805,LUSC-KR|3|170|0.0176471,COCA-CN|2|321|0.00623053	0.5	374	501	3	134670524	.	C	T	374	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2984;VD=1416;AF=0.4745;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.41214;SOR=0.97426;LSEQ=ACCATTGCTGCAGATGAGAG;RSEQ=TTCTCCCAGGTGGACTTTGG;CSQ=T|synonymous_variant|LOW|EPHB1|2047|Transcript|NM_004441.5|protein_coding|3/16||NM_004441.5:c.435C>T|NP_004432.1:p.Ser145%3D|807|435|145|S|agC/agT|rs7644369&COSV67660842||1||EntrezGene||YES||||3:g.134670524C>T|0.4587|0.6144|0.5229|0.5402|0.1939|0.3542|0.4539|0.4701|0.5255|0.6377|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2984:1416:730,686:792,769:1561,1416:0.4745:2,2:38:1:35.8:1:0.65974:1.03:60:44.677:0.4716:0:1.1	0/1:501:241:122,119:130,130:260,241:0.481:2,2:38.5:1:35.8:1:0.92882:1.03:60:47.2:0.4768:0:1.1
    1248. 

  1248. 3	134825326	134825326	C	A	exonic	EPHB1	.	nonsynonymous SNV	EPHB1:NM_004441:exon4:c.C842A:p.A281D	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.112	0.247	B	0.03	0.205	B	0.002	0.378	N	0.794	0.810	D	-1.525	0.005	N	-4.38	0.974	D	2.69	0.002	N	0.15	0.178	0.019	0.827	D	0.551	0.836	D	0.058	0.673	D	1.789	0.276	14.92	0.735	0.100	0.005	0.023	N	c	-0.629	-0.366	0.126	0.170	0.615	0.372	0	4.71	0.589	0.470	0.216	0.935	0.490	0.375	0.257	0.998	0.697	9.704	0.392	Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	186	3	134825326	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=982;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02524;SOR=0;LSEQ=ATTCAAGGCCAGCCAGGAAG;RSEQ=TGAAGGCTGCTCCCACTGCC;CSQ=A|missense_variant|MODERATE|EPHB1|2047|Transcript|NM_004441.5|protein_coding|4/16||NM_004441.5:c.842C>A|NP_004432.1:p.Ala281Asp|1214|842|281|A/D|gCt/gAt|||1||EntrezGene||YES||||3:g.134825326C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:982:0:0,0:571,411:982,0:0:2,0:38.2:1:36.4:1:1:0:60:121.75:1:0:0.1	0/1:186:2:1,1:105,79:184,2:0.0108:2,2:6:0:37:0:1:1.32704:60:4:0.0108:0:1
    1249. 

  1249. 3	134825428	134825428	C	G	exonic	EPHB1	.	nonsynonymous SNV	EPHB1:NM_004441:exon4:c.C944G:p.P315R	.	.	.	.	.	.	.	.	.	.	.	0.21	0.196	T	0.79	0.426	P	0.504	0.459	P	0.000	0.843	D	1	0.810	D	1.68	0.433	L	-4.45	0.975	D	-3.46	0.677	D	0.676	0.685	0.880	0.954	D	0.895	0.965	D	0.161	0.842	D	3.349	0.461	22.9	0.993	0.595	0.149	0.185	N	c	0.525	0.588	1.000	0.747	0.713	0.819	0	5.96	0.967	5.054	0.639	0.935	0.490	0.981	0.351	0.998	0.697	20.422	0.990	Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	188	3	134825428	.	C	G	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1063;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02248;SOR=0;LSEQ=CCGAGCGGACTTTGACCCTC;RSEQ=AGAAGTGGCATGCACTAGTA;CSQ=G|missense_variant|MODERATE|EPHB1|2047|Transcript|NM_004441.5|protein_coding|4/16||NM_004441.5:c.944C>G|NP_004432.1:p.Pro315Arg|1316|944|315|P/R|cCa/cGa|||1||EntrezGene||YES||||3:g.134825428C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1063:0:0,0:474,588:1062,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:188:2:1,1:78,108:186,2:0.0106:2,2:17:1:37:0:1:1.38:60:4:0.0107:0:2
    1250. 

  1250. 3	134880861	134880861	A	G	exonic	EPHB1	.	nonsynonymous SNV	EPHB1:NM_004441:exon7:c.A1424G:p.E475G	.	.	.	.	.	.	.	.	.	.	.	0.307	0.182	T	0.032	0.189	B	0.032	0.208	B	0.001	0.437	D	1.000	0.588	D	-0.145	0.044	N	0.57	0.544	T	-1.96	0.454	N	0.344	0.407	-1.028	0.210	T	0.069	0.283	T	0.018	0.404	T	3.111	0.434	22.5	0.994	0.648	0.968	0.706	D	c	-0.300	-0.036	1.000	0.747	0.653	0.482	0	5.54	0.828	4.208	0.580	1.199	0.960	1.000	0.715	0.958	0.437	15.847	0.786	Ephrin receptor ligand binding domain|Galactose-binding domain-like;Fibronectin type III|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	201	3	134880861	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1893;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00917;SOR=0;LSEQ=TTCCCTTGCTTTCTTTTAGG;RSEQ=ACACAATGAGTTCAACTCCT;CSQ=G|missense_variant&splice_region_variant|MODERATE|EPHB1|2047|Transcript|NM_004441.5|protein_coding|7/16||NM_004441.5:c.1424A>G|NP_004432.1:p.Glu475Gly|1796|1424|475|E/G|gAa/gGa|||1||EntrezGene||YES||||3:g.134880861A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1893:0:0,0:1118,775:1893,0:0:2,0:38.1:1:36.5:1:1:0:60:134.214:1:0:0.2	0/1:201:2:1,1:129,70:199,2:0.01:2,2:24:1:37:0:1:1.83698:60:4:0.01:0:1
    1251. 

  1251. 3	134898742	134898742	C	T	exonic	EPHB1	.	synonymous SNV	EPHB1:NM_004441:exon10:c.C1800T:p.Y600Y	0.74	0.4358	0.5083	0.4653	0.2748	0.7172	0.3184	0.3933	0.4206	rs1042787	rs1042787	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67654940;OCCURENCE=12(soft_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU4133192	COCA-CN|5|321|0.0155763	0.75	311	384	3	134898742	.	C	T	311	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1415;VD=652;AF=0.4608;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00226;LSEQ=TACATTGACCCCTTCACTTA;RSEQ=GAGGATCCCAACGAAGCTGT;CSQ=T|synonymous_variant|LOW|EPHB1|2047|Transcript|NM_004441.5|protein_coding|10/16||NM_004441.5:c.1800C>T|NP_004432.1:p.Tyr600%3D|2172|1800|600|Y|taC/taT|rs1042787&COSV67654940||1||EntrezGene||YES||||3:g.134898742C>T|0.4465|0.5012|0.5027|0.3096|0.7334|0.3101|0.395|0.4151|0.5244|0.7334|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1415:652:308,344:370,387:757,652:0.4608:2,2:39:1:33.3:1:0.55661:1.06776:60:10.439:0.4424:0:1.1	1/1:384:383:186,197:0,0:0,383:0.9974:0,2:39.3:1:36:1:1:0:60:75.6:0.9974:0:1.1
    1252. 

  1252. 3	134960005	134960005	G	T	exonic	EPHB1	.	nonsynonymous SNV	EPHB1:NM_004441:exon13:c.G2362T:p.V788L	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.998	0.715	D	0.995	0.818	D	0.000	0.843	D	1	0.810	D	0.74	0.190	N	-1.73	0.833	D	-1.28	0.322	N	0.748	0.744	0.274	0.871	D	0.607	0.861	D	0.078	0.731	D	6.276	0.867	29.0	0.998	0.851	0.980	0.786	D	c	0.575	0.577	1.000	0.747	0.693	0.558	0	4.88	0.630	4.271	0.585	1.048	0.713	1.000	0.715	0.957	0.436	18.213	0.898	Fibronectin type III|Immunoglobulin-like fold;Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV67667547;OCCURENCE=1(biliary_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	55	306	3	134960005	.	G	T	55	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2557;VD=1;AF=0.0004;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00059;SOR=0.02964;LSEQ=TTCAGGGAGGGAAGATCCCT;RSEQ=TGAGATGGACAGCTCCAGAG;CSQ=T|missense_variant|MODERATE|EPHB1|2047|Transcript|NM_004441.5|protein_coding|13/16||NM_004441.5:c.2362G>T|NP_004432.1:p.Val788Leu|2734|2362|788|V/L|Gtg/Ttg|COSV67667547||1||EntrezGene||YES||||3:g.134960005G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2557:1:1,0:1401,1155:2556,1:0.0004:2,0:47:0:11:0:1:0:60:0:0:0:8	0/1:306:4:2,2:184,118:302,4:0.0131:2,2:13.2:1:27.5:1:0.64649:1.55694:60:3:0.0099:0:1
    1253. 

  1253. 3	134967368	134967368	G	A	intronic	EPHB1	.	.	.	0.37	0.2490	0.2552	0.2386	0.2914	0.2867	0.2944	0.2304	0.25	rs11717042	rs11717042	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV67654946;OCCURENCE=3(haematopoietic_and_lymphoid_tissue),12(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU28582199	ESAD-UK|1|409|0.00244499,LICA-CN|1|402|0.00248756,LAML-KR|4|205|0.0195122,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.75	325	195	3	134967368	.	G	A	325	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1056;VD=514;AF=0.4867;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGTGTGAGTCTAGTGAAAC;RSEQ=GTGATCCCTAAATATGGCTG;CSQ=A|intron_variant|MODIFIER|EPHB1|2047|Transcript|NM_004441.5|protein_coding||14/15|NM_004441.5:c.2690+17G>A|||||||rs11717042&COSV67654946||1||EntrezGene||YES||||3:g.134967368G>A|0.2567|0.2623|0.2408|0.3274|0.2948|0.3034|0.2218|0.2412|0.3129|0.3558|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1056:514:180,334:210,329:539,514:0.4867:2,2:37.4:1:36.1:1:0.20175:1.1842:60:56.111:0.486:0:1.1	1/1:195:195:71,124:0,0:0,195:1:0,2:40.7:1:36.2:1:1:0:60:64:1:0:1.1
    1254. 

  1254. 3	138374239	138374239	T	G	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_001256045:exon13:c.A1741C:p.R581R,PIK3CB:NM_006219:exon22:c.A3205C:p.R1069R	0.078	0.0039	0	0	0	0.0723	0	0.0002	0.0010	rs28763907	rs28763907	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56686416;OCCURENCE=1(breast),1(stomach),2(haematopoietic_and_lymphoid_tissue)	733829	not_provided	MedGen:CN517202	criteria_provided,_single_submitter	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	1	MU11478877	LICA-CN|1|402|0.00248756,LAML-KR|2|205|0.0097561,BRCA-KR|1|50|0.02	0.25	248	287	3	138374239	.	T	G	248	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=365;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGCTGATCGTTAAGATC;RSEQ=GTAGTCTTTCCGAACTGTGT;CSQ=G|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|13/13||NM_001256045.2:c.1741A>C|NP_001242974.1:p.Arg581%3D|2087|1741|581|R|Aga/Cga|rs28763907&COSV56686416||-1||EntrezGene||||||3:g.138374239T>G|0.00566|0|2.895e-05|0|0.0721|0|0.0001411|0.002447|0.002059|0.0784|EAS|benign|0&1|1&1,G|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|24/24||NM_006219.3:c.3205A>C|NP_006210.1:p.Arg1069%3D|3560|3205|1069|R|Aga/Cga|rs28763907&COSV56686416||-1||EntrezGene||YES||||3:g.138374239T>G|0.00566|0|2.895e-05|0|0.0721|0|0.0001411|0.002447|0.002059|0.0784|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:365:0:0,0:201,164:365,0:0:2,0:38.5:1:36.2:1:1:0:60:72:1:0:0	0/1:287:119:71,48:98,68:166,119:0.4146:2,2:40:1:36:1:1:1.03:60:118:0.417:0:1.1
    1255. 

  1255. 3	138376490	138376490	A	G	intronic	PIK3CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	172	3	138376490	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=127;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.33009;SOR=0;LSEQ=TCCACCTGGTCAGATAAGAA;RSEQ=ATGTTAGAAGTGTTCAGCCT;CSQ=G|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||11/12|NM_001256045.2:c.1478+42T>C|||||||||-1||EntrezGene||||||3:g.138376490A>G||||||||||||||,G|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||22/23|NM_006219.3:c.2942+42T>C|||||||||-1||EntrezGene||YES||||3:g.138376490A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:127:0:0,0:71,56:127,0:0:2,0:37:1:35.7:1:1:0:60:30.75:1:0:0.1	0/1:172:2:1,1:102,68:170,2:0.0116:2,2:5:0:37:0:1:1.49633:60:4:0.0118:0:1
    1256. 

  1256. 3	138376505	138376505	C	A	intronic	PIK3CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	189	3	138376505	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=150;VD=2;AF=0.0133;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.19506;SOR=inf;LSEQ=AAGAAAATGTTAGAAGTGTT;RSEQ=AGCCTTGGCACAAGGGCAGT;CSQ=A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||11/12|NM_001256045.2:c.1478+27G>T|||||||||-1||EntrezGene||||||3:g.138376505C>A||||||||||||||,A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||22/23|NM_006219.3:c.2942+27G>T|||||||||-1||EntrezGene||YES||||3:g.138376505C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:150:2:1,1:81,67:148,2:0.0133:2,2:38:0:37:0:1:1.20741:60:4:0.0135:0:1	0/0:189:0:0,0:102,87:189,0:0:2,0:38.1:1:36.7:1:1:0:60:188:1:0:0.1
    1257. 

  1257. 3	138384064	138384064	G	A	intronic	PIK3CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	256	3	138384064	.	G	A	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=2;AF=0.0187;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08631;SOR=inf;LSEQ=TCCTGGAAGGAAAAAAATGG;RSEQ=CATAGAGTCATATTTTCCTT;CSQ=A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||8/12|NM_001256045.2:c.1041-19C>T|||||||||-1||EntrezGene||||||3:g.138384064G>A||||||||||||||,A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||19/23|NM_006219.3:c.2505-19C>T|||||||||-1||EntrezGene||YES||||3:g.138384064G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:23,82:105,2:0.0187:2,2:11:0:31:1:0.39993:3.51:60:4:0.019:0:1	0/0:256:0:0,0:76,179:255,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1258. 

  1258. 3	138384073	138384073	C	T	intronic	PIK3CB	.	.	.	0.45	0.0606	0.0597	0.0263	0.0331	0.4460	0.0507	0.0248	0.0560	rs2305268	rs2305268	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU761104	LICA-CN|3|402|0.00746269,COCA-CN|2|321|0.00623053	0.75	285	234	3	138384073	.	C	T	285	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=79;VD=34;AF=0.4304;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.00668;LSEQ=GAAAAAAATGGGCATAGAGT;RSEQ=ATATTTTCCTTAAAATGAAA;CSQ=T|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||8/12|NM_001256045.2:c.1041-28G>A|||||||rs2305268||-1||EntrezGene||||||3:g.138384073C>T|0.06865|0.05765|0.02246|0.0442|0.4409|0.04797|0.02034|0.06312|0.1053|0.4474|EAS|||,T|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||19/23|NM_006219.3:c.2505-28G>A|||||||rs2305268||-1||EntrezGene||YES||||3:g.138384073C>T|0.06865|0.05765|0.02246|0.0442|0.4409|0.04797|0.02034|0.06312|0.1053|0.4474|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:79:34:7,27:10,35:45,34:0.4304:2,2:27.9:1:36.6:1:1:1.10067:60:68:0.4359:0:1.1	1/1:234:232:64,168:0,0:0,232:0.9915:0,2:40.4:1:36.3:1:1:0:60:115:0.9957:0:1.1
    1259. 

  1259. 3	138413784	138413784	G	T	intronic	PIK3CB	.	.	.	0.	.	.	.	.	.	.	.	.	rs760263126	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	188	3	138413784	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=198;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.23657;SOR=0;LSEQ=AAACTGGTTCAGAAATAATG;RSEQ=GGGACAAAAGTAATCTAATT;CSQ=T|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||2/12|NM_001256045.2:c.307-35C>A|||||||rs760263126||-1||EntrezGene||||||3:g.138413784G>T|1.387e-05|0|0|0|0|5.048e-05|1.941e-05|0|0|5.048e-05|gnomAD_FIN|||,T|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||13/23|NM_006219.3:c.1771-35C>A|||||||rs760263126||-1||EntrezGene||YES||||3:g.138413784G>T|1.387e-05|0|0|0|0|5.048e-05|1.941e-05|0|0|5.048e-05|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:198:0:0,0:33,165:198,0:0:2,0:27.3:1:36.1:1:1:0:60:65:1:0:0.2	0/1:188:2:1,1:61,125:186,2:0.0106:2,2:50:1:37:0:0.552:2.04:60:4:0.0107:0:1
    1260. 

  1260. 3	138417747	138417747	A	G	splicing	PIK3CB	NM_006219:exon11:c.1770+2T>C;NM_001256045:exon2:c.306+2T>C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.138	0.693	25.4	0.995	0.683	0.973	0.737	D	c	1.152	1.013	1.000	0.747	0.156	0.027	0	5.68	0.880	8.947	0.927	1.140	0.893	1.000	0.715	0.987	0.523	15.931	0.794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	168	3	138417747	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.60978;SOR=0;LSEQ=TATAGAAACGATCTTTTGTT;RSEQ=CCTGAGCAACATCCTCAAGT;CSQ=G|splice_donor_variant|HIGH|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||2/12|NM_001256045.2:c.306+2T>C|||||||||-1||EntrezGene||||||3:g.138417747A>G||||||||||||||,G|splice_donor_variant|HIGH|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||13/23|NM_006219.3:c.1770+2T>C|||||||||-1||EntrezGene||YES||||3:g.138417747A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:47:0:0,0:29,18:47,0:0:2,0:27.9:1:36.2:1:1:0:60:94:1:0:0	0/1:168:2:1,1:108,58:166,2:0.0119:2,2:22.5:1:37:0:1:1.85482:60:4:0.0119:0:1
    1261. 

  1261. 3	138417773	138417773	C	A	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_001256045:exon2:c.G282T:p.W94C,PIK3CB:NM_006219:exon11:c.G1746T:p.W582C	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	3.645	0.943	H	-0.4	0.693	T	-12.0	0.996	D	0.92	0.957	0.375	0.887	D	0.619	0.866	D	0.140	0.823	D	7.303	0.948	34	0.994	0.637	0.955	0.648	D	c	0.978	0.928	1.0	0.983	0.706	0.609	0	5.91	0.952	7.568	0.814	0.892	0.403	1.000	0.715	1.000	0.888	20.296	0.985	Armadillo-type fold|Phosphoinositide 3-kinase, accessory (PIK) domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	222	3	138417773	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=2;AF=0.0357;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.04;SOR=inf;LSEQ=GCAACATCCTCAAGTTTATT;RSEQ=CACTTGATTGACAGCAGTAA;CSQ=A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|2/13||NM_001256045.2:c.282G>T|NP_001242974.1:p.Trp94Cys|628|282|94|W/C|tgG/tgT|||-1||EntrezGene||||||3:g.138417773C>A||||||||||||||,A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|13/24||NM_006219.3:c.1746G>T|NP_006210.1:p.Trp582Cys|2101|1746|582|W/C|tgG/tgT|||-1||EntrezGene||YES||||3:g.138417773C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:56:2:1,1:32,22:54,2:0.0357:2,2:51.5:1:37:0:1:1.4446:60:4:0.037:0:1	0/0:222:0:0,0:125,97:222,0:0:2,0:37.4:1:36.3:1:1:0:60:73:1:0:0.1
    1262. 

  1262. 3	138423254	138423254	G	A	intronic	PIK3CB	.	.	.	.	.	.	.	.	.	.	.	.	rs941207493	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	132	3	138423254	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=2;AF=0.0476;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.05721;SOR=inf;LSEQ=TAATGTGCACAACTCCATAA;RSEQ=AAAGGGCCATTTAAAACTCT;CSQ=A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding||1/12|NM_001256045.2:c.117+2747C>T|||||||rs941207493||-1||EntrezGene||||||3:g.138423254G>A||||||||||||||,A|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||12/23|NM_006219.3:c.1581+31C>T|||||||rs941207493||-1||EntrezGene||YES||||3:g.138423254G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:42:2:1,1:16,24:40,2:0.0476:2,2:50:1:37:0:1:1.49:60:4:0.0476:0:2	0/0:132:0:0,0:75,57:132,0:0:2,0:38.2:1:35.5:1:1:0:60:65:1:0:0
    1263. 

  1263. 3	138426004	138426004	A	G	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_001256045:exon1:c.T114C:p.D38D,PIK3CB:NM_006219:exon9:c.T1527C:p.D509D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	137	3	138426004	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.83365;SOR=0;LSEQ=TTAAATAATTAGCTTACCTT;RSEQ=TCGAAGGGAGGGTAATAATA;CSQ=G|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|1/13||NM_001256045.2:c.114T>C|NP_001242974.1:p.Asp38%3D|460|114|38|D|gaT/gaC|||-1||EntrezGene||||||3:g.138426004A>G||||||||||||||,G|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|11/24||NM_006219.3:c.1527T>C|NP_006210.1:p.Asp509%3D|1882|1527|509|D|gaT/gaC|||-1||EntrezGene||YES||||3:g.138426004A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:13:0:0,0:6,7:13,0:0:2,0:35.8:1:37:0:1:0:60:26:1:0:0.2	0/1:137:2:1,1:77,58:135,2:0.0146:2,2:60:1:37:0:1:1.32479:60:4:0.0148:0:1
    1264. 

  1264. 3	138426016	138426016	G	A	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_001256045:exon1:c.C102T:p.Y34Y,PIK3CB:NM_006219:exon9:c.C1515T:p.Y505Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	134	3	138426016	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.85354;SOR=0;LSEQ=CTTACCTTATCGAAGGGAGG;RSEQ=TAATAATAAGGTTGTTTTTT;CSQ=A|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|1/13||NM_001256045.2:c.102C>T|NP_001242974.1:p.Tyr34%3D|448|102|34|Y|taC/taT|||-1||EntrezGene||||||3:g.138426016G>A||||||||||||||,A|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|11/24||NM_006219.3:c.1515C>T|NP_006210.1:p.Tyr505%3D|1870|1515|505|Y|taC/taT|||-1||EntrezGene||YES||||3:g.138426016G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:5,6:11,0:0:2,0:45.8:1:37:0:1:0:60:22:1:0:0.2	0/1:134:2:1,1:70,62:132,2:0.0149:2,2:45.5:1:37:0:1:1.12801:60:4:0.0154:0:1
    1265. 

  1265. 3	138426068	138426068	G	T	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_001256045:exon1:c.C50A:p.A17E,PIK3CB:NM_006219:exon9:c.C1463A:p.A488E	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.988	0.604	D	0.965	0.695	D	0.000	0.843	D	1.000	0.810	D	2.705	0.794	M	-0.52	0.707	T	-3.48	0.679	D	0.903	0.893	-0.621	0.640	T	0.286	0.659	T	0.066	0.698	D	5.501	0.747	26.2	0.993	0.596	0.987	0.858	D	c	0.348	0.403	1.000	0.747	0.706	0.609	0	4.96	0.650	9.317	0.954	0.998	0.613	1.000	0.715	0.744	0.320	15.044	0.714	C2 domain|Phosphatidylinositol 3-kinase, C2 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	126	3	138426068	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.87065;SOR=0;LSEQ=ATTTAACATGCAAAGCTGTT;RSEQ=CATTTTCAGTATATGGATTT;CSQ=T|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|1/13||NM_001256045.2:c.50C>A|NP_001242974.1:p.Ala17Glu|396|50|17|A/E|gCa/gAa|||-1||EntrezGene||||||3:g.138426068G>T||||||||||||||,T|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|11/24||NM_006219.3:c.1463C>A|NP_006210.1:p.Ala488Glu|1818|1463|488|A/E|gCa/gAa|||-1||EntrezGene||YES||||3:g.138426068G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:3,6:9,0:0:2,0:38.6:1:37:0:1:0:60:18:1:0:0.2	0/1:126:2:1,1:51,73:124,2:0.0159:2,2:46.5:1:37:0:1:1.43:60:4:0.0164:0:1
    1266. 

  1266. 3	138426084	138426084	G	A	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_001256045:exon1:c.C34T:p.P12S,PIK3CB:NM_006219:exon9:c.C1447T:p.P483S	.	.	.	.	.	.	.	.	.	.	.	0.007	0.599	D	1.0	0.899	D	0.994	0.807	D	0.000	0.843	D	1	0.810	D	2.97	0.856	M	-0.74	0.732	T	-6.85	0.931	D	0.739	0.756	0.178	0.855	D	0.618	0.865	D	0.081	0.737	D	5.845	0.801	27.3	0.999	0.965	0.988	0.874	D	c	0.894	0.866	1.000	0.747	0.706	0.609	0	5.84	0.934	9.317	0.954	0.998	0.613	1.000	0.715	0.997	0.653	20.129	0.980	C2 domain|Phosphatidylinositol 3-kinase, C2 domain	.	.	ID=COSV104610813;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU48045465	MELA-AU|1|183|0.00546448	0.25	37	106	3	138426084	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00549;SOR=inf;LSEQ=TGTTGCATTTTCAGTATATG;RSEQ=ATTTGTTTGAACAGTTCCCA;CSQ=A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_001256045.2|protein_coding|1/13||NM_001256045.2:c.34C>T|NP_001242974.1:p.Pro12Ser|380|34|12|P/S|Cca/Tca|COSV104610813||-1||EntrezGene||||||3:g.138426084G>A|||||||||||||1|1,A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|11/24||NM_006219.3:c.1447C>T|NP_006210.1:p.Pro483Ser|1802|1447|483|P/S|Cca/Tca|COSV104610813||-1||EntrezGene||YES||||3:g.138426084G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:9:2:1,1:2,5:7,2:0.2222:2,2:28:0:37:0:1:2.24:60:4:0.2222:0:1	0/0:106:0:0,0:37,69:106,0:0:2,0:36.5:1:35.5:1:1:0:60:52:1:0:0.2
    1267. 

  1267. 3	138433568	138433568	C	T	intronic	PIK3CB	.	.	.	0.99	0.6127	0.6083	0.7291	0.4735	0.9907	0.6583	0.5586	0.6339	rs497900	rs497900	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU4126273	ESAD-UK|1|409|0.00244499,COCA-CN|5|321|0.0155763	1	262	144	3	138433568	.	C	T	262	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=18;AF=1;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.88889;SOR=inf;LSEQ=GCCCTGACATGAACCTGTAA;RSEQ=GAAGCAGACAAAAACAAAAA;CSQ=T|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||8/23|NM_006219.3:c.1051-7G>A|||||||rs497900||-1||EntrezGene||YES||||3:g.138433568C>T|0.6262|0.6194|0.7739|0.4887|0.9901|0.6648|0.5341|0.5918|0.6433|0.9901|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:18:18:8,10:0,0:0,18:1:0,2:44.1:1:36.3:1:1:0:60:36:1:0:1.1	1/1:144:143:46,97:0,0:0,143:0.9931:0,2:41:1:36.7:1:1:0:60:142:1:0:1.1
    1268. 

  1268. 3	138433606	138433606	T	C	intronic	PIK3CB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	99	3	138433606	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=2;AF=0.1818;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00917;SOR=inf;LSEQ=AAACAAAGTCATGAATACTG;RSEQ=ACCACGAAAAACATCTCTTT;CSQ=C|intron_variant|MODIFIER|PIK3CB|5291|Transcript|NM_006219.3|protein_coding||8/23|NM_006219.3:c.1051-45A>G|||||||||-1||EntrezGene||YES||||3:g.138433606T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:11:2:1,1:2,7:9,2:0.1818:2,2:48:1:37:0:0.49091:3.06:60:4:0.1818:0:2	0/0:99:0:0,0:29,70:99,0:0:2,0:37.2:1:36.3:1:1:0:60:98:1:0:1
    1269. 

  1269. 3	138452232	138452232	T	A	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_006219:exon6:c.A1021T:p.N341Y	.	.	.	.	.	.	.	.	.	.	.	0.021	0.491	D	0.153	0.265	B	0.139	0.319	B	0.000	0.629	D	1.000	0.508	D	1.5	0.380	L	-0.05	0.634	T	-2.02	0.465	N	0.392	0.456	-0.899	0.481	T	0.179	0.525	T	0.019	0.410	T	4.613	0.618	24.4	0.989	0.481	0.981	0.792	D	c	0.032	0.226	1.000	0.747	0.706	0.609	0	5.68	0.880	6.443	0.732	1.011	0.635	1.000	0.715	1.000	0.888	15.918	0.792	C2 domain|Phosphatidylinositol 3-kinase, C2 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	64	3	138452232	.	T	A	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.9118;SOR=0;LSEQ=TTCCTCTGTGTTAAGTTTAT;RSEQ=TCCCTTAACCAAGACAATTT;CSQ=A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|8/24||NM_006219.3:c.1021A>T|NP_006210.1:p.Asn341Tyr|1376|1021|341|N/Y|Aat/Tat|||-1||EntrezGene||YES||||3:g.138452232T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:0,3:3,0:0:0,0:23.3:1:33:1:1:0:60:6:1:0:0.3	0/1:64:2:1,1:30,32:62,2:0.0312:2,2:51:0:37:0:1:1.07:60:4:0.0328:0:1
    1270. 

  1270. 3	138461404	138461404	C	T	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_006219:exon3:c.G617A:p.C206Y	.	.	.	.	.	.	.	.	.	.	.	0.021	0.491	D	0.159	0.267	B	0.317	0.399	B	0.000	0.457	D	0.709	0.335	D	1.79	0.469	L	0.99	0.418	T	-1.42	0.350	N	0.34	0.475	-0.975	0.361	T	0.119	0.418	T	0.022	0.449	T	1.908	0.290	15.64	0.652	0.075	0.888	0.487	D	c	-0.646	-0.550	0.140	0.173	0.706	0.609	0	2.08	0.260	2.248	0.426	-0.569	0.046	1.000	0.715	0.508	0.272	18.681	0.915	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain|Ubiquitin-related domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	122	3	138461404	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=2;AF=0.0571;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04859;SOR=inf;LSEQ=AAAAATATAATCCTACCTGG;RSEQ=AGTTTTCAAAATGAACAGCT;CSQ=T|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|5/24||NM_006219.3:c.617G>A|NP_006210.1:p.Cys206Tyr|972|617|206|C/Y|tGc/tAc|||-1||EntrezGene||YES||||3:g.138461404C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:35:2:1,1:23,10:33,2:0.0571:2,2:25.5:1:37:0:0.53613:2.24016:60:4:0.0571:0:1	0/0:122:0:0,0:85,37:122,0:0:2,0:36.8:1:36.1:1:1:0:60:39.667:1:0:0.1
    1271. 

  1271. 3	138461420	138461420	C	A	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_006219:exon3:c.G601T:p.V201F	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.936	0.504	P	0.756	0.544	P	0.000	0.629	D	0.795	0.344	D	2.25	0.640	M	0.81	0.485	T	-3.09	0.634	D	0.667	0.678	-0.868	0.507	T	0.172	0.515	T	0.042	0.605	D	4.835	0.649	24.8	0.993	0.592	0.751	0.365	D	c	-0.124	-0.102	0.381	0.200	0.706	0.609	0	4.15	0.478	0.186	0.167	0.040	0.155	0.991	0.370	0.985	0.512	12.431	0.547	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain|Ubiquitin-related domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	142	3	138461420	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.59462;SOR=0;LSEQ=CTGGCAGTTTTCAAAATGAA;RSEQ=AGCTACGATGAGCTTTCCCC;CSQ=A|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|5/24||NM_006219.3:c.601G>T|NP_006210.1:p.Val201Phe|956|601|201|V/F|Gtt/Ttt|||-1||EntrezGene||YES||||3:g.138461420C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:29,13:42,0:0:2,0:37.6:1:35.8:1:1:0:60:41:1:0:0.1	0/1:142:2:1,1:90,50:140,2:0.0141:2,2:19.5:1:37:0:1:1.79204:60:4:0.0142:0:1
    1272. 

  1272. 3	138461506	138461506	A	G	exonic	PIK3CB	.	nonsynonymous SNV	PIK3CB:NM_006219:exon3:c.T515C:p.L172P	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.993	0.637	D	0.927	0.644	D	0.000	0.843	D	1	0.810	D	2.085	0.579	M	0.79	0.491	T	-3.99	0.739	D	0.956	0.955	-0.569	0.661	T	0.316	0.686	T	0.037	0.577	D	5.743	0.785	26.9	0.999	0.977	0.996	0.983	D	c	0.448	0.543	1.000	0.747	0.732	0.924	0	5.98	0.971	7.673	0.828	1.140	0.893	1.000	0.715	0.989	0.536	16.473	0.839	Ubiquitin-related domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	202	3	138461506	.	A	G	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=107;VD=2;AF=0.0187;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.11917;SOR=inf;LSEQ=CTGGTGGATATGTTTGTTTT;RSEQ=GCCAGTCCATCCAAGACAAT;CSQ=G|missense_variant|MODERATE|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|5/24||NM_006219.3:c.515T>C|NP_006210.1:p.Leu172Pro|870|515|172|L/P|cTa/cCa|||-1||EntrezGene||YES||||3:g.138461506A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:55,50:105,2:0.0187:2,2:51:0:31:1:1:1.09902:60:4:0.0187:0:1	0/0:202:0:0,0:96,106:202,0:0:2,0:39.5:1:36.9:1:1:0:60:404:1:0:0.2
    1273. 

  1273. 3	138461567	138461567	T	-	exonic	PIK3CB	.	frameshift deletion	PIK3CB:NM_006219:exon3:c.454delA:p.M152Cfs*21	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	165	3	138461566	.	AT	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=80;VD=2;AF=0.025;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.10572;SOR=inf;LSEQ=TTTCCTCGCTGAATTTGCGC;RSEQ=TTTTCTTCGAAATTCATTTA;CSQ=-|frameshift_variant|HIGH|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|5/24||NM_006219.3:c.454del|NP_006210.1:p.Met152CysfsTer21|809|454|152|M/X|Atg/tg|||-1||EntrezGene||YES||||3:g.138461571del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:33,45:78,2:0.025:2,2:19.5:1:37:1:1:1.36:60:4:0.026:0.0125:0	0/0:165:0:0,0:66,98:164,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1274. 

  1274. 3	138461580	138461580	T	C	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_006219:exon3:c.A441G:p.E147E	.	3.229e-05	0	0	0	0	0	6.66e-05	0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	151	3	138461580	.	T	C	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=2;AF=0.0339;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.07797;SOR=inf;LSEQ=TTGCGCATTTTTCTTCGAAA;RSEQ=TCATTTACTTCAGGATCCTT;CSQ=C|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|5/24||NM_006219.3:c.441A>G|NP_006210.1:p.Glu147%3D|796|441|147|E|gaA/gaG|rs1342209357||-1||EntrezGene||YES||||3:g.138461580T>C|7.967e-06|0|5.798e-05|0|0|0|0|0|0|5.798e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:59:2:1,1:20,37:57,2:0.0339:2,2:25:0:31:1:1:1.83:60:4:0.0345:0:1	0/0:151:0:0,0:56,95:151,0:0:2,0:37.6:1:36.5:1:1:0:60:302:1:0:0.2
    1275. 

  1275. 3	138478060	138478060	G	A	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_006219:exon1:c.C126T:p.I42I	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	336	3	138478060	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=154;VD=2;AF=0.013;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09833;SOR=inf;LSEQ=TCCCGAGGTACCTCCAACTG;RSEQ=ATATAAATCCCAGTGGGCAA;CSQ=A|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|3/24||NM_006219.3:c.126C>T|NP_006210.1:p.Ile42%3D|481|126|42|I|atC/atT|||-1||EntrezGene||YES||||3:g.138478060G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:154:2:1,1:97,55:152,2:0.013:2,2:5:0:37:0:1:1.75672:60:4:0.0133:0:1	0/0:336:0:0,0:191,144:335,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1276. 

  1276. 3	138478075	138478075	G	A	exonic	PIK3CB	.	synonymous SNV	PIK3CB:NM_006219:exon1:c.C111T:p.P37P	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100006029;OCCURENCE=1(lung)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU130900674	LUSC-US|1|485|0.00206186	0.25	37	367	3	138478075	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=185;VD=2;AF=0.0108;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.11192;SOR=inf;LSEQ=AACTGGATATAAATCCCAGT;RSEQ=GGCAAAAGGAAATCCACAGG;CSQ=A|synonymous_variant|LOW|PIK3CB|5291|Transcript|NM_006219.3|protein_coding|3/24||NM_006219.3:c.111C>T|NP_006210.1:p.Pro37%3D|466|111|37|P|ccC/ccT|COSV100006029||-1||EntrezGene||YES||||3:g.138478075G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:185:2:1,1:108,75:183,2:0.0108:2,2:26.5:1:37:0:1:1.43707:60:4:0.0108:0:1	0/0:367:0:0,0:194,173:367,0:0:2,0:38.9:1:36.6:1:1:0:60:90.75:1:0:0.1
    1277. 

  1277. 3	138664508	138664508	G	T	exonic	FOXL2	.	nonsynonymous SNV	FOXL2:NM_023067:exon1:c.C1057A:p.L353I	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.816	0.436	P	0.132	0.314	B	.	.	.	0.999	0.452	D	1.545	0.392	L	-3.52	0.947	D	-0.62	0.183	N	0.164	0.198	0.376	0.887	D	0.673	0.887	D	0.947	0.996	D	3.853	0.520	23.4	0.977	0.347	0.923	0.551	D	c	0.154	0.174	1.000	0.747	0.598	0.340	0	2.64	0.304	4.494	0.598	0.754	0.309	1.000	0.715	1.000	0.888	10.437	0.434	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	99	3	138664508	.	G	T	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=446;VD=1;AF=0.0022;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.08648;SOR=0.10967;LSEQ=AGAGCAATGCATCATGGCGA;RSEQ=CTCGGGCTGCCGGGCACAAG;CSQ=T|upstream_gene_variant|MODIFIER|FOXL2NB|401089|Transcript|NM_001040061.3|protein_coding|||||||||||1551|1||EntrezGene||YES||||3:g.138664508G>T||||||||||||||,T|missense_variant|MODERATE|FOXL2|668|Transcript|NM_023067.4|protein_coding|1/1||NM_023067.4:c.1057C>A|NP_075555.1:p.Leu353Ile|1472|1057|353|L/I|Ctc/Atc|||-1||EntrezGene||YES||||3:g.138664508G>T||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01391|103344930|Transcript|NR_121649.1|lncRNA|||||||||||1646|-1||EntrezGene||YES||||3:g.138664508G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:446:1:1,0:144,301:445,1:0.0022:2,0:62:0:11:0:0.32511:0:60:0:0:0:3	0/1:99:2:1,1:37,60:97,2:0.0202:2,2:46.5:1:37:0:1:1.61:60:4:0.0202:0:1
    1278. 

  1278. 3	142168331	142168331	C	T	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon47:c.G7875A:p.Q2625Q	0.99	0.8880	0.9702	0.7775	0.8079	0.9420	0.7995	0.8651	0.8510	rs1802904	rs1802904	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99377126;OCCURENCE=17(meninges),401(prostate)	99572	Seckel_syndrome_1|not_specified|not_provided	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU767958	LICA-CN|1|402|0.00248756,COCA-CN|5|321|0.0155763	1	258	146	3	142168331	.	C	T	258	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=40;VD=40;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTTTCATCAGTAGCTTC;RSEQ=TGTATAAGGTAATGCACATG;CSQ=T|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|47/47||NM_001184.4:c.7875G>A|NP_001175.2:p.Gln2625%3D|7904|7875|2625|Q|caG/caA|rs1802904&COSV99377126||-1||EntrezGene||YES||||3:g.142168331C>T|0.8581|0.9733|0.7565|0.7768|0.9333|0.8109|0.8561|0.8431|0.9373|0.9856|AFR|benign&benign/likely_benign|0&1|1&1,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282857.2|protein_coding||||||||||rs1802904&COSV99377126|1452|-1||EntrezGene||||||3:g.142168331C>T|0.8581|0.9733|0.7565|0.7768|0.9333|0.8109|0.8561|0.8431|0.9373|0.9856|AFR|benign&benign/likely_benign|0&1|1&1,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282859.2|protein_coding||||||||||rs1802904&COSV99377126|1452|-1||EntrezGene||||||3:g.142168331C>T|0.8581|0.9733|0.7565|0.7768|0.9333|0.8109|0.8561|0.8431|0.9373|0.9856|AFR|benign&benign/likely_benign|0&1|1&1,T|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|46/46||NM_001354579.2:c.7683G>A|NP_001341508.1:p.Gln2561%3D|7712|7683|2561|Q|caG/caA|rs1802904&COSV99377126||-1||EntrezGene||||||3:g.142168331C>T|0.8581|0.9733|0.7565|0.7768|0.9333|0.8109|0.8561|0.8431|0.9373|0.9856|AFR|benign&benign/likely_benign|0&1|1&1,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_019001.5|protein_coding||||||||||rs1802904&COSV99377126|1452|-1||EntrezGene||YES||||3:g.142168331C>T|0.8581|0.9733|0.7565|0.7768|0.9333|0.8109|0.8561|0.8431|0.9373|0.9856|AFR|benign&benign/likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:40:40:23,17:0,0:0,40:1:0,2:30.9:1:36:1:1:0:60:39:1:0:1	1/1:146:146:85,61:0,0:0,146:1:0,2:36.8:1:35.9:1:1:0:60:72:1:0:1.1
    1279. 

  1279. 3	142168417	142168417	G	A	exonic	ATR	.	stopgain	ATR:NM_001184:exon47:c.C7789T:p.Q2597X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.812	0.998	48	0.996	0.750	0.990	0.903	D	c	1.151	1.024	1.0	0.983	0.732	0.924	0	5.46	0.799	9.925	0.988	1.044	0.665	1.000	0.715	0.993	0.574	19.378	0.945	Phosphatidylinositol 3-/4-kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	156	3	142168417	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.57258;SOR=0;LSEQ=GATTACACCTTGTAGTCGCT;RSEQ=CTCAATGTCAAGAACATGGG;CSQ=A|stop_gained|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|47/47||NM_001184.4:c.7789C>T|NP_001175.2:p.Gln2597Ter|7818|7789|2597|Q/*|Cag/Tag|COSV53811722||-1||EntrezGene||YES||||3:g.142168417G>A|||||||||||||1|1,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282857.2|protein_coding||||||||||COSV53811722|1538|-1||EntrezGene||||||3:g.142168417G>A|||||||||||||1|1,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282859.2|protein_coding||||||||||COSV53811722|1538|-1||EntrezGene||||||3:g.142168417G>A|||||||||||||1|1,A|stop_gained|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|46/46||NM_001354579.2:c.7597C>T|NP_001341508.1:p.Gln2533Ter|7626|7597|2533|Q/*|Cag/Tag|COSV53811722||-1||EntrezGene||||||3:g.142168417G>A|||||||||||||1|1,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_019001.5|protein_coding||||||||||COSV53811722|1538|-1||EntrezGene||YES||||3:g.142168417G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:50:0:0,0:25,25:50,0:0:2,0:33.5:1:35.8:1:1:0:60:49:1:0:0.7	0/1:156:2:1,1:63,91:154,2:0.0128:2,2:38.5:1:37:0:1:1.44:60:4:0.0131:0:1.5
    1280. 

  1280. 3	142169475	142169475	C	T	intronic	ATR	.	.	.	0.0001	6.46e-05	0	0	0	0.0012	0	0	0	rs779195656	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	148	170	3	142169475	.	C	T	148	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=29;VD=16;AF=0.5517;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=inf;LSEQ=GGTGGATATGGAAGAGTATA;RSEQ=AAGGTCAGGAATAAATTAGA;CSQ=T|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||46/46|NM_001184.4:c.7762-1031G>A|||||||rs779195656||-1||EntrezGene||YES||||3:g.142169475C>T|3.981e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282857.2|protein_coding||||||||||rs779195656|2596|-1||EntrezGene||||||3:g.142169475C>T|3.981e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282859.2|protein_coding||||||||||rs779195656|2596|-1||EntrezGene||||||3:g.142169475C>T|3.981e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||,T|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||45/45|NM_001354579.2:c.7570-1031G>A|||||||rs779195656||-1||EntrezGene||||||3:g.142169475C>T|3.981e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||,T|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_019001.5|protein_coding||||||||||rs779195656|2596|-1||EntrezGene||YES||||3:g.142169475C>T|3.981e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:29:16:6,10:5,8:13,16:0.5517:2,2:38.7:1:37:0:1:1.04022:60:32:0.5517:0:1.5	0/0:170:0:0,0:77,93:170,0:0:2,0:40.1:1:36.4:1:1:0:60:169:1:0:0
    1281. 

  1281. 3	142169515	142169515	-	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	38	130	3	142169515	.	T	TA	38	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=20;VD=2;AF=0.1;SHIFT3=6;MSI=7;MSILEN=1;SSF=0.017;SOR=inf;LSEQ=ATGGTCAGTATTATGCAATT;RSEQ=AAAAAATCCTGATTAAGGGT;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||46/46|NM_001184.4:c.7762-1072dup|||||||rs1204158244||-1||EntrezGene||YES||||3:g.142169521dup||||||||||||||,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282857.2|protein_coding||||||||||rs1204158244|2636|-1||EntrezGene||||||3:g.142169521dup||||||||||||||,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_001282859.2|protein_coding||||||||||rs1204158244|2636|-1||EntrezGene||||||3:g.142169521dup||||||||||||||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||45/45|NM_001354579.2:c.7570-1072dup|||||||rs1204158244||-1||EntrezGene||||||3:g.142169521dup||||||||||||||,A|upstream_gene_variant|MODIFIER|XRN1|54464|Transcript|NM_019001.5|protein_coding||||||||||rs1204158244|2636|-1||EntrezGene||YES||||3:g.142169521dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:20:2:1,1:9,9:18,2:0.1:2,2:51.7:1:38.2:0:1:1:62:4:0.1:0:1	0/0:130:0:0,0:38,92:130,0:0:2,0:39.5:1:36.7:1:1:0:60:260:1:0:0
    1282. 

  1282. 3	142171957	142171957	A	G	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	174	3	142171957	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=2;AF=0.0667;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.02101;SOR=inf;LSEQ=TACAGCCCATATCAAGCTAT;RSEQ=CCTTCTACTAACCTTTTCAT;CSQ=G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||46/46|NM_001184.4:c.7761+13T>C|||||||||-1||EntrezGene||YES||||3:g.142171957A>G||||||||||||||,G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||45/45|NM_001354579.2:c.7569+13T>C|||||||||-1||EntrezGene||||||3:g.142171957A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:30:2:1,1:14,14:28,2:0.0667:2,2:11.5:1:37:0:1:1:60:4:0.0667:0:1	0/0:174:0:0,0:98,76:174,0:0:2,0:40.6:1:36.4:1:1:0:60:86:1:0:0
    1283. 

  1283. 3	142172011	142172011	T	C	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon46:c.A7720G:p.K2574E	.	.	.	.	.	.	.	.	.	.	.	0.033	0.443	D	0.965	0.541	D	0.444	0.441	B	0.000	0.843	D	1.000	0.588	D	1.95	0.526	M	3.92	0.035	T	-0.78	0.216	N	0.514	0.645	-0.886	0.493	T	0.176	0.521	T	0.029	0.514	D	3.777	0.511	23.4	0.995	0.684	0.969	0.715	D	c	0.172	0.248	1.000	0.517	0.732	0.924	0	5.0	0.661	6.079	0.707	0.913	0.425	1.000	0.715	0.974	0.471	14.709	0.687	Phosphatidylinositol 3-/4-kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	172	3	142172011	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=34;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.69647;SOR=0;LSEQ=AGTTTCATTCAGTGGCGCTT;RSEQ=GGAATGCCCTTTCACTGGTT;CSQ=C|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|46/47||NM_001184.4:c.7720A>G|NP_001175.2:p.Lys2574Glu|7749|7720|2574|K/E|Aaa/Gaa|||-1||EntrezGene||YES||||3:g.142172011T>C||||||||||||||,C|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|45/46||NM_001354579.2:c.7528A>G|NP_001341508.1:p.Lys2510Glu|7557|7528|2510|K/E|Aaa/Gaa|||-1||EntrezGene||||||3:g.142172011T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:34:0:0,0:15,19:34,0:0:2,0:38.2:1:36.2:1:1:0:60:33:1:0:0.1	0/1:172:2:1,1:76,94:170,2:0.0116:2,2:32.5:1:37:0:1:1.24:60:4:0.0118:0:1
    1284. 

  1284. 3	142176522	142176522	C	A	exonic	ATR	.	stopgain	ATR:NM_001184:exon45:c.G7579T:p.G2527X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.809	0.999	53	0.992	0.549	0.994	0.959	D	c	1.163	1.024	1.000	0.747	0.732	0.924	0	5.5	0.813	7.905	0.864	0.892	0.403	1.000	0.715	1.000	0.888	19.386	0.945	Phosphatidylinositol 3-/4-kinase, catalytic domain|Protein kinase-like domain	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	252	3	142176522	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=55;VD=3;AF=0.0545;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.00549;SOR=inf;LSEQ=TCGAAAAAGACCCTCTGTTC;RSEQ=CATAGGACCCATTCCATTAA;CSQ=A|stop_gained|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|45/47||NM_001184.4:c.7579G>T|NP_001175.2:p.Gly2527Ter|7608|7579|2527|G/*|Gga/Tga|||-1||EntrezGene||YES||||3:g.142176522C>A||||||||||||||,A|stop_gained|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|44/46||NM_001354579.2:c.7387G>T|NP_001341508.1:p.Gly2463Ter|7416|7387|2463|G/*|Gga/Tga|||-1||EntrezGene||||||3:g.142176522C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:55:3:1,2:23,29:52,3:0.0545:2,2:32.3:1:28.3:1:1:1.57346:60:2:0.0377:0:1.7	0/0:252:0:0,0:124,128:252,0:0:2,0:40.4:1:36:1:1:0:60:41:1:0:0.1
    1285. 

  1285. 3	142176632	142176632	T	C	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	125	3	142176632	.	T	C	25	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.92427;SOR=0;LSEQ=ATTTTATTACAAACTAACAA;RSEQ=GTTAGAATTTAAAAATCTTT;CSQ=C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||44/46|NM_001184.4:c.7504-35A>G|||||||rs747983560||-1||EntrezGene||YES||||3:g.142176632T>C|4.081e-06|0|0|0|0|0|9.02e-06|0|0|9.02e-06|gnomAD_NFE|||,C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||43/45|NM_001354579.2:c.7312-35A>G|||||||rs747983560||-1||EntrezGene||||||3:g.142176632T>C|4.081e-06|0|0|0|0|0|9.02e-06|0|0|9.02e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:0,5:5,0:0:0,0:34.4:1:37:0:1:0:60:10:1:0:0	0/1:125:2:1,1:38,85:123,2:0.016:2,2:8:1:25:0:0.52839:2.22:60:4:0.0165:0:1
    1286. 

  1286. 3	142178029	142178029	C	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	44	210	3	142178029	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.93153;SOR=0;LSEQ=TCTAAAATATTAAAAATAAA;RSEQ=ATTCAACCATAACAACGTAT;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||43/46|NM_001184.4:c.7349+40G>T|||||||||-1||EntrezGene||YES||||3:g.142178029C>A||||||||||||||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||42/45|NM_001354579.2:c.7157+40G>T|||||||||-1||EntrezGene||||||3:g.142178029C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:4,1:5,0:0:2,0:23.4:1:34.6:1:1:0:60:10:1:0:0	0/1:210:3:2,1:108,99:207,3:0.0143:2,2:46.7:1:28.3:1:1:1.83:60:2:0.0097:0:3
    1287. 

  1287. 3	142178144	142178144	C	T	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon43:c.G7274A:p.R2425Q	0.17	0.1332	0.0813	0.1160	0.0728	0.1017	0.1746	0.1584	0.1469	rs2229032	rs2229032	0.56	0.064	T	0.0	0.026	B	0.001	0.040	B	0.249	0.155	N	0.998	0.224	P	0.615	0.157	N	-1.0	0.760	T	0.04	0.065	N	0.019	0.223	-1.105	0.035	T	0.001	0.002	T	.	.	.	1.116	0.201	11.30	0.842	0.146	0.231	0.218	N	c	-1.517	-1.496	0.999	0.388	0.706	0.609	0	-9.12	0.006	0.037	0.136	-1.656	0.008	0.961	0.334	0.958	0.437	19.102	0.932	Phosphatidylinositol 3-/4-kinase, catalytic domain	ENSG00000120756.8	Artery_Aorta	ID=COSV63383988;OCCURENCE=6(meninges),1(stomach),3(haematopoietic_and_lymphoid_tissue),12(soft_tissue),2(kidney),1(thyroid),1(upper_aerodigestive_tract)	140173	Seckel_syndrome_1|not_specified|not_provided	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	0	MU586115	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,WT-US|2|102|0.0196078	0.25	264	296	3	142178144	.	C	T	264	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTGGGCAGGAGAAATTCT;RSEQ=GGAATACTTTGAGTTTTTCA;CSQ=T|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|43/47||NM_001184.4:c.7274G>A|NP_001175.2:p.Arg2425Gln|7303|7274|2425|R/Q|cGa/cAa|rs2229032&COSV63383988||-1||EntrezGene||YES||||3:g.142178144C>T|0.1306|0.07947|0.09939|0.07979|0.09815|0.1657|0.1599|0.1294|0.09569|0.172|EUR|benign|0&1|1&1,T|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|42/46||NM_001354579.2:c.7082G>A|NP_001341508.1:p.Arg2361Gln|7111|7082|2361|R/Q|cGa/cAa|rs2229032&COSV63383988||-1||EntrezGene||||||3:g.142178144C>T|0.1306|0.07947|0.09939|0.07979|0.09815|0.1657|0.1599|0.1294|0.09569|0.172|EUR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:30:0:0,0:16,14:30,0:0:2,0:40.5:1:37:0:1:0:60:60:1:0:0	1/0:296:162:81,81:68,66:134,162:0.5473:2,2:37.9:1:36.1:1:0.90758:1.03021:60:53:0.5445:0:1.1
    1288. 

  1288. 3	142183921	142183921	A	G	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	21	3	142183921	.	A	G	37	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAAATAAATAAAATAAA;RSEQ=GCAAACTATCTCCCAACCTT;CSQ=G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||41/46|NM_001184.4:c.7041+18T>C|||||||||-1||EntrezGene||YES||||3:g.142183921A>G||||||||||||||,G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||40/45|NM_001354579.2:c.6849+18T>C|||||||||-1||EntrezGene||||||3:g.142183921A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:21:2:1,1:15,4:19,2:0.0952:2,2:63.5:1:37:0:0.42857:3.46389:60:4:0.0952:0:1
    1289. 

  1289. 3	142185330	142185330	T	-	exonic	ATR	.	frameshift deletion	ATR:NM_001184:exon40:c.6733delA:p.M2245Cfs*6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	194	3	142185329	.	AT	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=15;VD=0;AF=0;SHIFT3=3;MSI=4;MSILEN=1;SSF=0.86129;SOR=0;LSEQ=CTTCTACCAGCTTTTTAAGC;RSEQ=TTTAAAATGAGTGCTCATGC;CSQ=-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|40/47||NM_001184.4:c.6733del|NP_001175.2:p.Met2245CysfsTer6|6762|6733|2245|M/X|Atg/tg|||-1||EntrezGene||YES||||3:g.142185333del||||||||||||||,-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|39/46||NM_001354579.2:c.6541del|NP_001341508.1:p.Met2181CysfsTer6|6570|6541|2181|M/X|Atg/tg|||-1||EntrezGene||||||3:g.142185333del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:5,10:15,0:0:2,0:29.7:1:37:0:1:0:60:30:1:0:0.1	0/1:194:2:1,1:54,138:192,2:0.0103:2,2:19:1:37:0:0.48769:2.54:60:4:0.0105:0:0
    1290. 

  1290. 3	142188362	142188362	G	A	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon38:c.C6369T:p.N2123N	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	124	3	142188362	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.88203;SOR=0;LSEQ=GTATGCTCTGTGATAACCTT;RSEQ=TTTATTTTACCCAAATCATT;CSQ=A|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|38/47||NM_001184.4:c.6369C>T|NP_001175.2:p.Asn2123%3D|6398|6369|2123|N|aaC/aaT|COSV99052509||-1||EntrezGene||YES||||3:g.142188362G>A|||||||||||||1|1,A|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|37/46||NM_001354579.2:c.6177C>T|NP_001341508.1:p.Asn2059%3D|6206|6177|2059|N|aaC/aaT|COSV99052509||-1||EntrezGene||||||3:g.142188362G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:39.6:1:37:0:1:0:60:16:1:0:0	0/1:124:2:1,1:56,66:122,2:0.0161:2,2:32:1:37:0:1:1.18:60:4:0.0169:0:1
    1291. 

  1291. 3	142203957	142203957	G	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	142	3	142203957	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=41;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.60115;SOR=0;LSEQ=CATCCTTACATATTTAATCT;RSEQ=CAAACATGCAGTTCTCATAC;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||36/46|NM_001184.4:c.6221+25C>T|||||||rs1425399613||-1||EntrezGene||YES||||3:g.142203957G>A|7.964e-06|0|2.893e-05|0|0|0|8.814e-06|0|0|2.893e-05|gnomAD_AMR|||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||35/45|NM_001354579.2:c.6029+25C>T|||||||rs1425399613||-1||EntrezGene||||||3:g.142203957G>A|7.964e-06|0|2.893e-05|0|0|0|8.814e-06|0|0|2.893e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:41:0:0,0:36,5:41,0:0:2,0:31.8:1:36.4:1:1:0:60:40:1:0:0.2	0/1:142:2:1,1:104,36:140,2:0.0141:2,2:45:0:37:0:0.4546:2.86325:60:4:0.0142:0:1
    1292. 

  1292. 3	142203965	142203965	G	A	intronic	ATR	.	.	.	0.0001	.	.	.	.	.	.	.	.	rs761581509	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	158	3	142203965	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.59316;SOR=0;LSEQ=CATATTTAATCTGCAAACAT;RSEQ=CAGTTCTCATACTCACCTGC;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||36/46|NM_001184.4:c.6221+17C>T|||||||rs761581509||-1||EntrezGene||YES||||3:g.142203965G>A|2.786e-05|0|0|0|0|0|6.164e-05|0|0|6.164e-05|gnomAD_NFE|||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||35/45|NM_001354579.2:c.6029+17C>T|||||||rs761581509||-1||EntrezGene||||||3:g.142203965G>A|2.786e-05|0|0|0|0|0|6.164e-05|0|0|6.164e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:47:0:0,0:42,5:47,0:0:2,0:32.7:1:35.4:1:1:0:60:22.5:1:0:0.2	0/1:158:2:1,1:114,42:156,2:0.0127:2,2:40.5:1:37:0:0.4715:2.69428:60:4:0.0127:0:1
    1293. 

  1293. 3	142204011	142204011	G	T	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon36:c.C6192A:p.L2064L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	229	3	142204011	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=142;VD=2;AF=0.0141;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.14586;SOR=inf;LSEQ=TGAAGAACTATATACCGGAT;RSEQ=AGATCACCTTGCTTTTCCAT;CSQ=T|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|36/47||NM_001184.4:c.6192C>A|NP_001175.2:p.Leu2064%3D|6221|6192|2064|L|ctC/ctA|COSV63387386||-1||EntrezGene||YES||||3:g.142204011G>T|||||||||||||1|1,T|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|35/46||NM_001354579.2:c.6000C>A|NP_001341508.1:p.Leu2000%3D|6029|6000|2000|L|ctC/ctA|COSV63387386||-1||EntrezGene||||||3:g.142204011G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:142:2:1,1:86,54:140,2:0.0141:2,2:12:0:37:0:1:1.58714:60:4:0.0143:0:1	0/0:229:0:0,0:147,82:229,0:0:2,0:40.6:1:36.5:1:1:0:60:113.5:1:0:0.1
    1294. 

  1294. 3	142204075	142204075	G	A	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon36:c.C6128T:p.A2043V	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	0.998	0.715	D	0.942	0.660	D	0.000	0.843	D	1	0.810	D	2.93	0.848	M	-1.02	0.763	T	-3.49	0.680	D	0.964	0.967	0.427	0.895	D	0.652	0.879	D	0.298	0.908	D	6.907	0.932	33	0.999	0.992	0.990	0.898	D	c	0.894	0.857	1.000	0.747	0.732	0.924	0	5.2	0.716	9.746	0.981	0.998	0.613	1.000	0.715	1.000	0.888	19.081	0.931	Armadillo-type fold|PIK-related kinase|PIK-related kinase, FAT	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	258	3	142204075	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=2;AF=0.0107;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.17604;SOR=inf;LSEQ=TCAATTTGTCATAGTACTTG;RSEQ=CAAGGTAAAAATGCCCATCC;CSQ=A|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|36/47||NM_001184.4:c.6128C>T|NP_001175.2:p.Ala2043Val|6157|6128|2043|A/V|gCc/gTc|||-1||EntrezGene||YES||||3:g.142204075G>A||||||||||||||,A|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|35/46||NM_001354579.2:c.5936C>T|NP_001341508.1:p.Ala1979Val|5965|5936|1979|A/V|gCc/gTc|||-1||EntrezGene||||||3:g.142204075G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:187:2:1,1:92,93:185,2:0.0107:2,2:70:0:37:0:1:1.01:60:4:0.0109:0:1	0/0:258:0:0,0:122,135:257,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1295. 

  1295. 3	142204119	142204119	C	A	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon36:c.G6084T:p.V2028V	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV100638637;OCCURENCE=1(skin)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU129834315	SKCM-US|1|466|0.00214592	0.25	37	208	3	142204119	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=151;VD=2;AF=0.0132;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.17623;SOR=inf;LSEQ=CATTCTGGCAGGCACGCGGT;RSEQ=ACATCCTATAAAAAAGAACA;CSQ=A|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|36/47||NM_001184.4:c.6084G>T|NP_001175.2:p.Val2028%3D|6113|6084|2028|V|gtG/gtT|COSV100638637||-1||EntrezGene||YES||||3:g.142204119C>A|||||||||||||1|1,A|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|35/46||NM_001354579.2:c.5892G>T|NP_001341508.1:p.Val1964%3D|5921|5892|1964|V|gtG/gtT|COSV100638637||-1||EntrezGene||||||3:g.142204119C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:151:2:1,1:60,89:149,2:0.0132:2,2:35.5:1:37:0:1:1.48:60:4:0.0134:0:1	0/0:208:0:0,0:78,130:208,0:0:2,0:38.5:1:36.5:1:1:0:60:103:1:0:0.1
    1296. 

  1296. 3	142215171	142215171	T	C	intronic	ATR	.	.	.	0.097	0.0286	0.0080	0.0116	0.0059	0.0196	0.0280	0.0442	0.0266	rs11719960	rs11719960	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63384221;OCCURENCE=5(soft_tissue)	167845	not_specified	MedGen:CN169374	no_assertion_criteria_provided	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	141	55	3	142215171	.	T	C	141	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=0;AF=0;SHIFT3=7;MSI=19;MSILEN=2;SSF=0.02048;SOR=0;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATGATGACATTTCC;CSQ=C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||34/46|NM_001184.4:c.5898+32A>G|||||||rs11719960&COSV63384221||-1||EntrezGene||YES||||3:g.142215171T>C|0.0001495|0|8.498e-05|0|0.0002704|0|0.0002084|0.0002653|0.0002005|0.003504|EA|likely_benign|0&1|1&1,C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||33/45|NM_001354579.2:c.5706+32A>G|||||||rs11719960&COSV63384221||-1||EntrezGene||||||3:g.142215171T>C|0.0001495|0|8.498e-05|0|0.0002704|0|0.0002084|0.0002653|0.0002005|0.003504|EA|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:9:0:0,0:5,4:9,0:0:2,0:32:1:31.4:1:1:0:60:8:1:0:2.3	0/1:55:21:7,14:15,18:33,21:0.3818:2,2:33.1:1:32.2:1:0.41034:1.65099:60:9.5:0.3725:0:2.3
    1297. 

  1297. 3	142215178	142215178	A	C	intronic	ATR	.	.	.	0.8	0.6677	0.7981	0.5208	0.6102	0.5442	0.7070	0.6159	0.6328	rs7620648	rs7620648	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63391396;OCCURENCE=1(liver)	167844	not_specified	MedGen:CN169374	no_assertion_criteria_provided	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU9890992	LICA-CN|1|402|0.00248756,COCA-CN|1|321|0.00311526	1	206	66	3	142215178	.	A	C	206	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=16;VD=15;AF=0.9375;SHIFT3=0;MSI=16;MSILEN=2;SSF=0.19512;SOR=0;LSEQ=ATATATATATATATATATAT;RSEQ=TGATGACATTTCCCTGGCCA;CSQ=C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||34/46|NM_001184.4:c.5898+25T>G|||||||rs7620648&COSV63391396||-1||EntrezGene||YES||||3:g.142215178A>C|0.5116|0.8447|0.4206|0.5226|0.436|0.525|0.5578|0.5251|0.3542|0.8447|gnomAD_AFR|likely_benign|0&1|1&1,C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||33/45|NM_001354579.2:c.5706+25T>G|||||||rs7620648&COSV63391396||-1||EntrezGene||||||3:g.142215178A>C|0.5116|0.8447|0.4206|0.5226|0.436|0.525|0.5578|0.5251|0.3542|0.8447|gnomAD_AFR|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:16:15:8,7:1,0:1,15:0.9375:0,2:22.3:1:35.3:1:1:0:60:14:1:0:1.7	1/1:66:66:30,36:0,0:0,66:1:0,2:35.6:1:34.1:1:1:0:60:10:1:0:2.3
    1298. 

  1298. 3	142215973	142215973	C	A	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon33:c.G5620T:p.D1874Y	.	.	.	.	.	.	.	.	.	.	.	0.058	0.377	T	0.973	0.556	D	0.663	0.511	P	0.001	0.431	D	0.999	0.450	D	2.05	0.567	M	-0.43	0.697	T	-1.72	0.408	N	0.319	0.404	-0.637	0.633	T	0.272	0.643	T	0.042	0.606	D	5.768	0.789	27.0	0.993	0.579	0.808	0.401	D	c	0.092	0.034	0.997	0.350	0.706	0.609	0	4.52	0.546	2.646	0.461	0.852	0.362	0.907	0.314	0.994	0.587	9.779	0.396	PIK-related kinase|PIK-related kinase, FAT	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	220	3	142215973	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=74;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.41757;SOR=0;LSEQ=AGAATCTTCTTGAGAACTGT;RSEQ=ACCTGGAGAATGCTGGAAAA;CSQ=A|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|33/47||NM_001184.4:c.5620G>T|NP_001175.2:p.Asp1874Tyr|5649|5620|1874|D/Y|Gac/Tac|||-1||EntrezGene||YES||||3:g.142215973C>A||||||||||||||,A|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|32/46||NM_001354579.2:c.5428G>T|NP_001341508.1:p.Asp1810Tyr|5457|5428|1810|D/Y|Gac/Tac|||-1||EntrezGene||||||3:g.142215973C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:74:0:0,0:34,40:74,0:0:2,0:42.2:1:37:0:1:0:60:148:1:0:0	0/1:220:3:1,2:94,123:217,3:0.0136:2,2:32.3:1:28.3:1:1:1.52563:60:2:0.0092:0:1.3
    1299. 

  1299. 3	142217590	142217590	T	C	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon32:c.A5407G:p.R1803G	.	6.457e-05	0	0	0	0	0	0.0001	0	.	.	0.501	0.077	T	0.026	0.181	B	0.02	0.179	B	0.000	0.629	D	1.000	0.548	D	1.05	0.269	L	-0.39	0.692	T	-0.73	0.206	N	0.502	0.547	-0.978	0.355	T	0.137	0.453	T	0.019	0.419	T	1.923	0.292	15.73	0.964	0.292	0.874	0.466	D	c	-0.286	-0.082	0.998	0.359	0.745	0.986	0	3.87	0.437	2.606	0.457	1.061	0.807	1.000	0.715	1.000	0.888	11.246	0.480	PIK-related kinase|PIK-related kinase, FAT	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	64	3	142217590	.	T	C	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=74;VD=2;AF=0.027;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.28573;SOR=inf;LSEQ=TAATAATAGCTGTCCCAGTC;RSEQ=GACACTCCATGTTGTAGATT;CSQ=C|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|32/47||NM_001184.4:c.5407A>G|NP_001175.2:p.Arg1803Gly|5436|5407|1803|R/G|Aga/Gga|rs1312287969||-1||EntrezGene||YES||||3:g.142217590T>C||||||||||||||,C|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|31/46||NM_001354579.2:c.5215A>G|NP_001341508.1:p.Arg1739Gly|5244|5215|1739|R/G|Aga/Gga|rs1312287969||-1||EntrezGene||||||3:g.142217590T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:74:2:1,1:38,34:72,2:0.027:2,2:30.5:1:31:1:1:1.11596:60:4:0.0278:0:1.5	0/0:64:0:0,0:26,38:64,0:0:2,0:37.1:1:36.8:1:1:0:60:128:1:0:0
    1300. 

  1300. 3	142218551	142218551	C	-	exonic	ATR	.	stopgain	ATR:NM_001184:exon31:c.5298delG:p.W1766*	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	116	3	142218550	.	TC	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=156;VD=2;AF=0.0128;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.32803;SOR=inf;LSEQ=GTACGTGTTTAATTCATCTG;RSEQ=CACTCGGACCTATTAAAAGA;CSQ=-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|31/47||NM_001184.4:c.5298del|NP_001175.2:p.Trp1766Ter|5327|5298|1766|W/X|tgG/tg|||-1||EntrezGene||YES||||3:g.142218552del||||||||||||||,-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|30/46||NM_001354579.2:c.5106del|NP_001341508.1:p.Trp1702Ter|5135|5106|1702|W/X|tgG/tg|||-1||EntrezGene||||||3:g.142218552del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:156:2:1,1:60,94:154,2:0.0128:2,2:40:1:37:1:1:1.56:60:4:0.013:0.0064:0	0/0:116:0:0,0:57,59:116,0:0:2,0:40.1:1:35.8:1:1:0:60:57:1:0:0.1
    1301. 

  1301. 3	142222284	142222284	A	G	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon30:c.T5208C:p.Y1736Y	0.42	0.3410	0.1968	0.3349	0.4570	0.3739	0.3724	0.4087	0.3947	rs2227931	rs2227931	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63386201;OCCURENCE=1(breast),11(meninges),3(large_intestine),1(biliary_tract),1(haematopoietic_and_lymphoid_tissue),1(stomach)	167839	Seckel_syndrome_1|not_specified|not_provided	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU761169	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526,BTCA-JP|1|239|0.0041841	0.5	191	73	3	142222284	.	A	G	191	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=1;AF=0.5;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.64324;SOR=0.66289;LSEQ=ATGGACTTTACTACACCATG;RSEQ=TAATGAATGATCTAGAAATT;CSQ=G|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|30/47||NM_001184.4:c.5208T>C|NP_001175.2:p.Tyr1736%3D|5237|5208|1736|Y|taT/taC|rs2227931&COSV63386201||-1||EntrezGene||YES||||3:g.142222284A>G|0.3601|0.2029|0.3181|0.462|0.3624|0.3888|0.404|0.3899|0.2657|0.462|gnomAD_ASJ|benign&likely_benign|0&1|1&1,G|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|29/46||NM_001354579.2:c.5016T>C|NP_001341508.1:p.Tyr1672%3D|5045|5016|1672|Y|taT/taC|rs2227931&COSV63386201||-1||EntrezGene||||||3:g.142222284A>G|0.3601|0.2029|0.3181|0.462|0.3624|0.3888|0.404|0.3899|0.2657|0.462|gnomAD_ASJ|benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:0,1:1,0:1,1:0.5:0,0:6:0:37:0:1:0:60:2:0.5:0:1	1/0:73:44:18,26:10,19:29,44:0.6027:2,2:38.9:1:35:1:0.62981:1.31:60:21:0.5915:0:1.2
    1302. 

  1302. 3	142223957	142223957	G	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	94	3	142223957	.	G	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=160;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.13604;SOR=0;LSEQ=TCAGGGCTATTTTCATTACA;RSEQ=TTGCCTTTCAATTATTATCT;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||29/46|NM_001184.4:c.5196+24C>T|||||||||-1||EntrezGene||YES||||3:g.142223957G>A||||||||||||||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||28/45|NM_001354579.2:c.5004+24C>T|||||||||-1||EntrezGene||||||3:g.142223957G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:160:0:0,0:100,60:160,0:0:2,0:33.8:1:36.5:1:1:0:60:159:1:0:0.2	0/1:94:2:1,1:59,33:92,2:0.0213:2,2:40.5:1:31:1:1:1.77616:60:4:0.0213:0:1
    1303. 

  1303. 3	142226836	142226836	C	T	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon28:c.G4968A:p.M1656I	.	.	.	.	.	.	.	.	.	.	.	0.071	0.351	T	0.967	0.544	D	0.776	0.553	P	0.000	0.843	D	1	0.810	D	2.615	0.767	M	2.04	0.208	T	-2.75	0.584	D	0.917	0.926	-1.025	0.220	T	0.122	0.423	T	0.032	0.537	D	5.044	0.679	25.2	0.997	0.839	0.983	0.817	D	c	0.722	0.720	1.000	0.747	0.651	0.465	0	5.35	0.762	7.695	0.834	0.935	0.490	1.000	0.715	1.000	0.888	19.055	0.930	PIK-related kinase|Tetratricopeptide-like helical domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	74	246	3	142226836	.	C	T	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=44;VD=4;AF=0.0909;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00047;SOR=inf;LSEQ=GTAATAAATGATTCAAAGTG;RSEQ=ATTACAGCTCGTGTGTATGC;CSQ=T|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|28/47||NM_001184.4:c.4968G>A|NP_001175.2:p.Met1656Ile|4997|4968|1656|M/I|atG/atA|||-1||EntrezGene||YES||||3:g.142226836C>T||||||||||||||,T|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|27/46||NM_001354579.2:c.4776G>A|NP_001341508.1:p.Met1592Ile|4805|4776|1592|M/I|atG/atA|||-1||EntrezGene||||||3:g.142226836C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:44:4:2,2:22,18:40,4:0.0909:2,2:13.5:1:37:0:1:1.21662:60:8:0.0952:0:1	0/0:246:0:0,0:143,103:246,0:0:2,0:39.2:1:35.4:1:1:0:60:29.75:1:0:0.1
    1304. 

  1304. 3	142226961	142226961	A	-	intronic	ATR	.	.	.	0.0007	.	.	.	.	.	.	.	.	rs774086025	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	176	3	142226960	.	TA	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=14;VD=0;AF=0;SHIFT3=6;MSI=7;MSILEN=1;SSF=0.8577;SOR=0;LSEQ=CCACAGTAGATACTAGATCA;RSEQ=AAAAAAGTTGAGTAATTAAA;CSQ=-|splice_polypyrimidine_tract_variant&intron_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding||27/46|NM_001184.4:c.4853-10del|||||||rs774086025||-1||EntrezGene||YES||||3:g.142226967del|2.478e-05|6.252e-05|0|0|5.554e-05|0|2.696e-05|0|3.595e-05|0.0007032|AA|||,-|splice_polypyrimidine_tract_variant&intron_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding||26/45|NM_001354579.2:c.4661-10del|||||||rs774086025||-1||EntrezGene||||||3:g.142226967del|2.478e-05|6.252e-05|0|0|5.554e-05|0|2.696e-05|0|3.595e-05|0.0007032|AA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:14:0:0,0:4,10:14,0:0:2,0:24.6:1:37:0:1:0:60:28:1:0:0	0/1:176:2:1,1:58,116:174,2:0.0114:2,2:38:1:37:0:1:1.99:60:4:0.0114:0:0
    1305. 

  1305. 3	142231282	142231282	G	A	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon27:c.C4672T:p.H1558Y	.	.	.	.	.	.	.	.	.	.	.	0.338	0.128	T	0.022	0.174	B	0.006	0.112	B	0.000	0.513	D	0.990	0.410	D	1.43	0.360	L	3.55	0.048	T	-1.15	0.295	N	0.366	0.437	-1.097	0.045	T	0.032	0.138	T	0.005	0.131	T	1.105	0.200	11.24	0.960	0.278	0.971	0.724	D	c	-0.301	-0.089	0.261	0.188	0.707	0.730	0	4.31	0.505	2.695	0.465	0.998	0.613	1.000	0.715	1.000	0.888	13.361	0.599	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	159	3	142231282	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=2;AF=0.0152;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20491;SOR=inf;LSEQ=TATGGTATGCTGATCGTCAT;RSEQ=CTTTAGAACTGCCATAATTT;CSQ=A|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|27/47||NM_001184.4:c.4672C>T|NP_001175.2:p.His1558Tyr|4701|4672|1558|H/Y|Cat/Tat|||-1||EntrezGene||YES||||3:g.142231282G>A||||||||||||||,A|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|26/46||NM_001354579.2:c.4480C>T|NP_001341508.1:p.His1494Tyr|4509|4480|1494|H/Y|Cat/Tat|||-1||EntrezGene||||||3:g.142231282G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:132:2:1,1:47,83:130,2:0.0152:2,2:12:1:37:0:1:1.76:60:4:0.0153:0:1	0/0:159:0:0,0:55,104:159,0:0:2,0:36.2:1:35.6:1:1:0:60:25.5:1:0:0.1
    1306. 

  1306. 3	142231294	142231294	C	G	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon27:c.G4660C:p.A1554P	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	1.0	0.899	D	0.993	0.797	D	0.000	0.843	D	1	0.810	D	2.57	0.754	M	3.57	0.047	T	-3.39	0.669	D	0.911	0.901	-0.761	0.574	T	0.194	0.548	T	0.083	0.741	D	6.854	0.929	33	0.998	0.866	0.997	0.986	D	c	0.820	0.786	1.000	0.747	0.707	0.730	0	5.4	0.779	7.168	0.770	0.892	0.403	1.000	0.715	1.000	0.888	19.176	0.936	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	134	3	142231294	.	C	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=99;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.3297;SOR=0;LSEQ=ATCGTCATGCTTTAGAACTG;RSEQ=CATAATTTCTGCATAAACCT;CSQ=G|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|27/47||NM_001184.4:c.4660G>C|NP_001175.2:p.Ala1554Pro|4689|4660|1554|A/P|Gca/Cca|||-1||EntrezGene||YES||||3:g.142231294C>G||||||||||||||,G|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|26/46||NM_001354579.2:c.4468G>C|NP_001341508.1:p.Ala1490Pro|4497|4468|1490|A/P|Gca/Cca|||-1||EntrezGene||||||3:g.142231294C>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:99:0:0,0:32,67:99,0:0:2,0:30.8:1:35.8:1:1:0:60:32:1:0:0	0/1:134:2:1,1:40,92:132,2:0.0149:2,2:39.5:1:31:1:0.51992:2.28:60:4:0.0152:0:2
    1307. 

  1307. 3	142234279	142234279	A	G	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon25:c.T4461C:p.F1487F	0.0001	.	.	.	.	.	.	.	.	rs139029532	rs139029532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	164	3	142234279	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=8;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.90888;SOR=0;LSEQ=CAAGATGCTGACCATTCTGC;RSEQ=AAGTTACTACCCAATTTACT;CSQ=G|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|25/47||NM_001184.4:c.4461T>C|NP_001175.2:p.Phe1487%3D|4490|4461|1487|F|ttT/ttC|rs139029532||-1||EntrezGene||YES||||3:g.142234279A>G||||||||||0.0001163|EA|||,G|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|24/46||NM_001354579.2:c.4269T>C|NP_001341508.1:p.Phe1423%3D|4298|4269|1423|F|ttT/ttC|rs139029532||-1||EntrezGene||||||3:g.142234279A>G||||||||||0.0001163|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:8:0:0,0:4,4:8,0:0:2,0:27.1:1:37:0:1:0:60:16:1:0:0	0/1:164:2:1,1:74,88:162,2:0.0122:2,2:28.5:1:37:0:1:1.19:60:4:0.0123:0:1
    1308. 

  1308. 3	142238583	142238583	C	T	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon24:c.G4310A:p.G1437D	.	.	.	.	.	.	.	.	.	.	.	0.071	0.351	T	0.112	0.247	B	0.05	0.239	B	0.005	0.331	N	0.766	0.341	D	1.495	0.376	L	3.96	0.034	T	-2.24	0.501	N	0.262	0.322	-0.962	0.388	T	0.012	0.048	T	0.004	0.089	T	3.171	0.440	22.7	0.983	0.397	0.937	0.587	D	c	-0.075	0.104	1.000	0.446	0.706	0.609	0	5.13	0.696	5.012	0.635	0.935	0.490	1.000	0.715	0.957	0.436	18.941	0.925	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	146	3	142238583	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.74563;SOR=0;LSEQ=TCCACAATTGGTGACCTGGG;RSEQ=CGTTGGTCTCCATCTCTCTA;CSQ=T|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|24/47||NM_001184.4:c.4310G>A|NP_001175.2:p.Gly1437Asp|4339|4310|1437|G/D|gGc/gAc|||-1||EntrezGene||YES||||3:g.142238583C>T||||||||||||||,T|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|23/46||NM_001354579.2:c.4118G>A|NP_001341508.1:p.Gly1373Asp|4147|4118|1373|G/D|gGc/gAc|||-1||EntrezGene||||||3:g.142238583C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:9,14:23,0:0:2,0:30.7:1:36:1:1:0:60:46:1:0:0.1	0/1:146:2:1,1:72,71:143,2:0.0137:2,2:25:1:37:0:1:1.01399:60:4:0.0141:0:1
    1309. 

  1309. 3	142238596	142238596	T	C	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon24:c.A4297G:p.M1433V	.	.	.	.	.	.	.	.	.	.	.	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.000	0.457	D	0.758	0.295	N	-1.15	0.009	N	4.09	0.030	T	0.08	0.060	N	0.249	0.309	-1.024	0.224	T	0.009	0.030	T	0.004	0.085	T	1.488	0.241	13.25	0.942	0.239	0.882	0.478	D	c	-0.089	0.106	0.999	0.379	0.732	0.924	0	5.13	0.696	5.731	0.680	1.061	0.807	1.000	0.715	1.000	0.888	9.730	0.393	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.5	31	141	3	142238596	.	T	C	31	v3;pSTD;q22.5;SN1.5	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=15;VD=1;AF=0.0667;SHIFT3=0;MSI=3;MSILEN=2;SSF=0.26314;SOR=4.87518;LSEQ=ACCTGGGCCGTTGGTCTCCA;RSEQ=CTCTCTACAGTCATAAATAG;CSQ=C|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|24/47||NM_001184.4:c.4297A>G|NP_001175.2:p.Met1433Val|4326|4297|1433|M/V|Atg/Gtg|||-1||EntrezGene||YES||||3:g.142238596T>C||||||||||||||,C|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|23/46||NM_001354579.2:c.4105A>G|NP_001341508.1:p.Met1369Val|4134|4105|1369|M/V|Atg/Gtg|||-1||EntrezGene||||||3:g.142238596T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:15:1:0,1:5,8:13,1:0.0667:2,0:60:0:11:0:1:0:60:0:0:0:1	0/1:141:2:1,1:68,71:139,2:0.0142:2,2:57:1:31:1:1:1.04:60:4:0.0146:0:1
    1310. 

  1310. 3	142259707	142259708	AA	-	intronic	ATR	.	.	.	0.016	0.0005	0.0001	0	0	0	0.0054	0.0002	0.0030	rs760044988	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	57	97	3	142259706	.	CAA	C	57	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=12;VD=2;AF=0.1667;SHIFT3=12;MSI=14;MSILEN=1;SSF=0.09248;SOR=6.08205;LSEQ=GTTAGTGCTACTGGAAAATG;RSEQ=AAAAAAAAAAAATTAATAAA;CSQ=-|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||18/46|NM_001184.4:c.3581+38_3581+39del|||||||rs201551475||-1||EntrezGene||YES||||3:g.142259719_142259720del|0.009105|0.00944|0.008954|0.005417|0.007333|0.007885|0.0104|0.007099|0.008881|0.0104|gnomAD_NFE|||,-|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||17/45|NM_001354579.2:c.3389+38_3389+39del|||||||rs201551475||-1||EntrezGene||||||3:g.142259719_142259720del|0.009105|0.00944|0.008954|0.005417|0.007333|0.007885|0.0104|0.007099|0.008881|0.0104|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:12:2:1,1:7,2:9,2:0.1667:2,2:56:1:37:0:0.49091:3.05504:60:4:0.1667:0:0	0/1:97:3:2,1:30,10:40,3:0.0309:2,2:43.7:1:36:1:1:1.48475:60:6:0.0312:0.0103:0.3
    1311. 

  1311. 3	142266640	142266640	G	A	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon16:c.C3284T:p.S1095L	.	.	.	.	.	.	.	.	.	rs1051324098	.	0.066	0.361	T	0.872	0.459	P	0.253	0.374	B	0.000	0.629	D	1	0.810	D	0.695	0.181	N	3.92	0.035	T	-1.83	0.429	N	0.562	0.600	-0.667	0.620	T	0.009	0.031	T	0.024	0.472	T	4.338	0.581	24.0	0.998	0.867	0.995	0.969	D	c	0.388	0.548	1.000	0.747	0.732	0.924	0	5.89	0.947	10.003	0.997	1.048	0.713	1.000	0.715	1.000	0.888	20.257	0.984	Armadillo-like helical	.	.	ID=COSV63383821;OCCURENCE=1(breast)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	212	3	142266640	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=24;VD=2;AF=0.0833;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00995;SOR=inf;LSEQ=ATGCAAATGAGGCAAGTATT;RSEQ=ACAAACCATTAAAAACCTGT;CSQ=A|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|16/47||NM_001184.4:c.3284C>T|NP_001175.2:p.Ser1095Leu|3313|3284|1095|S/L|tCa/tTa|rs1051324098&COSV63383428&COSV63383821||-1||EntrezGene||YES||||3:g.142266640G>A|||||||||||||0&1&1|0&1&1,A|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|15/46||NM_001354579.2:c.3092C>T|NP_001341508.1:p.Ser1031Leu|3121|3092|1031|S/L|tCa/tTa|rs1051324098&COSV63383428&COSV63383821||-1||EntrezGene||||||3:g.142266640G>A|||||||||||||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:24:2:1,1:12,10:22,2:0.0833:2,2:27.5:1:37:0:1:1.19087:60:4:0.0833:0:1	0/0:212:0:0,0:95,117:212,0:0:2,0:38.5:1:36.6:1:1:0:60:211:1:0:0
    1312. 

  1312. 3	142272585	142272585	A	G	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	94	3	142272585	.	A	G	31	d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTTAAGACAAAAAGCT;RSEQ=GAACAATAAAATTAACTGGT;CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding||11/46|NM_001184.4:c.2533-3T>C|||||||||-1||EntrezGene||YES||||3:g.142272585A>G||||||||||||||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding||10/45|NM_001354579.2:c.2341-3T>C|||||||||-1||EntrezGene||||||3:g.142272585A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:94:2:1,1:40,52:92,2:0.0213:2,2:53:1:31:1:1:1.3:60:4:0.022:0:1
    1313. 

  1313. 3	142274684	142274684	G	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	91	3	142274684	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=3;MSI=2;MSILEN=1;SSF=0.87951;SOR=0;LSEQ=TGAAAAGCAGAGCTTAAATA;RSEQ=GTTTTAAAGTATTAAATAAG;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||10/46|NM_001184.4:c.2341+35C>T|||||||||-1||EntrezGene||YES||||3:g.142274684G>A||||||||||||||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||9/45|NM_001354579.2:c.2149+35C>T|||||||||-1||EntrezGene||||||3:g.142274684G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:5,1:6,0:0:2,0:13.7:1:37:0:1:0:60:12:1:0:0.5	0/1:91:2:1,1:68,21:89,2:0.022:2,2:39.5:1:37:0:0.42711:3.18682:60:4:0.0241:0:1
    1314. 

  1314. 3	142274740	142274740	T	-	exonic	ATR	.	frameshift deletion	ATR:NM_001184:exon10:c.2320delA:p.I774Yfs*5	0.0084	6.653e-05	0.0002	0	0	0	0	0	0	rs757500301	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	363235	Endometrial_neoplasm	MeSH:D016889,MedGen:C0014170	no_assertion_provided	not_provided	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU4350843	LICA-FR|1|252|0.00396825,BTCA-JP|1|239|0.0041841	0.25	57	183	3	142274739	.	AT	A	57	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=21;VD=0;AF=0;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.72065;SOR=0;LSEQ=CAAGTTTTACTGGACTAGGT;RSEQ=TTTTTTTTTCAGTAGGAAAA;CSQ=-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|10/47||NM_001184.4:c.2320del|NP_001175.2:p.Ile774TyrfsTer5|2349|2320|774|I/X|Ata/ta|rs757500301&CD112378||-1||EntrezGene||YES||||3:g.142274749del|0.001253|0.0004699|0.0014|0.00217|0.001059|0.000618|0.001308|0.0009852|0.001762|0.00217|gnomAD_ASJ|not_provided||1&1,-|frameshift_variant|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|9/46||NM_001354579.2:c.2128del|NP_001341508.1:p.Ile710TyrfsTer5|2157|2128|710|I/X|Ata/ta|rs757500301&CD112378||-1||EntrezGene||||||3:g.142274749del|0.001253|0.0004699|0.0014|0.00217|0.001059|0.000618|0.001308|0.0009852|0.001762|0.00217|gnomAD_ASJ|not_provided||1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:21:0:0,0:14,7:21,0:0:2,0:34.7:1:35.9:1:1:0:60:42:1:0:0.3	0/1:183:3:2,1:116,64:180,3:0.0164:2,2:47.7:1:36.3:1:1:1.1:60:6:0.0164:0.0055:0
    1315. 

  1315. 3	142275342	142275342	G	A	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon9:c.C1961T:p.A654V	.	.	.	.	.	.	.	.	.	.	.	0.068	0.524	T	0.294	0.306	B	0.057	0.248	B	0.002	0.379	N	0.632	0.328	D	1.78	0.463	L	-0.12	0.646	T	-0.69	0.412	N	0.337	0.398	-0.787	0.559	T	0.139	0.458	T	0.009	0.234	T	2.847	0.403	21.6	0.998	0.882	0.894	0.496	D	c	-0.003	0.186	0.989	0.317	0.651	0.465	0	5.45	0.796	2.262	0.427	1.048	0.713	1.000	0.715	1.000	0.888	15.285	0.734	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	254	3	142275342	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=2;AF=0.0227;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.06565;SOR=inf;LSEQ=GCAGGGCCCAGTTGTAAACT;RSEQ=CTGTTCTCCACTCAAGGAAT;CSQ=A|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|9/47||NM_001184.4:c.1961C>T|NP_001175.2:p.Ala654Val|1990|1961|654|A/V|gCa/gTa|rs1231927463||-1||EntrezGene||YES||||3:g.142275342G>A|3.979e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||,A|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|8/46||NM_001354579.2:c.1769C>T|NP_001341508.1:p.Ala590Val|1798|1769|590|A/V|gCa/gTa|rs1231927463||-1||EntrezGene||||||3:g.142275342G>A|3.979e-06|6.155e-05|0|0|0|0|0|0|0|6.155e-05|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:88:2:1,1:44,42:86,2:0.0227:2,2:31:1:37:0:1:1.04708:60:4:0.023:0:1	0/0:254:0:0,0:114,140:254,0:0:2,0:38.9:1:36.6:1:1:0:60:253:1:0:0.1
    1316. 

  1316. 3	142275344	142275344	T	C	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon9:c.A1959G:p.T653T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	31	254	3	142275344	.	T	C	31	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=88;VD=2;AF=0.0227;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.06565;SOR=inf;LSEQ=AGGGCCCAGTTGTAAACTGC;RSEQ=GTTCTCCACTCAAGGAATAT;CSQ=C|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|9/47||NM_001184.4:c.1959A>G|NP_001175.2:p.Thr653%3D|1988|1959|653|T|acA/acG|||-1||EntrezGene||YES||||3:g.142275344T>C||||||||||||||,C|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|8/46||NM_001354579.2:c.1767A>G|NP_001341508.1:p.Thr589%3D|1796|1767|589|T|acA/acG|||-1||EntrezGene||||||3:g.142275344T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:88:2:1,1:43,43:86,2:0.0227:2,2:31:0:31:1:1:1:60:4:0.023:0:1	0/0:254:0:0,0:113,140:253,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1317. 

  1317. 3	142275351	142275351	C	T	exonic	ATR	.	stopgain	ATR:NM_001184:exon9:c.G1952A:p.W651X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.867	0.978	38	0.993	0.579	0.982	0.804	D	c	0.945	0.828	1.000	0.747	0.651	0.465	0	5.45	0.796	6.696	0.742	0.935	0.490	1.000	0.715	0.999	0.750	19.657	0.958	Armadillo-type fold	.	.	.	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	243	3	142275351	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=87;VD=2;AF=0.023;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.06891;SOR=inf;LSEQ=AGTTGTAAACTGCTGTTCTC;RSEQ=ACTCAAGGAATATTCTTCTT;CSQ=T|stop_gained|HIGH|ATR|545|Transcript|NM_001184.4|protein_coding|9/47||NM_001184.4:c.1952G>A|NP_001175.2:p.Trp651Ter|1981|1952|651|W/*|tGg/tAg|||-1||EntrezGene||YES||||3:g.142275351C>T||||||||||||||,T|stop_gained|HIGH|ATR|545|Transcript|NM_001354579.2|protein_coding|8/46||NM_001354579.2:c.1760G>A|NP_001341508.1:p.Trp587Ter|1789|1760|587|W/*|tGg/tAg|||-1||EntrezGene||||||3:g.142275351C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:87:2:1,1:42,43:85,2:0.023:2,2:68:1:37:0:1:1.02:60:4:0.0233:0:1	0/0:243:0:0,0:110,133:243,0:0:2,0:39.5:1:36.1:1:1:0:60:39.5:1:0:0.1
    1318. 

  1318. 3	142277427	142277427	A	G	intronic	ATR	.	.	.	0.17	0.1045	0.0645	0.0783	0.0582	0.0905	0.1217	0.1268	0.1195	rs73240318	rs73240318	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63383992;OCCURENCE=8(haematopoietic_and_lymphoid_tissue),2(lung),1(large_intestine),1(biliary_tract)	167814	not_specified	MedGen:CN169374	no_assertion_criteria_provided	Likely_benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU639590	LAML-KR|5|205|0.0243902,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526,BTCA-JP|1|239|0.0041841	0.25	184	64	3	142277427	.	A	G	184	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=4;MSI=3;MSILEN=1;SSF=0.00088;SOR=0;LSEQ=GATAGATAGATAGATAGATA;RSEQ=ATAAAACAAACCACACACAC;CSQ=G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||8/46|NM_001184.4:c.1885+39T>C|||||||rs73240318&COSV63383992||-1||EntrezGene||YES||||3:g.142277427A>G|0.07589|0.01972|0.04084|0.04959|0.06371|0.1053|0.09693|0.07366|0.06387|0.174|EUR|likely_benign|0&1|1&1,G|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||7/45|NM_001354579.2:c.1693+39T>C|||||||rs73240318&COSV63383992||-1||EntrezGene||||||3:g.142277427A>G|0.07589|0.01972|0.04084|0.04959|0.06371|0.1053|0.09693|0.07366|0.06387|0.174|EUR|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:6,4:10,0:0:2,0:35.1:1:35.8:1:1:0:60:20:1:0:0.2	1/0:64:35:24,11:20,9:29,35:0.5469:2,2:36.7:1:35.9:1:1:1.01823:60:34:0.5484:0:1.1
    1319. 

  1319. 3	142277454	142277454	G	T	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	100	3	142277454	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=13;VD=2;AF=0.1538;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01233;SOR=inf;LSEQ=CAAACCACACACACATTCTT;RSEQ=TGAGCACTTACAATAGCTAT;CSQ=T|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||8/46|NM_001184.4:c.1885+12C>A|||||||||-1||EntrezGene||YES||||3:g.142277454G>T||||||||||||||,T|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||7/45|NM_001354579.2:c.1693+12C>A|||||||||-1||EntrezGene||||||3:g.142277454G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:13:2:1,1:6,5:11,2:0.1538:2,2:11:0:37:0:1:1.18321:60:4:0.1538:0:1	0/0:100:0:0,0:62,38:100,0:0:2,0:35.8:1:36.7:1:1:0:60:99:1:0:1.1
    1320. 

  1320. 3	142277536	142277536	A	G	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon8:c.T1815C:p.D605D	0.41	0.3358	0.1941	0.3329	0.4470	0.3747	0.3638	0.4022	0.3837	rs2227929	rs2227929	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63386203;OCCURENCE=12(meninges),3(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(kidney),2(lung)	167813	Seckel_syndrome_1|not_specified	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU653857	LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|3|170|0.0176471,COCA-CN|1|321|0.00311526	0.5	221	151	3	142277536	.	A	G	221	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=4;AF=0.3636;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.37471;SOR=0.66288;LSEQ=GTGGTCAACTTTAAACAGCC;RSEQ=TCATCAGAATGGGAATAAAT;CSQ=G|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|8/47||NM_001184.4:c.1815T>C|NP_001175.2:p.Asp605%3D|1844|1815|605|D|gaT/gaC|rs2227929&COSV63386203||-1||EntrezGene||YES||||3:g.142277536A>G|0.3567|0.2009|0.3191|0.4543|0.3629|0.3827|0.3986|0.3872|0.2657|0.4543|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|7/46||NM_001354579.2:c.1623T>C|NP_001341508.1:p.Asp541%3D|1652|1623|541|D|gaT/gaC|rs2227929&COSV63386203||-1||EntrezGene||||||3:g.142277536A>G|0.3567|0.2009|0.3191|0.4543|0.3629|0.3827|0.3986|0.3872|0.2657|0.4543|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:11:4:1,3:4,3:7,4:0.3636:2,2:42.2:1:37:0:0.54545:3.51553:60:8:0.3636:0:1.2	0/1:151:70:37,33:40,41:81,70:0.4636:2,2:38:1:36.1:1:0.74472:1.15:60:69:0.4631:0:1.7
    1321. 

  1321. 3	142277575	142277575	A	T	exonic	ATR	.	synonymous SNV	ATR:NM_001184:exon8:c.T1776A:p.G592G	0.85	0.6300	0.7950	0.4976	0.5728	0.4851	0.5406	0.5824	0.5704	rs2227930	rs2227930	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV63383320;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),1(stomach),20(soft_tissue),1(pancreas),2(prostate),14(meninges),2(large_intestine)	167812	Seckel_syndrome_1|not_specified|not_provided	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU586118	ESAD-UK|1|409|0.00244499,PACA-CA|1|268|0.00373134,LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.75	254	127	3	142277575	.	A	T	254	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=1;AF=0.3333;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00107;SOR=0.00598;LSEQ=ATCCATGGAAGTGAGAGCAT;RSEQ=CCACATAAATCTTCCAGGAT;CSQ=T|synonymous_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding|8/47||NM_001184.4:c.1776T>A|NP_001175.2:p.Gly592%3D|1805|1776|592|G|ggT/ggA|rs2227930&COSV63383320||-1||EntrezGene||YES||||3:g.142277575A>T|0.5464|0.8003|0.4534|0.5643|0.4689|0.5515|0.5786|0.5547|0.4321|0.8533|AFR|benign&benign/likely_benign|0&1|1&1,T|synonymous_variant|LOW|ATR|545|Transcript|NM_001354579.2|protein_coding|7/46||NM_001354579.2:c.1584T>A|NP_001341508.1:p.Gly528%3D|1613|1584|528|G|ggT/ggA|rs2227930&COSV63383320||-1||EntrezGene||||||3:g.142277575A>T|0.5464|0.8003|0.4534|0.5643|0.4689|0.5515|0.5786|0.5547|0.4321|0.8533|AFR|benign&benign/likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:3:1:0,1:1,1:2,1:0.3333:2,0:30:0:37:0:1:0:60:2:0.3333:0:2	1/1:127:126:53,73:0,0:0,126:0.9921:0,2:39.5:1:36.5:1:1:0:60:62:1:0:1.4
    1322. 

  1322. 3	142278227	142278227	G	C	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon7:c.C1598G:p.T533S	.	.	.	.	.	.	.	.	.	.	.	0.43	0.095	T	0.005	0.119	B	0.003	0.080	B	0.001	0.424	N	0.790	0.292	N	1.87	0.498	L	3.99	0.033	T	-0.53	0.208	N	0.23	0.297	-1.011	0.267	T	0.009	0.034	T	0.006	0.167	T	2.054	0.308	16.56	0.973	0.329	0.865	0.456	D	c	-0.258	-0.052	0.959	0.284	0.651	0.465	0	4.99	0.658	1.469	0.347	1.048	0.713	1.000	0.715	0.994	0.587	11.035	0.468	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	138	3	142278227	.	G	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=21;VD=2;AF=0.0952;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01672;SOR=inf;LSEQ=AAAAATCCAATGACATCCAA;RSEQ=TTATCACTACAGAAGGTTTC;CSQ=C|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|7/47||NM_001184.4:c.1598C>G|NP_001175.2:p.Thr533Ser|1627|1598|533|T/S|aCt/aGt|||-1||EntrezGene||YES||||3:g.142278227G>C||||||||||||||,C|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|6/46||NM_001354579.2:c.1406C>G|NP_001341508.1:p.Thr469Ser|1435|1406|469|T/S|aCt/aGt|||-1||EntrezGene||||||3:g.142278227G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:21:2:1,1:8,11:19,2:0.0952:2,2:42.5:1:37:0:1:1.35:60:4:0.0952:0:1	0/0:138:0:0,0:58,80:138,0:0:2,0:40.8:1:35.3:1:1:0:60:45:1:0:0.1
    1323. 

  1323. 3	142279306	142279306	T	C	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	103	3	142279306	.	T	C	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.98077;SOR=0;LSEQ=CATGTTTAATTCTATAATTA;RSEQ=GAATATAGTAGAGAGATATT;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|ATR|545|Transcript|NM_001184.4|protein_coding||5/46|NM_001184.4:c.1350-10A>G|||||||rs1331220834||-1||EntrezGene||YES||||3:g.142279306T>C||||||||||||||,C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||5/45|NM_001354579.2:c.1349+779A>G|||||||rs1331220834||-1||EntrezGene||||||3:g.142279306T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:37:0:1:0:60:2:1:0:0	0/1:103:2:1,1:30,71:101,2:0.0194:2,2:38:1:37:0:0.51342:2.34:60:4:0.0196:0:1
    1324. 

  1324. 3	142281183	142281183	A	G	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon4:c.T1061C:p.L354P	.	.	.	.	.	.	.	.	.	.	.	0.004	0.784	D	0.994	0.647	D	0.87	0.600	P	0.033	0.250	N	1	0.810	D	1.67	0.430	L	-0.49	0.704	T	-1.26	0.857	N	0.904	0.894	-0.236	0.767	T	0.382	0.739	T	0.068	0.703	D	5.177	0.699	25.5	0.999	0.963	0.968	0.706	D	c	0.532	0.563	1.000	0.747	0.651	0.465	0	5.67	0.876	5.305	0.653	1.140	0.893	1.000	0.715	0.998	0.697	15.895	0.790	Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	331	3	142281183	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=56;VD=2;AF=0.0357;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.02062;SOR=inf;LSEQ=ACCCAGCTGGCACAAATTTA;RSEQ=GGAAATACTGCAGTAAATGG;CSQ=G|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|4/47||NM_001184.4:c.1061T>C|NP_001175.2:p.Leu354Pro|1090|1061|354|L/P|cTt/cCt|||-1||EntrezGene||YES||||3:g.142281183A>G||||||||||||||,G|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|4/46||NM_001354579.2:c.1061T>C|NP_001341508.1:p.Leu354Pro|1090|1061|354|L/P|cTt/cCt|||-1||EntrezGene||||||3:g.142281183A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:56:2:1,1:28,26:54,2:0.0357:2,2:41:1:37:0:1:1.07547:60:4:0.0357:0:1	0/0:331:0:0,0:167,164:331,0:0:2,0:40.4:1:36.7:1:1:0:60:662:1:0:0.1
    1325. 

  1325. 3	142281412	142281412	T	C	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon4:c.A832G:p.K278E	.	.	.	.	.	.	.	.	.	.	.	0.75	0.036	T	0.001	0.067	B	0.001	0.040	B	0.146	0.181	N	1	0.090	N	0.805	0.203	L	-0.17	0.656	T	0.34	0.038	N	0.186	0.227	-1.029	0.207	T	0.130	0.441	T	0.013	0.320	T	-0.783	0.041	0.047	0.833	0.142	0.640	0.320	D	c	-0.432	-0.246	0.799	0.241	0.651	0.465	0	4.18	0.483	1.452	0.345	0.054	0.162	0.995	0.385	0.894	0.377	11.950	0.520	Armadillo-like helical|Armadillo-type fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	140	3	142281412	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=15;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.81525;SOR=0;LSEQ=ATCCATTTCTACAAGGTGTT;RSEQ=TAATAATTCCAAAAATGAGC;CSQ=C|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|4/47||NM_001184.4:c.832A>G|NP_001175.2:p.Lys278Glu|861|832|278|K/E|Aaa/Gaa|||-1||EntrezGene||YES||||3:g.142281412T>C||||||||||||||,C|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|4/46||NM_001354579.2:c.832A>G|NP_001341508.1:p.Lys278Glu|861|832|278|K/E|Aaa/Gaa|||-1||EntrezGene||||||3:g.142281412T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:7,8:15,0:0:2,0:35.7:1:37:0:1:0:60:30:1:0:0.1	0/1:140:2:1,1:53,85:138,2:0.0143:2,2:30.5:1:31:1:1:1.6:60:4:0.0144:0:1
    1326. 

  1326. 3	142281612	142281612	A	G	exonic	ATR	.	nonsynonymous SNV	ATR:NM_001184:exon4:c.T632C:p.M211T	0.85	0.6291	0.7916	0.4964	0.5728	0.4845	0.5404	0.5832	0.5708	rs2227928	rs2227928	1.0	0.010	T	0.0	0.026	B	0.0	0.013	B	0.299	0.146	N	1.000	0.090	P	0.145	0.088	N	-0.14	0.650	T	-0.2	0.102	N	0.018	0.003	-0.930	0.442	T	0.000	0.000	T	.	.	.	-0.115	0.083	1.622	0.593	0.060	0.108	0.160	N	c	-0.764	-0.533	0.498	0.209	0.651	0.465	0	4.6	0.564	1.477	0.348	-0.247	0.091	0.937	0.323	0.958	0.437	4.074	0.093	.	ENSG00000242479.1|ENSG00000175054.10|ENSG00000242479.1|ENSG00000242479.1|ENSG00000242479.1|ENSG00000175054.10|ENSG00000242479.1|ENSG00000175054.10|ENSG00000242479.1|ENSG00000272565.1|ENSG00000242479.1|ENSG00000175054.10|ENSG00000114127.6	Adipose_Subcutaneous|Adipose_Subcutaneous|Artery_Tibial|Cells_Transformed_fibroblasts|Lung|Lung|Nerve_Tibial|Nerve_Tibial|Skin_Sun_Exposed_Lower_leg|Thyroid|Thyroid|Thyroid|Thyroid	ID=COSV63383325;OCCURENCE=14(meninges),3(large_intestine),1(biliary_tract),1(haematopoietic_and_lymphoid_tissue),1(stomach),20(soft_tissue),6(prostate)	99571	Seckel_syndrome_1|not_specified	MONDO:MONDO:0008869,MedGen:C4551474,OMIM:210600|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign/Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	MU586119	ESAD-UK|1|409|0.00244499,LICA-CN|2|402|0.00497512,LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.75	236	97	3	142281612	.	A	G	236	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=3;AF=0.6;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00194;SOR=0;LSEQ=CAATAATACGAGTAAGAACC;RSEQ=TTAATAAAGTGACTTCAATA;CSQ=G|missense_variant|MODERATE|ATR|545|Transcript|NM_001184.4|protein_coding|4/47||NM_001184.4:c.632T>C|NP_001175.2:p.Met211Thr|661|632|211|M/T|aTg/aCg|rs2227928&COSV63383325||-1||EntrezGene||YES||||3:g.142281612A>G|0.5484|0.797|0.4558|0.5669|0.4701|0.5516|0.5796|0.5553|0.4362|0.8517|AFR|benign/likely_benign&benign|0&1|1&1,G|missense_variant|MODERATE|ATR|545|Transcript|NM_001354579.2|protein_coding|4/46||NM_001354579.2:c.632T>C|NP_001341508.1:p.Met211Thr|661|632|211|M/T|aTg/aCg|rs2227928&COSV63383325||-1||EntrezGene||||||3:g.142281612A>G|0.5484|0.797|0.4558|0.5669|0.4701|0.5516|0.5796|0.5553|0.4362|0.8517|AFR|benign/likely_benign&benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:5:3:1,2:1,1:2,3:0.6:2,2:25:1:37:0:1:1.7321:60:6:0.6:0:1	1/1:97:97:62,35:0,0:0,97:1:0,2:31.8:1:35.8:1:1:0:60:31.333:1:0:1.1
    1327. 

  1327. 3	142284947	142284947	G	A	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	281	3	142284947	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=132;VD=2;AF=0.0152;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.10162;SOR=inf;LSEQ=CAGATGGCAAGTGAATGCAT;RSEQ=AATAACAGCACTTACCAATA;CSQ=A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||3/46|NM_001184.4:c.292+16C>T|||||||||-1||EntrezGene||YES||||3:g.142284947G>A||||||||||||||,A|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||3/45|NM_001354579.2:c.292+16C>T|||||||||-1||EntrezGene||||||3:g.142284947G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:132:2:1,1:85,45:130,2:0.0152:2,2:23:0:37:0:1:1.87927:60:4:0.0152:0:1	0/0:281:0:0,0:175,106:281,0:0:2,0:40:1:36.6:1:1:0:60:92.667:1:0:0
    1328. 

  1328. 3	142297479	142297479	T	C	intronic	ATR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	172	3	142297479	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=882;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0265;SOR=0;LSEQ=TGCAGGACCCAGGCTGGGCC;RSEQ=AGCCCTACCTGCCCAGCTCC;CSQ=C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001184.4|protein_coding||1/46|NM_001184.4:c.59+9A>G|||||||rs1309766255||-1||EntrezGene||YES||||3:g.142297479T>C||||||||||||||,C|intron_variant|MODIFIER|ATR|545|Transcript|NM_001354579.2|protein_coding||1/45|NM_001354579.2:c.59+9A>G|||||||rs1309766255||-1||EntrezGene||||||3:g.142297479T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:882:0:0,0:449,432:881,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:172:2:1,1:93,76:169,2:0.0116:2,2:23.5:1:37:0:1:1.22223:60:4:0.0121:0:1
    1329. 

  1329. 3	169981163	169981163	T	C	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	124	3	169981163	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.55685;SOR=0;LSEQ=TCATGTTCGTTTATTTTCTT;RSEQ=CAGTGTTCCCTTGTGTACCA;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|PRKCI|5584|Transcript|NM_002740.6|protein_coding||3/17|NM_002740.6:c.314-4T>C|||||||||1||EntrezGene||YES||||3:g.169981163T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:23,19:42,0:0:2,0:38:1:37:0:1:0:60:84:1:0:0.3	0/1:124:2:1,1:71,51:122,2:0.0161:2,2:33:1:37:0:1:1.38836:60:4:0.0163:0:1
    1330. 

  1330. 3	169981221	169981221	A	G	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	136	3	169981221	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.58275;SOR=0;LSEQ=TTGTCCAGGAGAAGATAGTG;RSEQ=GTGTTTATATACTTCATACC;CSQ=G|splice_donor_region_variant&intron_variant|LOW|PRKCI|5584|Transcript|NM_002740.6|protein_coding||4/17|NM_002740.6:c.364+4A>G|||||||||1||EntrezGene||YES||||3:g.169981221A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:22,20:42,0:0:2,0:37.6:1:35.6:1:1:0:60:84:1:0:0.4	0/1:136:2:1,1:68,66:134,2:0.0147:2,2:28.5:1:37:0:1:1.03008:60:4:0.0148:0:1
    1331. 

  1331. 3	169981223	169981223	T	C	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	135	3	169981223	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=41;VD=2;AF=0.0488;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.05325;SOR=inf;LSEQ=GTCCAGGAGAAGATAGTGAG;RSEQ=GTTTATATACTTCATACCTT;CSQ=C|splice_donor_region_variant&intron_variant|LOW|PRKCI|5584|Transcript|NM_002740.6|protein_coding||4/17|NM_002740.6:c.364+6T>C|||||||||1||EntrezGene||YES||||3:g.169981223T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:41:2:1,1:21,18:39,2:0.0488:2,2:68.5:1:37:0:1:1.16227:60:4:0.0541:0:1	0/0:135:0:0,0:68,67:135,0:0:2,0:43:1:36.2:1:1:0:60:66.5:1:0:0.1
    1332. 

  1332. 3	169981239	169981239	A	G	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	127	3	169981239	.	A	G	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=37;VD=2;AF=0.0541;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.04983;SOR=inf;LSEQ=TGAGTGTTTATATACTTCAT;RSEQ=CCTTTTACAAGAGTTACTAT;CSQ=G|intron_variant|MODIFIER|PRKCI|5584|Transcript|NM_002740.6|protein_coding||4/17|NM_002740.6:c.364+22A>G|||||||||1||EntrezGene||YES||||3:g.169981239A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:2:1,1:19,16:35,2:0.0541:2,2:7:0:37:0:1:1.18197:60:4:0.0541:0:1	0/0:127:0:0,0:62,65:127,0:0:2,0:41.6:1:36.5:1:1:0:60:126:1:0:0.1
    1333. 

  1333. 3	169991120	169991120	C	T	exonic	PRKCI	.	nonsynonymous SNV	PRKCI:NM_002740:exon7:c.C638T:p.A213V	.	.	.	.	.	.	.	.	.	.	.	0.146	0.250	T	0.0	0.026	B	0.0	0.013	B	0.396	0.045	N	1	0.090	N	0.03	0.081	N	-0.31	0.680	T	-0.55	0.168	N	0.058	0.041	-0.979	0.353	T	0.110	0.397	T	0.012	0.295	T	1.765	0.273	14.78	0.978	0.358	0.169	0.194	N	c	-0.705	-0.591	0.000	0.038	0.372	0.050	0	2.79	0.317	1.949	0.397	0.036	0.152	0.461	0.264	0.583	0.285	2.787	0.050	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	218	3	169991120	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=2;AF=0.0107;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.21258;SOR=inf;LSEQ=ATCCATGCATTCTGACCATG;RSEQ=ACAGACAGGTAAGAGTGGTG;CSQ=T|missense_variant|MODERATE|PRKCI|5584|Transcript|NM_002740.6|protein_coding|7/18||NM_002740.6:c.638C>T|NP_002731.4:p.Ala213Val|884|638|213|A/V|gCa/gTa|||1||EntrezGene||YES||||3:g.169991120C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:187:2:1,1:87,98:185,2:0.0107:2,2:42.5:1:37:0:1:1.13:60:4:0.0109:0:1	0/0:218:0:0,0:97,121:218,0:0:2,0:36.4:1:36.8:1:1:0:60:217:1:0:0.1
    1334. 

  1334. 3	169993099	169993099	C	T	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	41	3	169993099	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.72695;SOR=0;LSEQ=AGATAATTTGTCTTATTGTA;RSEQ=ATTATATCATTAGCTTTTTA;CSQ=T|intron_variant|MODIFIER|PRKCI|5584|Transcript|NM_002740.6|protein_coding||8/17|NM_002740.6:c.705+24C>T|||||||||1||EntrezGene||YES||||3:g.169993099C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:3,4:7,0:0:2,0:27.4:1:35.3:1:1:0:60:14:1:0:0.1	0/1:41:2:1,1:19,20:39,2:0.0488:2,2:36:1:31:1:1:1.05:60:4:0.0513:0:1
    1335. 

  1335. 3	170011126	170011126	G	T	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	178	3	170011126	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=100;VD=2;AF=0.02;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.12856;SOR=inf;LSEQ=TTCCAGTTACTAACTTTCAA;RSEQ=AATGCAAAGTGTATAATTTA;CSQ=T|intron_variant|MODIFIER|PRKCI|5584|Transcript|NM_002740.6|protein_coding||13/17|NM_002740.6:c.1292-45G>T|||||||||1||EntrezGene||YES||||3:g.170011126G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:100:2:1,1:70,28:98,2:0.02:2,2:39:1:37:0:0.49798:2.47401:60:4:0.0206:0:1	0/0:178:0:0,0:127,51:178,0:0:2,0:35:1:35.8:1:1:0:60:43.5:1:0:0.1
    1336. 

  1336. 3	170011135	170011135	G	A	intronic	PRKCI	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	204	3	170011135	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=127;VD=2;AF=0.0157;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.1465;SOR=inf;LSEQ=CTAACTTTCAAGAATGCAAA;RSEQ=TGTATAATTTATTGCTTTAA;CSQ=A|intron_variant|MODIFIER|PRKCI|5584|Transcript|NM_002740.6|protein_coding||13/17|NM_002740.6:c.1292-36G>A|||||||rs1405772819||1||EntrezGene||YES||||3:g.170011135G>A|4.339e-06|0|0|0|0|0|0|0|3.894e-05|3.894e-05|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:127:2:1,1:84,41:125,2:0.0157:2,2:10:0:37:0:1:2.03631:60:4:0.016:0:1.5	0/0:204:0:0,0:141,63:204,0:0:2,0:35.5:1:36.2:1:1:0:60:101:1:0:0.1
    1337. 

  1337. 3	170011268	170011268	C	T	exonic	PRKCI	.	synonymous SNV	PRKCI:NM_002740:exon14:c.C1389T:p.D463D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	58	278	3	170011268	.	C	T	58	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=244;VD=3;AF=0.0123;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.2645;SOR=3.44057;LSEQ=GGGAGCTCCGATAACCCTGA;RSEQ=CAGAACACAGAGGATTATCT;CSQ=T|synonymous_variant|LOW|PRKCI|5584|Transcript|NM_002740.6|protein_coding|14/18||NM_002740.6:c.1389C>T|NP_002731.4:p.Asp463%3D|1635|1389|463|D|gaC/gaT|||1||EntrezGene||YES||||3:g.170011268C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:244:3:1,2:105,136:241,3:0.0123:2,2:48.3:1:37:0:1:1.54148:60:6:0.0125:0:1	0/0:278:1:1,0:110,167:277,1:0.0036:2,0:22:0:37:0:0.39928:0:60:2:0.0036:0:1
    1338. 

  1338. 3	170011287	170011287	C	A	exonic	PRKCI	.	nonsynonymous SNV	PRKCI:NM_002740:exon14:c.C1408A:p.L470I	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.998	0.715	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	0.53	0.137	N	0.63	0.531	T	-1.84	0.431	N	0.535	0.574	-0.747	0.581	T	0.241	0.609	T	0.046	0.625	D	5.408	0.733	26.0	0.996	0.752	0.979	0.777	D	c	0.667	0.663	1.000	0.747	0.615	0.372	0	4.95	0.648	7.568	0.814	0.935	0.490	1.000	0.715	0.999	0.750	18.563	0.910	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	231	3	170011287	.	C	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=2;AF=0.0127;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.16311;SOR=inf;LSEQ=ACCAGAACACAGAGGATTAT;RSEQ=TCTTCCAAGGTAATTTGGAG;CSQ=A|missense_variant|MODERATE|PRKCI|5584|Transcript|NM_002740.6|protein_coding|14/18||NM_002740.6:c.1408C>A|NP_002731.4:p.Leu470Ile|1654|1408|470|L/I|Ctc/Atc|||1||EntrezGene||YES||||3:g.170011287C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:157:2:1,1:61,94:155,2:0.0127:2,2:23:0:37:0:1:1.54:60:4:0.0129:0:1	0/0:231:0:0,0:78,153:231,0:0:2,0:35.1:1:36.2:1:1:0:60:56.75:1:0:0.2
    1339. 

  1339. 3	170015132	170015132	T	A	exonic	PRKCI	.	nonsynonymous SNV	PRKCI:NM_002740:exon16:c.T1538A:p.F513Y	.	.	.	.	.	.	.	.	.	.	.	0.286	0.152	T	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	1.2	0.304	L	-0.27	0.674	T	-2.6	0.559	D	0.715	0.719	-0.523	0.678	T	0.310	0.681	T	0.065	0.696	D	5.735	0.783	26.9	0.990	0.493	0.985	0.836	D	c	0.562	0.617	1.000	0.517	0.732	0.924	0	5.51	0.817	7.639	0.824	1.061	0.807	1.000	0.715	1.000	0.888	15.922	0.793	Protein kinase domain|Protein kinase-like domain|Serine/threonine/dual specificity protein kinase, catalytic  domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	136	3	170015132	.	T	A	37	v3;f0.01;pSTD;q22.5;SN1.5;NM5.25	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=1;AF=0.0078;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.52281;SOR=0.52879;LSEQ=TTGTCATCCTCAAACAGGAT;RSEQ=TGCTGATATTCAGGGACACC;CSQ=A|missense_variant|MODERATE|PRKCI|5584|Transcript|NM_002740.6|protein_coding|16/18||NM_002740.6:c.1538T>A|NP_002731.4:p.Phe513Tyr|1784|1538|513|F/Y|tTt/tAt|||1||EntrezGene||YES||||3:g.170015132T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:128:1:1,0:65,62:127,1:0.0078:2,0:34:0:11:0:1:0:60:0:0:0:6	0/1:136:2:1,1:58,76:134,2:0.0147:2,2:30.5:1:37:0:1:1.31:60:4:0.0149:0:1
    1340. 

  1340. 3	170016857	170016857	T	A	exonic	PRKCI	.	synonymous SNV	PRKCI:NM_002740:exon17:c.T1662A:p.S554S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	219	3	170016857	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=154;VD=2;AF=0.013;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.16981;SOR=inf;LSEQ=GGTTTGGACAACTTTGATTC;RSEQ=CAGTTTACTAATGAACCTGT;CSQ=A|synonymous_variant|LOW|PRKCI|5584|Transcript|NM_002740.6|protein_coding|17/18||NM_002740.6:c.1662T>A|NP_002731.4:p.Ser554%3D|1908|1662|554|S|tcT/tcA|||1||EntrezGene||YES||||3:g.170016857T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:154:2:1,1:60,92:152,2:0.013:2,2:38.5:1:37:0:1:1.53:60:4:0.0131:0:1	0/0:219:0:0,0:93,126:219,0:0:2,0:37.6:1:36.8:1:1:0:60:218:1:0:0
    1341. 

  1341. 3	178919227	178919227	C	T	exonic	PIK3CA	.	stopgain	PIK3CA:NM_006218:exon4:c.C712T:p.Q238X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.063	0.980	38	0.998	0.920	0.976	0.756	D	c	1.003	0.892	1.000	0.454	0.732	0.924	0	5.56	0.836	7.455	0.796	0.935	0.490	1.000	0.715	0.994	0.587	19.905	0.970	Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain|Ubiquitin-related domain	.	.	ID=COSV55984796;OCCURENCE=1(large_intestine)	.	.	.	.	.	Likely pathogenic	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	174	3	178919227	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.8748;SOR=0;LSEQ=GTATGTTGCTATCCTCTGAA;RSEQ=AACTAAAACTCTGTGTTTTA;CSQ=T|stop_gained|HIGH|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|4/21||NM_006218.4:c.712C>T|NP_006209.2:p.Gln238Ter|1035|712|238|Q/*|Caa/Taa|COSV55984796||1||EntrezGene||YES||||3:g.178919227C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:12:0:0,0:6,6:12,0:0:2,0:44.6:1:37:0:1:0:60:24:1:0:0	0/1:174:2:1,1:80,92:172,2:0.0115:2,2:44:1:37:0:1:1.15:60:4:0.0116:0:1
    1342. 

  1342. 3	178921311	178921311	C	T	intronic	PIK3CA	.	.	.	0.0067	0.0007	0	0	0	0.0130	0	0	0	rs17849082	rs17849082	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55873360;OCCURENCE=1(meninges)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	127	3	178921311	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=14;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.81064;SOR=0;LSEQ=AAACCTTACAGGAAATGGCT;RSEQ=GCCCCCTTAATCTCTTACAG;CSQ=T|intron_variant|MODIFIER|PIK3CA|5290|Transcript|NM_006218.4|protein_coding||4/20|NM_006218.4:c.814-21C>T|||||||rs17849082&COSV55873360||1||EntrezGene||YES||||3:g.178921311C>T|0.0006413|0|3.37e-05|0|0.007764|0|9.341e-06|0.0003634|0.0003671|0.007764|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:14:0:0,0:12,2:14,0:0:2,0:24.5:1:37:0:1:0:60:28:1:0:0	0/1:127:2:1,1:85,40:125,2:0.0157:2,2:57:0:37:0:0.54318:2.11128:60:4:0.0159:0:1
    1343. 

  1343. 3	178921495	178921495	C	A	exonic	PIK3CA	.	nonsynonymous SNV	PIK3CA:NM_006218:exon5:c.C977A:p.S326Y	.	.	.	.	.	.	.	.	.	.	.	0.009	0.574	D	0.859	0.453	P	0.425	0.435	B	0.000	0.497	D	1	0.810	D	0.695	0.181	N	-0.99	0.759	T	-3.01	0.625	D	0.762	0.756	-0.518	0.680	T	0.314	0.684	T	0.046	0.625	D	4.974	0.669	25.1	0.991	0.520	0.973	0.736	D	c	0.278	0.366	1.000	0.427	0.732	0.924	0	5.4	0.779	4.605	0.606	0.892	0.403	1.000	0.715	0.995	0.604	19.540	0.952	Phosphatidylinositol 3-kinase, C2 domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	158	3	178921495	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=18;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.80539;SOR=0;LSEQ=TGGAGAAACATCTACAAAAT;RSEQ=CCTTTGGGTTATAAATAGTG;CSQ=A|missense_variant|MODERATE|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|5/21||NM_006218.4:c.977C>A|NP_006209.2:p.Ser326Tyr|1300|977|326|S/Y|tCc/tAc|COSV55902503||1||EntrezGene||YES||||3:g.178921495C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:18:0:0,0:6,12:18,0:0:2,0:23.1:1:36.3:1:1:0:60:36:1:0:0.7	0/1:158:2:1,1:56,100:156,2:0.0127:2,2:35:0:37:0:1:1.78:60:4:0.0128:0:1
    1344. 

  1344. 3	178922274	178922274	C	A	intronic	PIK3CA	.	.	.	0.9	0.6189	0.8533	0.5203	0.6689	0.2710	0.4851	0.5604	0.5509	rs2699896	rs2699896	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55874930;OCCURENCE=1(breast),2(meninges),40(large_intestine),20(soft_tissue),1(pancreas),1(upper_aerodigestive_tract)	251012	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU23553863	LAML-KR|1|205|0.00487805,COCA-CN|2|321|0.00623053,BRCA-KR|1|50|0.02	0.5	154	40	3	178922274	.	C	A	154	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=1;AF=0.25;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.37647;SOR=0.37617;LSEQ=GTGTATACATTAGTATATAC;RSEQ=TACTTTTTTCTTTTAGATCT;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PIK3CA|5290|Transcript|NM_006218.4|protein_coding||5/20|NM_006218.4:c.1060-17C>A|||||||rs2699896&COSV55874930||1||EntrezGene||YES||||3:g.178922274C>A|0.5552|0.8648|0.4871|0.6291|0.2627|0.486|0.584|0.5745|0.5599|0.9017|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:4:1:1,0:2,1:3,1:0.25:2,0:34:0:37:0:1:0:60:2:0.25:0:1	0/1:40:19:12,7:14,7:21,19:0.475:2,2:36.9:1:36.4:1:1:1.16217:60:38:0.475:0:1.4
    1345. 

  1345. 3	178928255	178928255	A	G	exonic	PIK3CA	.	nonsynonymous SNV	PIK3CA:NM_006218:exon9:c.A1441G:p.S481G	.	.	.	.	.	.	.	.	.	.	.	0.106	0.296	T	0.001	0.067	B	0.001	0.040	B	0.000	0.843	D	1	0.810	D	1.365	0.343	L	-1.14	0.779	T	-0.7	0.199	N	0.375	0.436	-0.726	0.592	T	0.266	0.637	T	0.037	0.572	D	2.338	0.342	18.41	0.994	0.618	0.985	0.836	D	c	-0.083	0.149	0.238	0.185	0.707	0.730	0	5.64	0.864	7.104	0.765	1.199	0.960	1.000	0.715	1.000	0.888	15.854	0.786	Phosphatidylinositol 3-kinase, C2 domain	.	.	ID=COSV56002542;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU114915277	COCA-CN|1|321|0.00311526	0.25	37	237	3	178928255	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=81;VD=2;AF=0.0247;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.06428;SOR=inf;LSEQ=AGTTGGAGTTTGACTGGTTC;RSEQ=GCAGTGTGGTAAAGTTCCCA;CSQ=G|missense_variant|MODERATE|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|9/21||NM_006218.4:c.1441A>G|NP_006209.2:p.Ser481Gly|1764|1441|481|S/G|Agc/Ggc|COSV56002542||1||EntrezGene||YES||||3:g.178928255A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:81:2:1,1:45,34:79,2:0.0247:2,2:33.5:1:37:0:1:1.31889:60:4:0.0247:0:1	0/0:237:0:0,0:135,102:237,0:0:2,0:37.7:1:35.9:1:1:0:60:46.4:1:0:0.1
    1346. 

  1346. 3	178937515	178937515	C	A	exonic	PIK3CA	.	nonsynonymous SNV	PIK3CA:NM_006218:exon12:c.C1903A:p.L635I	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.999	0.916	D	0.000	0.843	D	1	0.810	D	2.995	0.861	M	-1.39	0.804	T	-1.92	0.446	N	0.731	0.729	0.462	0.900	D	0.686	0.892	D	0.192	0.863	D	6.508	0.897	31	0.996	0.745	0.956	0.651	D	c	0.821	0.780	0.008	0.117	0.732	0.924	0	5.1	0.688	3.670	0.541	0.892	0.403	1.000	0.715	0.998	0.697	11.865	0.516	Armadillo-type fold|Phosphoinositide 3-kinase, accessory (PIK) domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	99	3	178937515	.	C	A	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.91351;SOR=0;LSEQ=TTTCTCAGTATTTAATTCAG;RSEQ=TAGTACAGGTAAAATAATGT;CSQ=A|missense_variant|MODERATE|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|12/21||NM_006218.4:c.1903C>A|NP_006209.2:p.Leu635Ile|2226|1903|635|L/I|Cta/Ata|||1||EntrezGene||YES||||3:g.178937515C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3:0:0,0:1,2:3,0:0:2,0:19.3:1:37:0:1:0:60:6:1:0:0	0/1:99:3:1,2:32,64:96,3:0.0303:2,2:33.3:1:28.3:1:1:1:60:2:0.0213:0:2.7
    1347. 

  1347. 3	178941872	178941872	C	A	exonic	PIK3CA	.	nonsynonymous SNV	PIK3CA:NM_006218:exon15:c.C2191A:p.Q731K	.	.	.	.	.	.	.	.	.	.	.	0.983	0.020	T	0.047	0.206	B	0.023	0.188	B	0.000	0.843	D	1	0.810	D	0.69	0.170	N	-1.4	0.805	T	-0.44	0.146	N	0.778	0.770	-0.617	0.641	T	0.314	0.685	T	0.060	0.680	D	2.306	0.338	18.20	0.723	0.096	0.991	0.918	D	c	-0.030	0.221	1.000	0.747	0.706	0.609	0	6.02	0.975	7.483	0.800	0.935	0.490	1.000	0.715	0.999	0.750	20.537	0.992	Protein kinase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	211	3	178941872	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=16;VD=2;AF=0.125;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00468;SOR=inf;LSEQ=CCTTTTTTTTTAATCAGGTA;RSEQ=AGATGAAGTTTTTAGTTGAG;CSQ=A|missense_variant|MODERATE|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|15/21||NM_006218.4:c.2191C>A|NP_006209.2:p.Gln731Lys|2514|2191|731|Q/K|Cag/Aag|||1||EntrezGene||YES||||3:g.178941872C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:16:2:1,1:7,7:14,2:0.125:2,2:17.5:1:37:0:1:1:60:4:0.1333:0:1.5	0/0:211:0:0,0:125,86:211,0:0:2,0:39:1:35.6:1:1:0:60:29.143:1:0:0.1
    1348. 

  1348. 3	178942431	178942431	C	G	intronic	PIK3CA	.	.	.	0.97	0.6499	0.9127	0.5484	0.7119	0.2930	0.4939	0.5800	0.5724	rs2699889	rs2699889	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55874955;OCCURENCE=20(soft_tissue),1(upper_aerodigestive_tract),32(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	220	130	3	178942431	.	C	G	220	PASS	STATUS=Deletion;SAMPLE=LibM078FTT;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATATTTTAAAATAAATTT;RSEQ=AGGGTAAAATAATAATAAAG;CSQ=G|intron_variant|MODIFIER|PIK3CA|5290|Transcript|NM_006218.4|protein_coding||15/20|NM_006218.4:c.2295-57C>G|||||||rs2699889&COSV55874955||1||EntrezGene||YES||||3:g.178942431C>G||||||||||0.9697|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:130:73:52,21:39,18:57,73:0.5615:2,2:36.2:1:35.6:1:0.84731:1.14:60:35.5:0.5635:0:1.1
    1349. 

  1349. 3	178947118	178947118	C	T	exonic	PIK3CA	.	stopgain	PIK3CA:NM_006218:exon18:c.C2554T:p.R852X	0.0002	.	.	.	.	.	.	.	.	rs758795044	.	.	.	.	.	.	.	.	.	.	0.000	0.843	D	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.217	0.981	38	0.995	0.707	0.794	0.391	D	c	0.394	0.235	0.073	0.156	0.732	0.924	0	2.95	0.331	1.838	0.386	-0.336	0.073	0.994	0.380	0.997	0.653	12.257	0.538	Phosphatidylinositol 3-/4-kinase, catalytic domain|Protein kinase-like domain	.	.	.	931843	Cowden_syndrome	MONDO:MONDO:0016063,MedGen:C0018553,OMIM:PS158350,Orphanet:ORPHA201,SNOMED_CT:58037000	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	312	3	178947118	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=87;VD=2;AF=0.023;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04712;SOR=inf;LSEQ=TGGGACTTATTGAGGTGGTG;RSEQ=GAAATTCTCACACTATTATG;CSQ=T|stop_gained|HIGH|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|18/21||NM_006218.4:c.2554C>T|NP_006209.2:p.Arg852Ter|2877|2554|852|R/*|Cga/Tga|rs758795044||1||EntrezGene||YES||||3:g.178947118C>T|8.039e-06|0|2.907e-05|0|0|4.645e-05|0|0|0|4.645e-05|gnomAD_FIN|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:87:2:1,1:40,45:85,2:0.023:2,2:40.5:1:37:0:1:1.12:60:4:0.0241:0:1	0/0:312:0:0,0:173,139:312,0:0:2,0:37.8:1:35.4:1:1:0:60:30.2:1:0:0.1
    1350. 

  1350. 3	178951930	178951930	C	A	exonic	PIK3CA	.	synonymous SNV	PIK3CA:NM_006218:exon21:c.C2985A:p.A995A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	125	3	178951930	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=49;VD=2;AF=0.0408;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.07813;SOR=inf;LSEQ=CTAGCTATTCGACAGCATGC;RSEQ=AATCTCTTCATAAATCTTTT;CSQ=A|synonymous_variant|LOW|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|21/21||NM_006218.4:c.2985C>A|NP_006209.2:p.Ala995%3D|3308|2985|995|A|gcC/gcA|COSV55903150||1||EntrezGene||YES||||3:g.178951930C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:49:2:1,1:35,12:47,2:0.0408:2,2:57:1:37:0:0.46429:2.84199:60:4:0.0426:0:1	0/0:125:0:0,0:93,32:125,0:0:2,0:35.5:1:36.1:1:1:0:60:250:1:0:0.1
    1351. 

  1351. 3	178952089	178952089	T	C	exonic	PIK3CA	.	synonymous SNV	PIK3CA:NM_006218:exon21:c.T3144C:p.H1048H	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV105063731;OCCURENCE=1(central_nervous_system)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	250	3	178952089	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=106;VD=2;AF=0.0189;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.08807;SOR=inf;LSEQ=CAAATGAATGATGCACATCA;RSEQ=GGTGGCTGGACAACAAAAAT;CSQ=C|synonymous_variant|LOW|PIK3CA|5290|Transcript|NM_006218.4|protein_coding|21/21||NM_006218.4:c.3144T>C|NP_006209.2:p.His1048%3D|3467|3144|1048|H|caT/caC|COSV55905780||1||EntrezGene||YES||||3:g.178952089T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:106:2:1,1:54,50:104,2:0.0189:2,2:16.5:1:37:0:1:1.07919:60:4:0.0189:0:1	0/0:250:0:0,0:105,145:250,0:0:2,0:39.6:1:36.6:1:1:0:60:82.333:1:0:0.1
    1352. 

  1352. 3	181430211	181430211	C	T	exonic	SOX2	.	synonymous SNV	SOX2:NM_003106:exon1:c.C63T:p.G21G	0.0008	.	.	.	.	.	.	.	.	rs781707393	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	48	3	181430211	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=561;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=3;SSF=0.00609;SOR=0;LSEQ=CAGCAAACTTCGGGGGGCGG;RSEQ=GGCGGCAACTCCACCGCGGC;CSQ=T|synonymous_variant|LOW|SOX2|6657|Transcript|NM_003106.4|protein_coding|1/1||NM_003106.4:c.63C>T|NP_003097.1:p.Gly21%3D|499|63|21|G|ggC/ggT|rs781707393||1||EntrezGene||YES||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_004053.3|lncRNA||3/4|NR_004053.3:n.768-2762C>T|||||||rs781707393||1||EntrezGene||||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075089.1|lncRNA||3/3|NR_075089.1:n.767+12540C>T|||||||rs781707393||1||EntrezGene||||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075090.1|lncRNA||2/2|NR_075090.1:n.482-27146C>T|||||||rs781707393||1||EntrezGene||||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075091.1|lncRNA||6/7|NR_075091.1:n.783-2762C>T|||||||rs781707393||1||EntrezGene||YES||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075092.1|lncRNA||6/6|NR_075092.1:n.782+12540C>T|||||||rs781707393||1||EntrezGene||||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075093.1|lncRNA||4/4|NR_075093.1:n.473-27146C>T|||||||rs781707393||1||EntrezGene||||||3:g.181430211C>T|1.368e-05|0|0|0|0.0001228|0|1.051e-05|0|0|0.0001228|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:561:0:0,0:464,97:561,0:0:2,0:33.7:1:36.5:1:1:0:60:186:1:0:0.2	0/1:48:2:1,1:43,3:46,2:0.0417:2,2:20.5:1:37:0:0.16135:12.5566:60:4:0.0417:0:1
    1353. 

  1353. 3	181431051	181431051	C	T	exonic	SOX2	.	synonymous SNV	SOX2:NM_003106:exon1:c.C903T:p.G301G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	101	3	181431051	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=525;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.02581;SOR=0;LSEQ=TCCCAGCACTACCAGAGCGG;RSEQ=CCGGTGCCCGGCACGGCCAT;CSQ=T|synonymous_variant|LOW|SOX2|6657|Transcript|NM_003106.4|protein_coding|1/1||NM_003106.4:c.903C>T|NP_003097.1:p.Gly301%3D|1339|903|301|G|ggC/ggT|||1||EntrezGene||YES||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_004053.3|lncRNA||3/4|NR_004053.3:n.768-1922C>T|||||||||1||EntrezGene||||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075089.1|lncRNA||3/3|NR_075089.1:n.767+13380C>T|||||||||1||EntrezGene||||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075090.1|lncRNA||2/2|NR_075090.1:n.482-26306C>T|||||||||1||EntrezGene||||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075091.1|lncRNA||6/7|NR_075091.1:n.783-1922C>T|||||||||1||EntrezGene||YES||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075092.1|lncRNA||6/6|NR_075092.1:n.782+13380C>T|||||||||1||EntrezGene||||||3:g.181431051C>T||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075093.1|lncRNA||4/4|NR_075093.1:n.473-26306C>T|||||||||1||EntrezGene||||||3:g.181431051C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:525:0:0,0:232,293:525,0:0:2,0:38.1:1:36.7:1:1:0:60:261.5:1:0:0.4	0/1:101:2:1,1:44,55:99,2:0.0198:2,2:46.5:1:37:0:1:1.25:60:4:0.0198:0:1
    1354. 

  1354. 3	181431155	181431155	A	C	ncRNA_intronic	SOX2-OT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	55	3	181431155	.	A	C	25	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=194;VD=2;AF=0.0103;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.60633;SOR=inf;LSEQ=TTTCAAAGAAAAACGAGGGA;RSEQ=ATGGGAGGGGTGCAAAAGAG;CSQ=C|3_prime_UTR_variant|MODIFIER|SOX2|6657|Transcript|NM_003106.4|protein_coding|1/1||NM_003106.4:c.*53A>C||1443|||||||1||EntrezGene||YES||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_004053.3|lncRNA||3/4|NR_004053.3:n.768-1818A>C|||||||||1||EntrezGene||||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075089.1|lncRNA||3/3|NR_075089.1:n.767+13484A>C|||||||||1||EntrezGene||||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075090.1|lncRNA||2/2|NR_075090.1:n.482-26202A>C|||||||||1||EntrezGene||||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075091.1|lncRNA||6/7|NR_075091.1:n.783-1818A>C|||||||||1||EntrezGene||YES||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075092.1|lncRNA||6/6|NR_075092.1:n.782+13484A>C|||||||||1||EntrezGene||||||3:g.181431155A>C||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SOX2-OT|347689|Transcript|NR_075093.1|lncRNA||4/4|NR_075093.1:n.473-26202A>C|||||||||1||EntrezGene||||||3:g.181431155A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:194:2:2,0:62,130:192,2:0.0103:2,0:11.5:1:25:0:0.10769:0:60:4:0.0115:0:1.5	0/0:55:0:0,0:16,39:55,0:0:2,0:31.9:1:33.1:1:1:0:60:8.167:1:0:0.2
    1355. 

  1355. 3	183209737	183209737	A	G	exonic	KLHL6	.	nonsynonymous SNV	KLHL6:NM_130446:exon7:c.T1844C:p.V615A	.	.	.	.	.	.	.	.	.	.	.	0.158	0.239	T	0.0	0.026	B	0.0	0.013	B	0.000	0.486	D	0.822	0.348	D	0.895	0.225	L	-0.8	0.739	T	-0.27	0.114	N	0.079	0.111	-0.813	0.544	T	0.184	0.533	T	0.017	0.387	T	1.563	0.250	13.65	0.955	0.264	0.922	0.550	D	c	-0.327	-0.125	0.999	0.392	0.719	0.830	0	4.5	0.542	5.501	0.664	1.140	0.893	1.000	0.715	0.811	0.340	11.489	0.494	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	149	3	183209737	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1638;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00691;SOR=0;LSEQ=AGACAGACACTGCTCCGGGC;RSEQ=CGATCCTGCGGATGTGGGTG;CSQ=G|missense_variant|MODERATE|KLHL6|89857|Transcript|NM_130446.4|protein_coding|7/7||NM_130446.4:c.1844T>C|NP_569713.2:p.Val615Ala|1897|1844|615|V/A|gTg/gCg|||-1||EntrezGene||YES||||3:g.183209737A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1638:0:0,0:975,663:1638,0:0:2,0:34.6:1:35.4:1:1:0:60:32.429:1:0:0.1	0/1:149:2:1,1:82,65:147,2:0.0134:2,2:49.5:1:37:0:1:1.25955:60:4:0.0138:0:1
    1356. 

  1356. 3	183211906	183211906	A	G	exonic	KLHL6	.	synonymous SNV	KLHL6:NM_130446:exon5:c.T1311C:p.N437N	0.87	0.5713	0.8114	0.6065	0.5667	0.7741	0.3972	0.4564	0.4501	rs1520101	rs1520101	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58066416;OCCURENCE=1(large_intestine),1(urinary_tract)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU103694	COCA-CN|5|321|0.0155763	0.75	356	211	3	183211906	.	A	G	356	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=1631;VD=868;AF=0.5322;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.0109;LSEQ=AAGGGGTCGTAGGTCTCCAC;RSEQ=TTGTTGATTCTCTGTAAGCC;CSQ=G|synonymous_variant|LOW|KLHL6|89857|Transcript|NM_130446.4|protein_coding|5/7||NM_130446.4:c.1311T>C|NP_569713.2:p.Asn437%3D|1364|1311|437|N|aaT/aaC|rs1520101&COSV58066416||-1||EntrezGene||YES||||3:g.183211906A>G|0.5573|0.8177|0.6126|0.5312|0.7966|0.3926|0.4744|0.5412|0.6494|0.8722|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:1631:868:440,428:377,386:763,868:0.5322:2,2:39.6:1:36.5:1:0.61988:1.05:60:85.8:0.5363:0:1.1	1/1:211:209:113,96:0,0:0,209:0.9905:0,2:38.3:1:36.7:1:1:0:60:103.5:0.9904:0:1
    1357. 

  1357. 3	183226072	183226072	G	A	exonic	KLHL6	.	synonymous SNV	KLHL6:NM_130446:exon3:c.C684T:p.Y228Y	0.25	0.0767	0.2244	0.0477	0.0033	0.1790	0.0083	0.0019	0.0286	rs16857707	rs16857707	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58066575;OCCURENCE=1(breast),1(stomach),1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU794080	LICA-CN|2|402|0.00497512,LUSC-KR|1|170|0.00588235,GACA-JP|1|585|0.0017094,BRCA-KR|1|50|0.02	0.25	248	268	3	183226072	.	G	A	248	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=3049;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCTGAGCCTCCTCGGTCAC;RSEQ=TAAAGGTCATCACTCTTCAA;CSQ=A|synonymous_variant|LOW|KLHL6|89857|Transcript|NM_130446.4|protein_coding|3/7||NM_130446.4:c.684C>T|NP_569713.2:p.Tyr228%3D|737|684|228|Y|taC/taT|rs16857707&COSV58066575||-1||EntrezGene||YES||||3:g.183226072G>A|0.04634|0.2255|0.05299|0.00387|0.1749|0.00716|0.001812|0.02478|0.07784|0.2451|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:3049:0:0,0:1344,1689:3033,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/0:268:138:40,98:50,80:130,138:0.5149:2,2:35.5:1:35:1:0.12054:1.52877:60:22:0.5197:0:1.5
    1358. 

  1358. 3	183226186	183226186	C	T	exonic	KLHL6	.	synonymous SNV	KLHL6:NM_130446:exon3:c.G570A:p.K190K	0.18	0.0335	0.0728	0.0394	0.0033	0.1796	0.0083	0.0017	0.0234	rs61447052	rs61447052	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58065123;OCCURENCE=1(breast),1(stomach)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU586201	LUSC-KR|1|170|0.00588235,BRCA-KR|1|50|0.02	0.25	250	232	3	183226186	.	C	T	250	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2869;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTAACTCTGAACCTGCTT;RSEQ=TTTAGACTGTCCAGCGAGTG;CSQ=T|synonymous_variant|LOW|KLHL6|89857|Transcript|NM_130446.4|protein_coding|3/7||NM_130446.4:c.570G>A|NP_569713.2:p.Lys190%3D|623|570|190|K|aaG/aaA|rs61447052&COSV58065123||-1||EntrezGene||YES||||3:g.183226186C>T|0.03501|0.07192|0.04566|0.002586|0.1745|0.00716|0.001314|0.02006|0.07776|0.1786|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2869:0:0,0:1357,1511:2868,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:232:113:49,64:55,64:119,113:0.4871:2,2:37.4:1:36.8:1:0.69329:1.12189:60:226:0.4871:0:2.1
    1359. 

  1359. 3	183226213	183226213	A	G	exonic	KLHL6	.	synonymous SNV	KLHL6:NM_130446:exon3:c.T543C:p.A181A	0.33	0.0994	0.3031	0.0513	0.0033	0.1794	0.0083	0.0025	0.0346	rs16857710	rs16857710	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV58065134;OCCURENCE=1(breast),1(stomach)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU586202	LUSC-KR|1|170|0.00588235,BRCA-KR|1|50|0.02	0.25	244	210	3	183226213	.	A	G	244	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2769;VD=3;AF=0.0011;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0.00114;LSEQ=CTGTCCAGCGAGTGTGTGTC;RSEQ=GCCAGCCTCAGTATTCCAAC;CSQ=G|synonymous_variant|LOW|KLHL6|89857|Transcript|NM_130446.4|protein_coding|3/7||NM_130446.4:c.543T>C|NP_569713.2:p.Ala181%3D|596|543|181|A|gcT/gcC|rs16857710&COSV58065134||-1||EntrezGene||YES||||3:g.183226213A>G|0.05299|0.3101|0.05781|0.004375|0.1749|0.007206|0.002409|0.03086|0.07813|0.3298|AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2769:3:1,2:1186,1579:2765,3:0.0011:2,2:51.3:1:28.3:1:1:1.502:60:2:0.0007:0:1	0/1:210:103:47,56:49,58:107,103:0.4905:2,2:36:1:36.5:1:1:1.00657:60:206:0.4905:0:1.9
    1360. 

  1360. 3	183245630	183245630	C	A	intronic	KLHL6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	25	82	3	183245630	.	C	A	25	v3;f0.01;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1047;VD=2;AF=0.0019;SHIFT3=0;MSI=3;MSILEN=2;SSF=0.02841;SOR=0.07699;LSEQ=ACTGAGCCAGTTTGTTCACA;RSEQ=ACCTGGAAGAGGTTAGCAGC;CSQ=A|splice_donor_region_variant&intron_variant|LOW|KLHL6|89857|Transcript|NM_130446.4|protein_coding||2/6|NM_130446.4:c.459+3G>T|||||||||-1||EntrezGene||YES||||3:g.183245630C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1047:2:2,0:595,450:1045,2:0.0019:2,0:28.5:1:24:1:0.50939:0:60:1:0.001:0:1	0/1:82:2:1,1:51,29:80,2:0.0244:2,2:60:1:25:0:1:1.74584:60:4:0.0244:0:1
    1361. 

  1361. 3	183245674	183245674	G	A	exonic	KLHL6	.	stopgain	KLHL6:NM_130446:exon2:c.C418T:p.Q140X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.116	0.192	N	1	0.810	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.961	0.971	37	0.998	0.901	0.848	0.436	D	c	1.060	0.923	1.000	0.747	0.731	0.878	0	5.7	0.886	3.636	0.538	1.048	0.713	1.000	0.715	0.996	0.625	16.121	0.811	BTB/POZ domain|SKP1/BTB/POZ domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	128	3	183245674	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1384;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00712;SOR=0;LSEQ=CAGGACCCGCTGGACATTCT;RSEQ=CTTGGTGATCAGCGCCTTGC;CSQ=A|stop_gained|HIGH|KLHL6|89857|Transcript|NM_130446.4|protein_coding|2/7||NM_130446.4:c.418C>T|NP_569713.2:p.Gln140Ter|471|418|140|Q/*|Cag/Tag|||-1||EntrezGene||YES||||3:g.183245674G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1384:0:0,0:771,613:1384,0:0:2,0:40.3:1:36.3:1:1:0:60:71.842:1:0:0.1	0/1:128:2:1,1:72,54:126,2:0.0156:2,2:59:1:37:0:1:1.33029:60:4:0.0157:0:1
    1362. 

  1362. 3	183245691	183245691	T	-	exonic	KLHL6	.	frameshift deletion	KLHL6:NM_130446:exon2:c.401delA:p.K134Rfs*3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	140	3	183245690	.	CT	C	37	v3;f0.01;p8;pSTD;q22.5;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1481;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.00741;SOR=0;LSEQ=TTCTGCTTGGTGATCAGCGC;RSEQ=TGCTGGTGTACGTGTAGTCC;CSQ=-|frameshift_variant|HIGH|KLHL6|89857|Transcript|NM_130446.4|protein_coding|2/7||NM_130446.4:c.401del|NP_569713.2:p.Lys134ArgfsTer3|454|401|134|K/X|aAg/ag|||-1||EntrezGene||YES||||3:g.183245692del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1481:0:0,0:803,677:1480,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:140:2:1,1:75,63:138,2:0.0143:2,2:18:1:37:0:1:1.18898:60:4:0.0148:0:0
    1363. 

  1363. 3	183245766	183245766	T	C	exonic	KLHL6	.	nonsynonymous SNV	KLHL6:NM_130446:exon2:c.A326G:p.Y109C	0.	.	.	.	.	.	.	.	.	rs780725237	.	0.171	0.227	T	0.002	0.090	B	0.014	0.158	B	0.000	0.504	D	1.000	0.511	D	0.515	0.136	N	-0.26	0.672	T	-2.03	0.466	N	0.53	0.622	-0.887	0.492	T	0.176	0.521	T	0.019	0.418	T	4.126	0.553	23.8	0.992	0.558	0.913	0.530	D	c	-0.059	0.171	1.000	0.747	0.731	0.878	0	5.83	0.930	4.715	0.614	1.049	0.752	1.000	0.715	0.987	0.523	16.216	0.820	BTB/POZ domain|SKP1/BTB/POZ domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	144	3	183245766	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1499;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00763;SOR=0;LSEQ=TAATAATGATCCTTTTCTCA;RSEQ=ACTTTTCCTTTAAATCGTTG;CSQ=C|missense_variant|MODERATE|KLHL6|89857|Transcript|NM_130446.4|protein_coding|2/7||NM_130446.4:c.326A>G|NP_569713.2:p.Tyr109Cys|379|326|109|Y/C|tAt/tGt|rs780725237||-1||EntrezGene||YES||||3:g.183245766T>C|3.978e-06|0|0|0|0|0|8.798e-06|0|0|8.798e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1499:0:0,0:796,702:1498,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:144:2:1,1:67,75:142,2:0.0139:2,2:38.5:1:37:0:1:1.12:60:4:0.0141:0:1
    1364. 

  1364. 3	185784121	185784121	C	T	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	155	3	185784121	.	C	T	37	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=2;AF=0.2857;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.00161;SOR=inf;LSEQ=CCATGTATGTATATTTTATG;RSEQ=ACAGTCTATCTGTATAGATG;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-260G>A|||||||||-1||EntrezGene||YES||||3:g.185784121C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:7:2:1,1:2,3:5,2:0.2857:2,2:31:1:37:0:1:1.41:60:4:0.3333:0:1	0/0:155:0:0,0:66,87:153,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1365. 

  1365. 3	185784186	185784186	T	C	intronic	ETV5	.	.	.	0.059	0.0160	0.0029	0.0530	0	0.0626	0.0249	0.0147	0.0193	rs76742690	rs76742690	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114159569	LAML-KR|1|205|0.00487805	0.25	225	135	3	185784186	.	T	C	225	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02316;SOR=0;LSEQ=TGAGACCAATTATCTGCAAA;RSEQ=AGCACTAACATATACATAAA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-325A>G|||||||rs76742690||-1||EntrezGene||YES||||3:g.185784186T>C||||||||||0.0595|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:1,4:5,0:0:2,0:19.8:1:37:0:1:0:60:10:1:0:0.2	1/0:135:73:34,39:21,41:62,73:0.5407:2,2:38.2:1:36.5:1:0.16098:1.7:60:72:0.5373:0:1.2
    1366. 

  1366. 3	185784364	185784364	T	C	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	98	3	185784364	.	T	C	37	d5;v3;f0.01;p8;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.9798;SOR=0;LSEQ=CATAACATTCCTAGGAATAA;RSEQ=CAGGAAACCTATAGGCCATA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-503A>G|||||||||-1||EntrezGene||YES||||3:g.185784364T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:37:0:1:0:60:2:1:0:0	0/1:98:2:1,1:49,47:96,2:0.0204:2,2:45.5:1:37:0:1:1.04212:60:4:0.0204:0:1
    1367. 

  1367. 3	185784415	185784415	G	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	102	3	185784415	.	G	A	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.98058;SOR=0;LSEQ=ATCTCAAAATTGTTTTCAGA;RSEQ=GAAAAGAAAGAAAAAAGATT;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-554C>T|||||||||-1||EntrezGene||YES||||3:g.185784415G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:58:0:37:0:1:0:60:2:1:0:0	0/1:102:2:1,1:51,49:100,2:0.0196:2,2:50.5:1:37:0:1:1.04042:60:4:0.0204:0:1
    1368. 

  1368. 3	185785242	185785242	C	T	intronic	ETV5	.	.	.	0.075	0.0192	0.0668	0.0036	0	0	0	0.0002	0.0052	rs112798278	rs112798278	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	13	3	185785242	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=158;VD=2;AF=0.0127;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.85332;SOR=inf;LSEQ=AATAAACAACAACAAAAAAA;RSEQ=CTAAAAAAATTAGCCAGGCG;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-1381G>A|||||||rs112798278||-1||EntrezGene||YES||||3:g.185785242C>T||||||||||0.0749|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:158:2:1,1:71,85:156,2:0.0127:2,2:43:0:37:0:1:1.2:60:4:0.0129:0:1	0/0:13:0:0,0:6,7:13,0:0:2,0:40.2:1:36.1:1:1:0:60:26:1:0:0.6
    1369. 

  1369. 3	185785398	185785398	-	A	intronic	ETV5	.	.	.	.	0.0061	0.0013	0.0233	0.0278	0.0015	0.0814	0.0041	0.0164	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	126	37	3	185785398	.	C	CA	126	MSI12;MSI12	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=40;VD=13;AF=0.325;SHIFT3=14;MSI=15;MSILEN=1;SSF=0.00056;SOR=16.8176;LSEQ=GCAACAGAGCAAGACTGTCT;RSEQ=AAAAAAAAAAAAAAGTGAAA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-1538dup|||||||rs908859546||-1||EntrezGene||YES||||3:g.185785412dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:40:13:4,8:8,11:19,13:0.325:2,2:39.7:1:34.1:1:0.71721:1.43716:60.2:26:0.4333:0.05:0.6	0/1:37:1:1,0:24,9:33,1:0.027:2,0:72.8:0:40.2:0:1:0:65.2:2:0.0345:0:1.1
    1370. 

  1370. 3	185785534	185785534	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	rs1043195466	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	171	3	185785534	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=15;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.84481;SOR=0;LSEQ=ACCTGGATATACCTCACTGT;RSEQ=TAAATTTCTATAACTTAAAA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-1673T>C|||||||rs1043195466||-1||EntrezGene||YES||||3:g.185785534A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:15:0:0,0:7,8:15,0:0:2,0:22.4:1:36.2:1:1:0:60:30:1:0:0.3	0/1:171:2:1,1:107,62:169,2:0.0117:2,2:48:1:37:0:1:1.71995:60:4:0.0119:0:2
    1371. 

  1371. 3	185785548	185785548	C	G	intronic	ETV5	.	.	.	0.84	0.7308	0.5493	0.75	0.8311	0.4783	0.8156	0.8364	0.7929	rs4234587	rs4234587	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	225	173	3	185785548	.	C	G	225	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=3;AF=0.3;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.26387;SOR=0.51172;LSEQ=CACTGTATAAATTTCTATAA;RSEQ=TTAAAAAGACATCGGAAACA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-1687G>C|||||||rs4234587||-1||EntrezGene||YES||||3:g.185785548C>G||||||||||0.837|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:10:3:1,2:3,4:7,3:0.3:2,2:16:1:37:0:1:1.44135:60:6:0.3:0:1	0/1:173:79:49,30:54,39:93,79:0.4566:2,2:38.1:1:35.7:1:0.64137:1.18:60:38.5:0.4556:0:1.1
    1372. 

  1372. 3	185785608	185785608	G	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	199	3	185785608	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=2;AF=0.1818;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00251;SOR=inf;LSEQ=AAACCAGGGGGAAAGAATCT;RSEQ=CAGTAGTCAGAAAACACCAG;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-1747C>T|||||||||-1||EntrezGene||YES||||3:g.185785608G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:11:2:1,1:6,3:9,2:0.1818:2,2:48.5:1:37:0:1:1.87089:60:4:0.2:0:1.5	0/0:199:0:0,0:115,84:199,0:0:2,0:37.3:1:36.3:1:1:0:60:98.5:1:0:0.3
    1373. 

  1373. 3	185785996	185785996	T	C	intronic	ETV5	.	.	.	0.84	0.7316	0.5515	0.7494	0.8311	0.4795	0.8160	0.8364	0.7933	rs9831938	rs9831938	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	257	260	3	185785996	.	T	C	257	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=21;VD=9;AF=0.4286;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.26083;SOR=0.67431;LSEQ=GAAACTGGCTATATATATTA;RSEQ=GATACAGTCATTTGGTTGAA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2135A>G|||||||rs9831938||-1||EntrezGene||YES||||3:g.185785996T>C||||||||||0.837|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:21:9:4,5:3,9:12,9:0.4286:2,2:18.2:1:37:0:0.39721:2.3:60:18:0.4286:0:1.2	1/0:260:137:51,86:45,77:122,137:0.5269:2,2:35.5:1:36.3:1:1:1.01:60:67.5:0.5273:0:1.1
    1374. 

  1374. 3	185786040	185786040	T	C	intronic	ETV5	.	.	.	0.46	0.0805	0.0803	0.1687	0.0265	0.4727	0.0865	0.0336	0.0764	rs79587697	rs79587697	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	242	203	3	185786040	.	T	C	242	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.03279;SOR=0;LSEQ=AACCATTAGAAATTACATAA;RSEQ=ATGTAAATATATAAGGTCTT;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2179A>G|||||||rs79587697||-1||EntrezGene||YES||||3:g.185786040T>C||||||||||0.4613|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:3,2:5,0:0:2,0:24.2:1:37:0:1:0:60:10:1:0:0.2	1/0:203:102:41,61:37,64:101,102:0.5025:2,2:34.5:1:36.4:1:0.66572:1.16:60:50:0.5:0:1.1
    1375. 

  1375. 3	185786239	185786239	T	C	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	235	3	185786239	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=36;VD=2;AF=0.0556;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01722;SOR=inf;LSEQ=AGGTGATTTTCTTTTTTTGC;RSEQ=CATCTATAGTTTGATAATAA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2378A>G|||||||||-1||EntrezGene||YES||||3:g.185786239T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:36:2:1,1:23,11:34,2:0.0556:2,2:16:0:37:0:1:2.045:60:4:0.0556:0:1	0/0:235:0:0,0:125,110:235,0:0:2,0:35.4:1:36.5:1:1:0:60:234:1:0:0.1
    1376. 

  1376. 3	185786269	185786269	-	T	intronic	ETV5	.	.	.	0.46	0.0669	0.0320	0.1695	0.0265	0.4746	0.0870	0.0333	0.0745	rs11404969	rs11404969	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	255	277	3	185786269	.	G	GT	255	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=64;VD=0;AF=0;SHIFT3=6;MSI=7;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGATAATAAATATGCACT;RSEQ=TTTTTTAACAAGATAGAATA;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2409dup|||||||rs11404969||-1||EntrezGene||YES||||3:g.185786275dup||||||||||0.4623|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:64:0:0,0:44,20:64,0:0:2,0:27.3:1:35.2:1:1:0:60:20.333:1:0:0.2	1/0:277:140:85,54:78,59:137,140:0.5054:2,2:33:1:35.8:1:0.54068:1.19:60.2:69:0.5111:0.0975:0.3
    1377. 

  1377. 3	185786297	185786297	G	T	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	340	3	185786297	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=145;VD=2;AF=0.0138;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.08895;SOR=inf;LSEQ=ACAAGATAGAATAAAAACCT;RSEQ=TTGCTACTAGTCGAGTTTCC;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2436C>A|||||||||-1||EntrezGene||YES||||3:g.185786297G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:145:2:1,1:100,43:143,2:0.0138:2,2:35.5:1:37:0:0.51628:2.3105:60:4:0.014:0:1.5	0/0:340:0:0,0:207,133:340,0:0:2,0:32.8:1:36.1:1:1:0:60:67:1:0:0.6
    1378. 

  1378. 3	185786406	185786406	G	A	intronic	ETV5	.	.	.	0.94	0.8810	0.8710	0.9344	0.8808	0.9548	0.9030	0.8706	0.8829	rs4234588	rs4234588	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	329	539	3	185786406	.	G	A	329	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=652;VD=309;AF=0.4739;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0.00166;LSEQ=TGTAGAAGGGAAAGCCTGCC;RSEQ=TGCCTTAGTAGGGAAGTGAC;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2545C>T|||||||rs4234588||-1||EntrezGene||YES||||3:g.185786406G>A||||||||||0.9444|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:652:309:170,139:192,151:343,309:0.4739:2,2:42.1:1:36:1:0.81331:1.03962:60:50.5:0.469:0:1.1	1/1:539:538:279,259:0,0:0,538:0.9981:0,2:36.6:1:36.3:1:1:0:60:66.25:1:0:1.1
    1379. 

  1379. 3	185786799	185786799	A	C	intronic	ETV5	.	.	.	.	9.681e-05	0	0	0	0	0	0.0001	0.0010	rs762047306	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	183	3	185786799	.	A	C	37	d5;v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.95756;SOR=0;LSEQ=ATTCTTGAATAGCTTTAATA;RSEQ=AATAGTTTGAATTTGATTTG;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-2938T>G|||||||rs762047306||-1||EntrezGene||YES||||3:g.185786799A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:4:0:0,0:2,2:4,0:0:2,0:21.5:1:37:0:1:0:60:8:1:0:0	0/1:183:2:1,1:102,79:181,2:0.0109:2,2:36.5:1:37:0:1:1.28931:60:4:0.011:0:1
    1380. 

  1380. 3	185786904	185786904	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	270	3	185786904	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=30;VD=2;AF=0.0667;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.0097;SOR=inf;LSEQ=GAAGAGATCTGTGTACAGAT;RSEQ=GAACACTGTTTACATCAGGG;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3043T>C|||||||||-1||EntrezGene||YES||||3:g.185786904A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:30:2:1,1:16,12:28,2:0.0667:2,2:16:0:37:0:1:1.32044:60:4:0.0667:0:1	0/0:270:0:0,0:149,121:270,0:0:2,0:37.2:1:36.5:1:1:0:60:134:1:0:0.2
    1381. 

  1381. 3	185787309	185787309	T	A	intronic	ETV5	.	.	.	0.42	0.1163	0.2767	0.0523	0.0674	0.0635	0.0247	0.0550	0.0685	rs199620828	rs199620828	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	215	101	3	185787309	.	T	A	215	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=186;VD=86;AF=0.4624;SHIFT3=0;MSI=7;MSILEN=1;SSF=0;SOR=inf;LSEQ=TGTTTTTTTTTTTTTTTTTT;RSEQ=AAAAAAAGTCTAAAAAAAGA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3448A>T|||||||rs199620828||-1||EntrezGene||YES||||3:g.185787309T>A||||||||||0.4167|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:186:86:17,69:17,78:95,86:0.4624:2,2:28.7:1:33.6:1:0.84934:1.13:60:9.75:0.4483:0:2.4	0/0:101:0:0,0:19,46:65,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1382. 

  1382. 3	185787334	185787334	A	G	intronic	ETV5	.	.	.	0.19	0.1316	0.1847	0.0673	0.14	0.0457	0.0849	0.1249	0.1157	rs7631721	rs7631721	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	205	72	3	185787334	.	A	G	205	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=128;VD=68;AF=0.5312;SHIFT3=0;MSI=8;MSILEN=1;SSF=0;SOR=inf;LSEQ=AAAGTCTAAAAAAAGACTTA;RSEQ=AAAAAAGTCTTGCTCTGTCA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3473T>C|||||||rs7631721||-1||EntrezGene||YES||||3:g.185787334A>G||||||||||0.1853|AFR|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:128:68:22,46:15,44:59,68:0.5312:2,2:25.7:1:33.8:1:0.43744:1.4:60:7.5:0.5042:0:2.4	0/0:72:0:0,0:10,62:72,0:0:2,0:29.9:1:36.8:1:1:0:60:144:1:0:1.7
    1383. 

  1383. 3	185787356	185787356	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	49	3	185787356	.	C	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=113;VD=2;AF=0.0177;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.48524;SOR=inf;LSEQ=AAAAAGTCTTGCTCTGTCAC;RSEQ=CAGGCTGGAGTGCAGTGACT;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3495G>T|||||||||-1||EntrezGene||YES||||3:g.185787356C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:113:2:1,1:63,48:111,2:0.0177:2,2:40.5:1:31:1:1:1.3093:60:4:0.0182:0:2.5	0/0:49:0:0,0:8,41:49,0:0:2,0:41.2:1:36.2:1:1:0:60:48:1:0:1.2
    1384. 

  1384. 3	185787600	185787600	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	48	3	185787600	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=404;VD=0;AF=0;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.01107;SOR=0;LSEQ=ACCCAGCTGATGAAGGTATT;RSEQ=TTTTTATTTTTTGTTGAGAC;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3739G>T|||||||||-1||EntrezGene||YES||||3:g.185787600C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:404:0:0,0:185,219:404,0:0:2,0:37.8:1:35.6:1:1:0:60:49.5:1:0:0.1	0/1:48:2:1,1:18,28:46,2:0.0417:2,2:17:1:37:0:1:1.54:60:4:0.0435:0:1
    1385. 

  1385. 3	185787762	185787762	-	T	intronic	ETV5	.	.	.	.	0.0009	0.0008	0.0054	0	0	0	0.0010	0.0011	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	62	22	3	185787762	.	A	AT	62	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=154;VD=3;AF=0.0195;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.66828;SOR=inf;LSEQ=CCTGCCATCATGCCTGGCTA;RSEQ=TTTTTTTTTTGTATTTTTAG;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3902dup|||||||rs879291697||-1||EntrezGene||YES||||3:g.185787772dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:154:3:3,0:111,32:143,3:0.0195:2,0:20.1:1:39.2:1:1:0:63.6:6:0.0208:0.013:0.4	0/0:22:0:0,0:18,4:22,0:0:2,0:26.6:1:35.3:1:1:0:60:21:1:0:0.2
    1386. 

  1386. 3	185787782	185787782	G	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	25	3	185787782	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=195;VD=2;AF=0.0103;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.78518;SOR=inf;LSEQ=ATTTTTTTTTTGTATTTTTA;RSEQ=TAGAGATAGGGTTTCACCAC;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-3921C>T|||||||||-1||EntrezGene||YES||||3:g.185787782G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:195:2:1,1:172,21:193,2:0.0103:2,2:15:1:37:0:0.21343:8.02495:60:4:0.0105:0:1	0/0:25:0:0,0:22,3:25,0:0:2,0:32:1:35.6:1:1:0:60:50:1:0:0.2
    1387. 

  1387. 3	185788988	185788988	A	-	intronic	ETV5	.	.	.	.	0.0026	0.0014	0.0073	0.0086	0.0013	0.0253	0.0009	0.0030	rs774748036	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112232171	BTCA-SG|17|71|0.239437	0.5	250	384	3	185788987	.	GA	G	250	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1606;VD=114;AF=0.071;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.10896;SOR=0.762;LSEQ=AGTAAACACAATGCTCACAG;RSEQ=AAAAAAAAAAGGAGAAAAGG;CSQ=-|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-5127del|||||||rs774748036||-1||EntrezGene||YES||||3:g.185788998del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1606:114:56,58:720,746:1466,114:0.071:2,2:37.5:1:36.7:1:1:1:60:228:0.0721:0.0037:0.1	0/1:384:35:21,14:189,158:347,35:0.0911:2,2:35.3:1:36.9:1:0.59517:1.25:60:70:0.0919:0.013:0.2
    1388. 

  1388. 3	185789571	185789571	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	58	3	185789571	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=521;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00988;SOR=0;LSEQ=GGAGTTTGAGACCAGCCTGA;RSEQ=CAACACGGTGAAACCTGTAA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-5710G>T|||||||||-1||EntrezGene||YES||||3:g.185789571C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:521:0:0,0:165,356:521,0:0:2,0:41.6:1:36.4:1:1:0:60:73.429:1:0:0.1	0/1:58:2:1,1:17,39:56,2:0.0345:2,2:38:1:37:0:0.52813:2.26:60:4:0.0351:0:1
    1389. 

  1389. 3	185789948	185789948	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	30	3	185789948	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.75565;SOR=inf;LSEQ=CAGATCACCATGTGAGTTCC;RSEQ=TAAATGAGGTCAGGAGTTTG;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-6087G>T|||||||||-1||EntrezGene||YES||||3:g.185789948C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:114,84:198,2:0.01:2,2:32:1:37:0:1:1.35502:60:4:0.0101:0:1	0/0:30:0:0,0:22,8:30,0:0:2,0:33.4:1:37:0:1:0:59:60:1:0:0
    1390. 

  1390. 3	185790160	185790160	-	A	intronic	ETV5	.	.	.	0.28	0.1825	0.2976	0.1035	0.1573	0.0472	0.1477	0.1396	0.1356	rs531761453	rs11418453	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	217	108	3	185790160	.	C	CA	217	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=Insertion;DP=108;VD=60;AF=0.5556;SHIFT3=11;MSI=12;MSILEN=1;SSF=0;SOR=20.9245;LSEQ=GACAGAGTGAGACTCTATCT;RSEQ=AAAAAAAAAAAGAAAAAAAA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-6300dup|||||||rs11418453||-1||EntrezGene||YES||||3:g.185790171dup||||||||||0.2829|AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:108:60:39,21:14,6:20,60:0.5556:2,2:37.5:1:36.9:1:0.78865:1.2529:60.8:120:0.566:0.0093:0.6	0/1:108:6:5,1:30,14:44,6:0.0556:2,2:40.4:1:37.3:1:0.65402:2.3:64:12:0.0638:0:0.4
    1391. 

  1391. 3	185790172	185790174	GAA	AAG	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	50	137	3	185790172	.	GAA	AAG	50	p8	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Complex;DP=141;VD=3;AF=0.0213;SHIFT3=0;MSI=8;MSILEN=1;SSF=0.1291;SOR=inf;LSEQ=CTCTATCTCAAAAAAAAAAA;RSEQ=AAAAAAGATATGCAAATAAA;CSQ=AAG|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.651-6313_651-6311delinsCTT|||||||||-1||EntrezGene||YES||||3:g.185790172_185790174delinsAAG||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:141:3:3,0:79,58:137,3:0.0213:2,0:5.3:1:31.8:1:0.2668:0:60:6:0.0246:0.0142:0.7	0/0:137:0:0,0:96,38:134,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1392. 

  1392. 3	185790752	185790752	C	T	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	81	3	185790752	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=162;VD=2;AF=0.0123;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.44353;SOR=inf;LSEQ=CCAACATGGTAATATCCCAC;RSEQ=TCTACTGAAAATACAAAAAT;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6854G>A|||||||||-1||EntrezGene||YES||||3:g.185790752C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:162:2:1,1:91,69:160,2:0.0123:2,2:26.5:1:31:1:1:1.31655:60:4:0.0125:0:1	0/0:81:0:0,0:37,44:81,0:0:2,0:34.7:1:36.5:1:1:0:60:80:1:0:0.2
    1393. 

  1393. 3	185790813	185790813	A	C	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	83	3	185790813	.	A	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=178;VD=2;AF=0.0112;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.46428;SOR=inf;LSEQ=CTCCTGTAATCTTAGCTACT;RSEQ=GGGAGGCTAAGGCAGGAGAA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6793T>G|||||||||-1||EntrezGene||YES||||3:g.185790813A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:178:2:1,1:88,88:176,2:0.0112:2,2:8:0:37:0:1:1:60:4:0.0115:0:3	0/0:83:0:0,0:40,43:83,0:0:2,0:38.7:1:34:1:1:0:60:19.75:1:0:0.8
    1394. 

  1394. 3	185790829	185790829	G	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	82	3	185790829	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=169;VD=2;AF=0.0118;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.45246;SOR=inf;LSEQ=TACTAGGGAGGCTAAGGCAG;RSEQ=AGAATCGTTTGAACTCGGGA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6777C>T|||||||||-1||EntrezGene||YES||||3:g.185790829G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:169:2:1,1:82,85:167,2:0.0118:2,2:42:1:37:0:1:1.04:60:4:0.0119:0:1.5	0/0:82:0:0,0:43,39:82,0:0:2,0:38.4:1:35.8:1:1:0:60:40:1:0:1
    1395. 

  1395. 3	185790845	185790845	C	T	intronic	ETV5	.	.	.	0.54	0.0737	0.0340	0.2273	0.0298	0.5506	0.0872	0.0340	0.0806	rs9942039	rs9942039	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	223	75	3	185790845	.	C	T	223	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=169;VD=72;AF=0.426;SHIFT3=5;MSI=3;MSILEN=1;SSF=0.0146;SOR=0.52437;LSEQ=GCAGGAGAATCGTTTGAACT;RSEQ=GGGAGGGGGAGGTTTTAGTA;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6761G>A|||||||rs9942039||-1||EntrezGene||YES||||3:g.185790845C>T||||||||||0.5377|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:169:72:30,42:47,50:97,72:0.426:2,2:38:1:36.2:1:0.43589:1.31385:60:144:0.426:0:1.8	1/0:75:44:27,17:15,15:30,44:0.5867:2,2:39.9:1:33:1:0.35099:1.58:60:10:0.5714:0:1.9
    1396. 

  1396. 3	185790895	185790895	T	C	intronic	ETV5	.	.	.	0.62	0.2821	0.4188	0.3640	0.2053	0.6244	0.1998	0.1852	0.2312	rs7622914	rs7622914	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	257	83	3	185790895	.	T	C	257	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=141;VD=141;AF=1;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=TGCACCACTGCACTCCAGCC;RSEQ=GTGCGATGGAGTGAGACTCC;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6711A>G|||||||rs7622914||-1||EntrezGene||YES||||3:g.185790895T>C||||||||||0.6181|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:141:141:56,85:0,0:0,141:1:0,2:38.4:1:36.1:1:1:0:60:69.5:1:0:1.5	1/0:83:48:24,24:19,16:35,48:0.5783:2,2:33.8:1:34.9:1:0.8245:1.18504:60:23:0.5679:0:1.9
    1397. 

  1397. 3	185790922	185790922	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	89	3	185790922	.	A	G	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=109;VD=2;AF=0.0183;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.3018;SOR=inf;LSEQ=TGGAGTGAGACTCCGTCTCA;RSEQ=AACAAAACAAAACAAAACAA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6684T>C|||||||||-1||EntrezGene||YES||||3:g.185790922A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:109:2:1,1:40,67:107,2:0.0183:2,2:5:0:37:0:1:1.67:60:4:0.0183:0:1	0/0:89:0:0,0:48,41:89,0:0:2,0:34.8:1:36.3:1:1:0:60:88:1:0:0.9
    1398. 

  1398. 3	185790935	185790935	-	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	105	3	185790935	.	C	CA	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=107;VD=2;AF=0.0187;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.25355;SOR=inf;LSEQ=CGTCTCAAAACAAAACAAAA;RSEQ=AAAACAAAAAATATTAGTGT;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6670dup|||||||||-1||EntrezGene||YES||||3:g.185790939dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:107:2:1,1:35,69:104,2:0.0187:2,2:19.4:0:37.7:0:1:1.96:61.2:4:0.0192:0:1	0/0:105:0:0,0:59,46:105,0:0:2,0:33.3:1:35.7:1:1:0:60:34:1:0:0.7
    1399. 

  1399. 3	185791112	185791112	C	T	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	141	3	185791112	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=65;VD=2;AF=0.0308;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.09851;SOR=inf;LSEQ=TTTTCAAAAAGTAAAATTGT;RSEQ=ATAGAAGCTAACATTTACTG;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6494G>A|||||||||-1||EntrezGene||YES||||3:g.185791112C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:65:2:1,1:44,19:63,2:0.0308:2,2:12.5:1:37:0:0.52404:2.28269:60:4:0.0317:0:1	0/0:141:0:0,0:93,48:141,0:0:2,0:36:1:35.7:1:1:0:60:27.2:1:0:0.2
    1400. 

  1400. 3	185791347	185791348	CT	-	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	282	3	185791346	.	ACT	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=139;VD=2;AF=0.0144;SHIFT3=4;MSI=3;MSILEN=2;SSF=0.10848;SOR=inf;LSEQ=TTCTACAATCATTTAAAAAT;RSEQ=CTCTGGATGAGAGATAATAA;CSQ=-|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+6258_650+6259del|||||||||-1||EntrezGene||YES||||3:g.185791351_185791352del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:139:2:1,1:43,94:137,2:0.0144:2,2:11.5:1:37:1:0.53446:2.17:60:4:0.0147:0.0072:0	0/0:282:0:0,0:120,162:282,0:0:2,0:37.6:1:36.3:1:1:0:60:93:1:0:0.1
    1401. 

  1401. 3	185791646	185791646	C	T	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	404	3	185791646	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=2;AF=0.0144;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.06518;SOR=inf;LSEQ=ACCATAAGTGACCTGGCAAA;RSEQ=TTCCATGTACAGTCACCCCA;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+5960G>A|||||||||-1||EntrezGene||YES||||3:g.185791646C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:139:2:1,1:59,78:137,2:0.0144:2,2:39.5:1:37:0:1:1.32:60:4:0.0144:0:1	0/0:404:0:0,0:179,225:404,0:0:2,0:38.7:1:36.5:1:1:0:60:100:1:0:0.1
    1402. 

  1402. 3	185791866	185791866	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	157	3	185791866	.	A	G	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.98734;SOR=0;LSEQ=ATAAGTAAGGCCAAAAGTAG;RSEQ=TTTGTTGAAGACAATATTGT;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+5740T>C|||||||||-1||EntrezGene||YES||||3:g.185791866A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:25:0:1:0:60:2:1:0:0	0/1:157:2:1,1:71,83:154,2:0.0127:2,2:31:1:37:0:1:1.17:60:4:0.0131:0:1
    1403. 

  1403. 3	185792384	185792384	C	G	intronic	ETV5	.	.	.	0.56	0.1472	0.2218	0.2947	0.0894	0.5675	0.1113	0.0613	0.1178	rs77579672	rs77579672	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV60507073;OCCURENCE=1(liver)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	185	74	3	185792384	.	C	G	185	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=1;AF=0.5;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.69789;SOR=0.8072;LSEQ=TATTAGAAAACCCAAACTCA;RSEQ=CAATGTACAAAATATAATAC;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+5222G>C|||||||rs77579672&COSV60507073||-1||EntrezGene||YES||||3:g.185792384C>G||||||||||0.5565|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:2:1:1,0:1,0:1,1:0.5:0,0:64:0:37:0:1:0:60:2:0.5:0:1	1/0:74:41:9,32:8,25:33,41:0.5541:2,2:33.4:1:34.6:1:1:1.13578:60:19.5:0.5417:0:1
    1404. 

  1404. 3	185792926	185792926	C	G	intronic	ETV5	.	.	.	0.54	0.0733	0.0339	0.2273	0.0298	0.5479	0.0873	0.0339	0.0798	rs76078136	rs76078136	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	242	241	3	185792926	.	C	G	242	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=34;VD=15;AF=0.4412;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.2838;SOR=0.75815;LSEQ=ATGAAATGCTAAAAACAAAC;RSEQ=CTCTTAAGACTCAGAACTAA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+4680G>C|||||||rs76078136||-1||EntrezGene||YES||||3:g.185792926C>G||||||||||0.5377|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:34:15:12,3:14,4:18,15:0.4412:2,2:25.2:1:35.3:1:1:1.14:60:14:0.4242:0:1	1/0:241:123:73,50:63,54:117,123:0.5104:2,2:36.9:1:35:1:0.43501:1.25:60:19.5:0.5065:0:1.1
    1405. 

  1405. 3	185792986	185792986	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	334	3	185792986	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=2;AF=0.0244;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.03847;SOR=inf;LSEQ=CCATTACAAGAACATCATTC;RSEQ=GTCTGTCAAAGAAGGATCCA;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+4620T>C|||||||||-1||EntrezGene||YES||||3:g.185792986A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:82:2:1,1:48,32:80,2:0.0244:2,2:67:1:37:0:1:1.49237:60:4:0.025:0:1	0/0:334:0:0,0:198,136:334,0:0:2,0:34.7:1:36.8:1:1:0:60:668:1:0:0.4
    1406. 

  1406. 3	185793626	185793626	T	C	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	345	3	185793626	.	T	C	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=83;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.42075;SOR=0;LSEQ=GTTTTAACCTCTTTGGTTGA;RSEQ=GTCAAGTAAGTGAGAAAGCA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+3980A>G|||||||||-1||EntrezGene||YES||||3:g.185793626T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:83:0:0,0:25,58:83,0:0:2,0:28.7:1:36.3:1:1:0:60:82:1:0:0.1	0/1:345:4:2,2:135,206:341,4:0.0116:2,2:44.5:1:37:0:0.65087:1.52:60:8:0.0117:0:1
    1407. 

  1407. 3	185793888	185793888	T	C	intronic	ETV5	.	.	.	0.54	0.0732	0.0338	0.2249	0.0298	0.5498	0.0869	0.0338	0.0815	rs60978794	rs60978794	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	251	258	3	185793888	.	T	C	251	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=19;VD=11;AF=0.5789;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.31194;SOR=1.41652;LSEQ=GGAAAAAACATTTTTTCAGC;RSEQ=GGTCTTTCAGGATAAGTGGC;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+3718A>G|||||||rs60978794||-1||EntrezGene||YES||||3:g.185793888T>C||||||||||0.5377|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:19:11:5,6:3,5:8,11:0.5789:2,2:52.5:1:33.5:1:1:1.37:60:10:0.5556:0:1.2	0/1:258:127:56,71:61,69:130,127:0.4922:2,2:36.5:1:36:1:0.70744:1.12036:60:30.75:0.49:0:1.1
    1408. 

  1408. 3	185794183	185794183	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	139	3	185794183	.	C	A	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=209;VD=0;AF=0;SHIFT3=3;MSI=1;MSILEN=1;SSF=0.15885;SOR=0;LSEQ=ACCTGCTCTGTTTCTGACCC;RSEQ=TGGGCCAGCTCACCTCTGCT;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+3423G>T|||||||||-1||EntrezGene||YES||||3:g.185794183C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:209:0:0,0:120,89:209,0:0:2,0:41.1:1:36.2:1:1:0:60:51.25:1:0:0.1	0/1:139:2:1,1:57,80:137,2:0.0144:2,2:32:1:31:1:1:1.4:60:4:0.0147:0:1
    1409. 

  1409. 3	185794412	185794412	G	C	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	184	3	185794412	.	G	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=70;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.52398;SOR=0;LSEQ=TTTGACTAGATTACATTTTA;RSEQ=CTATTTACGGTATAATTTTA;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+3194C>G|||||||||-1||EntrezGene||YES||||3:g.185794412G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:70:0:0,0:24,46:70,0:0:2,0:31.4:1:35.2:1:1:0:60:34:1:0:0.2	0/1:184:2:1,1:108,74:182,2:0.0109:2,2:34.5:1:37:0:1:1.45636:60:4:0.011:0:1
    1410. 

  1410. 3	185794846	185794846	T	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	373	3	185794846	.	T	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=102;VD=2;AF=0.0196;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04576;SOR=inf;LSEQ=GGTTGCTGAATGTAGGACCC;RSEQ=GTATTTGGCTATGTGAGCTT;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+2760A>T|||||||||-1||EntrezGene||YES||||3:g.185794846T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:102:2:1,1:55,45:100,2:0.0196:2,2:19:0:37:0:1:1.2198:60:4:0.0233:0:1	0/0:373:0:0,0:177,196:373,0:0:2,0:37:1:32.5:1:1:0:60:7.289:1:0:0.3
    1411. 

  1411. 3	185794946	185794946	G	T	intronic	ETV5	.	.	.	0.56	0.1469	0.2218	0.2936	0.0894	0.5682	0.1108	0.0615	0.1163	rs6777779	rs6777779	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	227	212	3	185794946	.	G	T	227	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=50;VD=26;AF=0.52;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.26134;SOR=1.28312;LSEQ=CTCTGCCTATGTCACAGGGC;RSEQ=GTTAAAAGTTTCAAATGAGA;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+2660C>A|||||||rs6777779||-1||EntrezGene||YES||||3:g.185794946G>T||||||||||0.5565|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:50:26:9,17:4,19:23,26:0.52:2,2:41:1:36:1:0.20918:2.47:60:25:0.5319:0:2.2	0/1:212:97:34,63:49,66:115,97:0.4575:2,2:34.9:1:34.5:1:0.32291:1.37358:60:18.4:0.4577:0:1.8
    1412. 

  1412. 3	185794966	185794966	A	G	intronic	ETV5	.	.	.	0.54	0.0735	0.0337	0.2267	0.0298	0.5541	0.0868	0.0338	0.0815	rs76124850	rs76124850	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	224	185	3	185794966	.	A	G	224	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=20;AF=0.5714;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.04574;SOR=1.99357;LSEQ=GGTTAAAAGTTTCAAATGAG;RSEQ=CTCTCTTTACTTCTATCATG;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+2640T>C|||||||rs76124850||-1||EntrezGene||YES||||3:g.185794966A>G||||||||||0.5367|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:35:20:6,14:2,12:14,20:0.5714:2,2:34:1:33.2:1:0.42205:2.5:60:9:0.5625:0:2.4	0/1:185:74:21,53:46,65:111,74:0.4:2,2:34.6:1:36.2:1:0.08611:1.7805:60:73:0.3967:0:2
    1413. 

  1413. 3	185795199	185795199	A	G	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	170	3	185795199	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=11;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.88183;SOR=0;LSEQ=ACTTTTACAAATATCAAACC;RSEQ=GGGATTTTGGTCTGTCTCAT;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+2407T>C|||||||||-1||EntrezGene||YES||||3:g.185795199A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:11:0:0,0:6,5:11,0:0:2,0:36.3:1:35.9:1:1:0:60:22:1:0:0.2	0/1:170:2:1,1:106,62:168,2:0.0118:2,2:26.5:1:37:0:1:1.70396:60:4:0.0119:0:1
    1414. 

  1414. 3	185795333	185795333	T	C	intronic	ETV5	.	.	.	0.62	0.3050	0.4987	0.3660	0.2053	0.6259	0.2005	0.1853	0.2367	rs4686728	rs4686728	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	269	364	3	185795333	.	T	C	269	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=105;VD=105;AF=1;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=ATAGACAAAGGCAGTAGGAA;RSEQ=AGAATTTGGTAATACATGCT;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+2273A>G|||||||rs4686728||-1||EntrezGene||YES||||3:g.185795333T>C||||||||||0.6181|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:105:105:79,26:0,0:0,105:1:0,2:33.2:1:36.5:1:1:0:60:104:1:0:1.1	0/1:364:172:101,71:116,75:191,172:0.4725:2,2:37.4:1:36.3:1:0.74801:1.08701:60:171:0.4737:0:1.1
    1415. 

  1415. 3	185795855	185795855	A	C	intronic	ETV5	.	.	.	0.62	0.2708	0.3771	0.3578	0.2053	0.6255	0.2006	0.1859	0.2334	rs12638263	rs12638263	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	354	405	3	185795855	.	A	C	354	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=881;VD=881;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=ATCAATCCCAGGAATCCAAA;RSEQ=CTCCTTCCTTCTCAGGGGGC;CSQ=C|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+1751T>G|||||||rs12638263||-1||EntrezGene||YES||||3:g.185795855A>C||||||||||0.6181|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:881:881:356,525:0,0:0,881:1:0,2:39.8:1:36.2:1:1:0:60:66.769:1:0:1.1	0/1:405:186:89,97:107,112:219,186:0.4593:2,2:38.4:1:36.6:1:0.84261:1.04115:60:185:0.466:0:1
    1416. 

  1416. 3	185796139	185796139	A	G	intronic	ETV5	.	.	.	0.56	0.1700	0.3032	0.2916	0.0894	0.5675	0.1109	0.0616	0.1224	rs60445894	rs60445894	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	265	338	3	185796139	.	A	G	265	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=176;VD=98;AF=0.5568;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.06523;SOR=1.3481;LSEQ=GACCCCACACTTCCTCCCCA;RSEQ=TTTCCCCATAACCCTTGCAG;CSQ=G|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+1467T>C|||||||rs60445894||-1||EntrezGene||YES||||3:g.185796139A>G||||||||||0.5565|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:176:98:71,27:53,25:78,98:0.5568:2,2:30.2:1:36.1:1:0.61812:1.24:60:48:0.5549:0:1.1	0/1:338:163:90,73:101,74:175,163:0.4822:2,2:34.4:1:36.1:1:0.66177:1.10672:60:162:0.4939:0:1
    1417. 

  1417. 3	185796323	185796323	A	-	intronic	ETV5	.	.	.	.	0.0003	0.0007	0	0	0	0.0008	0	0	rs900913728	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	132	320	3	185796322	.	TA	T	132	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=200;VD=12;AF=0.06;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.02342;SOR=2.84811;LSEQ=ATTTGAATTAGTTGCCAACT;RSEQ=AAAAAAAAAGTCTACAATTT;CSQ=-|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+1283del|||||||rs539512780||-1||EntrezGene||YES||||3:g.185796332del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:12:8,4:98,90:188,12:0.06:2,2:27.8:1:36.9:1:0.38373:1.83:60:24:0.0603:0.025:0.2	0/1:320:7:6,1:151,162:313,7:0.0219:2,2:31.4:1:36.7:1:0.06296:6.41:60:14:0.0219:0.0063:0.7
    1418. 

  1418. 3	185796347	185796347	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	49	325	3	185796347	.	C	A	49	Bias	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=254;VD=3;AF=0.0118;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02148;SOR=0.26602;LSEQ=AAAAAAGTCTACAATTTTTA;RSEQ=ATAAAAAACCAAGTAACCAA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+1259G>T|||||||||-1||EntrezGene||YES||||3:g.185796347C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:254:3:3,0:152,99:251,3:0.0118:2,0:17:1:33:1:0.28364:0:60:6:0.0128:0:2.3	0/1:325:14:14,0:155,156:311,14:0.0431:2,1:29.6:1:13:1:0.00011:0:60:0.167:0.0072:0:4.9
    1419. 

  1419. 3	185796765	185796765	C	T	intronic	ETV5	.	.	.	0.59	0.0752	0.0341	0.2225	0.0298	0.6025	0.0857	0.0328	0.0825	rs7430047	rs7430047	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	335	412	3	185796765	.	C	T	335	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=617;VD=615;AF=0.9968;SHIFT3=0;MSI=4;MSILEN=1;SSF=0;SOR=317.55;LSEQ=TATATTCTTCCCACTCCCGC;RSEQ=CCATTGTGGCCCCCACACCG;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+841G>A|||||||rs7430047||-1||EntrezGene||YES||||3:g.185796765C>T||||||||||0.5853|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:617:615:280,335:0,0:0,615:0.9968:0,2:36:1:36.2:1:1:0:60:86.857:0.9984:0:1.6	0/1:412:202:115,87:111,99:210,202:0.4903:2,2:35.7:1:35.7:1:0.42916:1.18:60:49.5:0.4853:0:1.3
    1420. 

  1420. 3	185796785	185796785	G	A	intronic	ETV5	.	.	.	0.11	0.0768	0.0682	0.0420	0.0927	0.0799	0.0800	0.0819	0.0825	rs4077189	rs4077189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	285	404	3	185796785	.	G	A	285	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=593;VD=264;AF=0.4452;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=CCCATTGTGGCCCCCACACC;RSEQ=ATCCACCTAACACAAGATAG;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||7/12|NM_004454.3:c.650+821C>T|||||||rs4077189||-1||EntrezGene||YES||||3:g.185796785G>A||||||||||0.1103|EUR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:593:264:125,139:148,180:328,264:0.4452:2,2:33.7:1:35.5:1:0.61908:1.09:60:36.714:0.4408:0:2.1	0/0:404:0:0,0:213,191:404,0:0:2,0:36.4:1:36.1:1:1:0:60:39.4:1:0:0.8
    1421. 

  1421. 3	185797958	185797958	C	A	intronic	ETV5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	54	3	185797958	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=195;VD=2;AF=0.0103;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.61261;SOR=inf;LSEQ=CATTAGCATGGTTACCAGGT;RSEQ=CAGCAGAAAGCTAGTTTGCA;CSQ=A|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||6/12|NM_004454.3:c.363-65G>T|||||||||-1||EntrezGene||YES||||3:g.185797958C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:195:2:1,1:63,130:193,2:0.0103:2,2:62.5:1:37:0:0.54983:2.06:60:4:0.0103:0:1	0/0:54:0:0,0:14,40:54,0:0:2,0:38.7:1:35.9:1:1:0:60:108:1:0:0.2
    1422. 

  1422. 3	185798025	185798025	C	T	intronic	ETV5	.	.	.	0.14	0.1185	0.1375	0.0668	0.0927	0.0655	0.0904	0.1234	0.1135	rs77805826	rs77805826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	169	18	3	185798025	.	C	T	169	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=26;AF=0.5532;SHIFT3=0;MSI=1;MSILEN=1;SSF=1e-05;SOR=inf;LSEQ=ATTAACATAGTTAAATCGCT;RSEQ=GTAGCCCCGAGGGGATATTT;CSQ=T|intron_variant|MODIFIER|ETV5|2119|Transcript|NM_004454.3|protein_coding||6/12|NM_004454.3:c.363-132G>A|||||||rs77805826||-1||EntrezGene||YES||||3:g.185798025C>T||||||||||0.1382|EUR|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:47:26:1,25:0,21:21,26:0.5532:1,1:43.2:1:36:1:1:0:60:25:0.5435:0:1.1	0/0:18:0:0,0:1,17:18,0:0:1,0:26.8:1:37:0:1:0:60:36:1:0:0.2
    1423. 

  1423. 3	187442700	187442700	C	A	ncRNA_intronic	LOC100131635	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	208	3	187442700	.	C	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2376;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00051;SOR=0;LSEQ=CCCTCCACATCCCCGCAGGT;RSEQ=AGAGAGCGGCCTCAAGAGGC;CSQ=A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001130845.2|protein_coding||9/9|NM_001130845.2:c.1977+29G>T|||||||||-1||EntrezGene||YES||||3:g.187442700C>A||||||||||||||,A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001134738.1|protein_coding||7/7|NM_001134738.1:c.1809+29G>T|||||||||-1||EntrezGene||||||3:g.187442700C>A||||||||||||||,A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001706.5|protein_coding||9/9|NM_001706.5:c.1977+29G>T|||||||||-1||EntrezGene||||||3:g.187442700C>A||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-7459C>A|||||||||1||EntrezGene||YES||||3:g.187442700C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2376:0:0,0:1535,841:2376,0:0:2,0:35.1:1:36.7:1:1:0:60:138.765:1:0:0.1	0/1:208:3:1,2:144,61:205,3:0.0144:2,2:44.7:1:37:0:0.21843:4.68151:60:6:0.0146:0:1.3
    1424. 

  1424. 3	187443259	187443259	G	A	ncRNA_intronic	LOC100131635	.	.	.	0.0007	9.842e-05	0.0001	0	0	0.0006	0	6.741e-05	0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU68659415	PBCA-DE|1|499|0.00200401	0.25	85	74	3	187443259	.	G	A	85	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1294;VD=5;AF=0.0039;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0508;SOR=0.14014;LSEQ=CCCGCTCCGCTCGCCTGCCC;RSEQ=CTCCGCTCGCCTGCCCACTC;CSQ=A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001130845.2|protein_coding||8/9|NM_001130845.2:c.1839+28C>T|||||||rs1308092010||-1||EntrezGene||YES||||3:g.187443259G>A|5.23e-05|0|0|0|5.482e-05|0|1.779e-05|0|0.0003287|0.0003287|gnomAD_SAS|||,A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001134738.1|protein_coding||6/7|NM_001134738.1:c.1671+28C>T|||||||rs1308092010||-1||EntrezGene||||||3:g.187443259G>A|5.23e-05|0|0|0|5.482e-05|0|1.779e-05|0|0.0003287|0.0003287|gnomAD_SAS|||,A|intron_variant|MODIFIER|BCL6|604|Transcript|NM_001706.5|protein_coding||8/9|NM_001706.5:c.1839+28C>T|||||||rs1308092010||-1||EntrezGene||||||3:g.187443259G>A|5.23e-05|0|0|0|5.482e-05|0|1.779e-05|0|0.0003287|0.0003287|gnomAD_SAS|||,A|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-6900G>A|||||||rs1308092010||1||EntrezGene||YES||||3:g.187443259G>A|5.23e-05|0|0|0|5.482e-05|0|1.779e-05|0|0.0003287|0.0003287|gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1294:5:3,2:834,453:1287,5:0.0039:2,2:29.8:1:37:0:1:1.22715:60:10:0.004:0:2.6	0/1:74:2:1,1:53,19:72,2:0.027:2,2:26:1:37:0:0.4702:2.74437:60:4:0.0278:0:1
    1425. 

  1425. 3	187443314	187443314	G	A	exonic	BCL6	.	synonymous SNV	BCL6:NM_001134738:exon6:c.C1644T:p.C548C,BCL6:NM_001130845:exon8:c.C1812T:p.C604C,BCL6:NM_001706:exon8:c.C1812T:p.C604C	0.098	0.0825	0.0627	0.0334	0.0397	0.1091	0.0834	0.0952	0.0713	rs61732778	rs61732778	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51652282;OCCURENCE=1(large_intestine)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU133766	ESAD-UK|1|409|0.00244499,LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526	0.25	363	133	3	187443314	.	G	A	363	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=2247;VD=1091;AF=0.4855;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=AATCTGGCTCCGCAGGTTTC;RSEQ=CATTTGTAGGGCTTCTCTCC;CSQ=A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001130845.2|protein_coding|8/10||NM_001130845.2:c.1812C>T|NP_001124317.1:p.Cys604%3D|2273|1812|604|C|tgC/tgT|rs61732778&COSV51650391&COSV51652282||-1||EntrezGene||YES||||3:g.187443314G>A|0.0677|0.06262|0.0312|0.04368|0.1043|0.08303|0.07592|0.06254|0.05719|0.1043|gnomAD_EAS||0&1&1|1&1&1,A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001134738.1|protein_coding|6/8||NM_001134738.1:c.1644C>T|NP_001128210.1:p.Cys548%3D|1693|1644|548|C|tgC/tgT|rs61732778&COSV51650391&COSV51652282||-1||EntrezGene||||||3:g.187443314G>A|0.0677|0.06262|0.0312|0.04368|0.1043|0.08303|0.07592|0.06254|0.05719|0.1043|gnomAD_EAS||0&1&1|1&1&1,A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001706.5|protein_coding|8/10||NM_001706.5:c.1812C>T|NP_001697.2:p.Cys604%3D|1920|1812|604|C|tgC/tgT|rs61732778&COSV51650391&COSV51652282||-1||EntrezGene||||||3:g.187443314G>A|0.0677|0.06262|0.0312|0.04368|0.1043|0.08303|0.07592|0.06254|0.05719|0.1043|gnomAD_EAS||0&1&1|1&1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-6845G>A|||||||rs61732778&COSV51650391&COSV51652282||1||EntrezGene||YES||||3:g.187443314G>A|0.0677|0.06262|0.0312|0.04368|0.1043|0.08303|0.07592|0.06254|0.05719|0.1043|gnomAD_EAS||0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:2247:1091:577,514:616,529:1145,1091:0.4855:2,2:38.8:1:36:1:0.67173:1.03732:60:46.435:0.4877:0:1.1	0/0:133:0:0,0:79,54:133,0:0:2,0:33.8:1:35.7:1:1:0:60:43.333:1:0:0.2
    1426. 

  1426. 3	187443371	187443371	C	T	exonic	BCL6	.	synonymous SNV	BCL6:NM_001134738:exon6:c.G1587A:p.R529R,BCL6:NM_001130845:exon8:c.G1755A:p.R585R,BCL6:NM_001706:exon8:c.G1755A:p.R585R	0.	6.458e-05	0	0	0	0	0	0.0001	0	rs767829359	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99215301;OCCURENCE=1(biliary_tract)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	25	177	3	187443371	.	C	T	25	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2618;VD=1;AF=0.0004;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01147;SOR=0.03354;LSEQ=TGGGTTTTCAGGTTGGCTGG;RSEQ=CGGTTGAACTGGGCCCCACA;CSQ=T|synonymous_variant|LOW|BCL6|604|Transcript|NM_001130845.2|protein_coding|8/10||NM_001130845.2:c.1755G>A|NP_001124317.1:p.Arg585%3D|2216|1755|585|R|cgG/cgA|rs767829359&COSV99215301||-1||EntrezGene||YES||||3:g.187443371C>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1,T|synonymous_variant|LOW|BCL6|604|Transcript|NM_001134738.1|protein_coding|6/8||NM_001134738.1:c.1587G>A|NP_001128210.1:p.Arg529%3D|1636|1587|529|R|cgG/cgA|rs767829359&COSV99215301||-1||EntrezGene||||||3:g.187443371C>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1,T|synonymous_variant|LOW|BCL6|604|Transcript|NM_001706.5|protein_coding|8/10||NM_001706.5:c.1755G>A|NP_001697.2:p.Arg585%3D|1863|1755|585|R|cgG/cgA|rs767829359&COSV99215301||-1||EntrezGene||||||3:g.187443371C>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1,T|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-6788C>T|||||||rs767829359&COSV99215301||1||EntrezGene||YES||||3:g.187443371C>T|3.977e-06|0|0|0|0|0|8.791e-06|0|0|8.791e-06|gnomAD_NFE||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2618:1:1,0:1340,1274:2614,1:0.0004:2,0:48:0:37:0:1:0:60:2:0.0004:0:1	0/1:177:2:1,1:88,87:175,2:0.0113:2,2:34.5:1:25:0:1:1.01143:60:4:0.0116:0:1
    1427. 

  1427. 3	187443433	187443433	A	G	ncRNA_intronic	LOC100131635	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51652581;OCCURENCE=1(stomach)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU121237633	GACA-JP|1|585|0.0017094	0.25	101	187	3	187443433	.	A	G	101	f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2202;VD=8;AF=0.0036;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.1813;SOR=0.33752;LSEQ=CTCACCTATTACCAAGAAAA;RSEQ=GGGAAAAAGAAAAGCCATAT;CSQ=G|splice_polypyrimidine_tract_variant&intron_variant|LOW|BCL6|604|Transcript|NM_001130845.2|protein_coding||7/9|NM_001130845.2:c.1709-16T>C|||||||COSV51652581||-1||EntrezGene||YES||||3:g.187443433A>G|||||||||||||1|1,G|splice_polypyrimidine_tract_variant&intron_variant|LOW|BCL6|604|Transcript|NM_001134738.1|protein_coding||5/7|NM_001134738.1:c.1541-16T>C|||||||COSV51652581||-1||EntrezGene||||||3:g.187443433A>G|||||||||||||1|1,G|splice_polypyrimidine_tract_variant&intron_variant|LOW|BCL6|604|Transcript|NM_001706.5|protein_coding||7/9|NM_001706.5:c.1709-16T>C|||||||COSV51652581||-1||EntrezGene||||||3:g.187443433A>G|||||||||||||1|1,G|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-6726A>G|||||||COSV51652581||1||EntrezGene||YES||||3:g.187443433A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2202:8:4,4:1024,1169:2193,8:0.0036:2,2:42.4:1:33.8:1:1:1.14:60:7:0.0032:0:1.2	0/1:187:2:1,1:89,96:185,2:0.0107:2,2:34.5:1:37:0:1:1.08:60:4:0.0108:0:1
    1428. 

  1428. 3	187447032	187447032	G	A	exonic	BCL6	.	synonymous SNV	BCL6:NM_001134738:exon4:c.C1161T:p.N387N,BCL6:NM_001130845:exon5:c.C1161T:p.N387N,BCL6:NM_001706:exon5:c.C1161T:p.N387N	0.81	0.5310	0.1832	0.7482	0.7086	0.7937	0.6955	0.6432	0.6496	rs1056932	rs1056932	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV51649553;OCCURENCE=1(breast),1(large_intestine),18(soft_tissue)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU794210	COCA-CN|6|321|0.0186916	0.75	391	331	3	187447032	.	G	A	391	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4165;VD=1957;AF=0.4699;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTCTGGTTTGGCATTCTG;RSEQ=TTGAGGCTGTTGAGCACGAT;CSQ=A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001130845.2|protein_coding|5/10||NM_001130845.2:c.1161C>T|NP_001124317.1:p.Asn387%3D|1622|1161|387|N|aaC/aaT|rs1056932&COSV51649553||-1||EntrezGene||YES||||3:g.187447032G>A|0.6575|0.1692|0.7755|0.7017|0.7967|0.6939|0.6586|0.6756|0.6519|0.7967|gnomAD_EAS||0&1|1&1,A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001134738.1|protein_coding|4/8||NM_001134738.1:c.1161C>T|NP_001128210.1:p.Asn387%3D|1210|1161|387|N|aaC/aaT|rs1056932&COSV51649553||-1||EntrezGene||||||3:g.187447032G>A|0.6575|0.1692|0.7755|0.7017|0.7967|0.6939|0.6586|0.6756|0.6519|0.7967|gnomAD_EAS||0&1|1&1,A|synonymous_variant|LOW|BCL6|604|Transcript|NM_001706.5|protein_coding|5/10||NM_001706.5:c.1161C>T|NP_001697.2:p.Asn387%3D|1269|1161|387|N|aaC/aaT|rs1056932&COSV51649553||-1||EntrezGene||||||3:g.187447032G>A|0.6575|0.1692|0.7755|0.7017|0.7967|0.6939|0.6586|0.6756|0.6519|0.7967|gnomAD_EAS||0&1|1&1,A|intron_variant&non_coding_transcript_variant|MODIFIER|LOC100131635|100131635|Transcript|NR_034062.1|lncRNA||2/2|NR_034062.1:n.294-3127G>A|||||||rs1056932&COSV51649553||1||EntrezGene||YES||||3:g.187447032G>A|0.6575|0.1692|0.7755|0.7017|0.7967|0.6939|0.6586|0.6756|0.6519|0.7967|gnomAD_EAS||0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:4165:1957:1045,912:1180,1022:2202,1957:0.4699:2,2:37.4:1:35.8:1:0.92557:1.00765:60:43.477:0.466:0:1.1	1/1:331:331:179,152:0,0:0,331:1:0,2:36.7:1:36:1:1:0:60:46.286:1:0:1.1
    1429. 

  1429. 3	189590824	189590825	GG	CA	intronic	TP63	.	.	.	0.33	.	.	.	.	.	.	.	.	rs371757788	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	0	3	189590824	.	GG	CA	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=Complex;DP=2;VD=2;AF=1;SHIFT3=0;MSI=3;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTAGGAGGCATGAGTGA;RSEQ=GTGACTTTATTTGGATCAGC;CSQ=CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114978.2|protein_coding||10/12|NM_001114978.2:c.1349+40_1349+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114979.2|protein_coding||10/10|NM_001114979.2:c.1349+40_1349+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114980.2|protein_coding||8/11|NM_001114980.2:c.1067+40_1067+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114981.2|protein_coding||8/10|NM_001114981.2:c.1067+40_1067+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114982.2|protein_coding||8/8|NM_001114982.2:c.1067+40_1067+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329144.2|protein_coding||10/11|NM_001329144.2:c.1349+40_1349+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329145.2|protein_coding||8/9|NM_001329145.2:c.1067+40_1067+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329146.2|protein_coding||7/10|NM_001329146.2:c.812+40_812+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329148.2|protein_coding||10/13|NM_001329148.2:c.1337+40_1337+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329149.2|protein_coding||8/9|NM_001329149.2:c.1055+40_1055+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329150.2|protein_coding||7/8|NM_001329150.2:c.800+40_800+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329964.2|protein_coding||10/13|NM_001329964.2:c.1343+40_1343+41delinsCA|||||||rs371757788||1||EntrezGene||||||3:g.189590824_189590825delinsCA||||||||||||||,CA|intron_variant|MODIFIER|TP63|8626|Transcript|NM_003722.5|protein_coding||10/13|NM_003722.5:c.1349+40_1349+41delinsCA|||||||rs371757788||1||EntrezGene||YES||||3:g.189590824_189590825delinsCA||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:37:0:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1430. 

  1430. 3	189604149	189604149	T	G	intronic	TP63	.	.	.	0.79	0.7438	0.7563	0.5489	0.7152	0.5839	0.7131	0.7740	0.7179	rs1554131	rs1554131	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	251059	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15728052	COCA-CN|4|321|0.0124611	0.5	37	0	3	189604149	.	T	G	37	d5;v3;pSTD	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCACTCTTCAGTGTCCC;RSEQ=TGCTCACCATTATTTCCATG;CSQ=G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114978.2|protein_coding||10/12|NM_001114978.2:c.1350-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|downstream_gene_variant|MODIFIER|TP63|8626|Transcript|NM_001114979.2|protein_coding||||||||||rs1554131|4857|1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114980.2|protein_coding||8/11|NM_001114980.2:c.1068-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114981.2|protein_coding||8/10|NM_001114981.2:c.1068-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|downstream_gene_variant|MODIFIER|TP63|8626|Transcript|NM_001114982.2|protein_coding||||||||||rs1554131|4857|1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329144.2|protein_coding||10/11|NM_001329144.2:c.1350-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329145.2|protein_coding||8/9|NM_001329145.2:c.1068-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329146.2|protein_coding||7/10|NM_001329146.2:c.813-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329148.2|protein_coding||10/13|NM_001329148.2:c.1338-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329149.2|protein_coding||8/9|NM_001329149.2:c.1056-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329150.2|protein_coding||7/8|NM_001329150.2:c.801-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329964.2|protein_coding||10/13|NM_001329964.2:c.1344-34T>G|||||||rs1554131||1||EntrezGene||||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1,G|intron_variant|MODIFIER|TP63|8626|Transcript|NM_003722.5|protein_coding||10/13|NM_003722.5:c.1350-34T>G|||||||rs1554131||1||EntrezGene||YES||||3:g.189604149T>G|0.7103|0.7462|0.5008|0.6861|0.5954|0.6955|0.7891|0.7371|0.7177|0.7945|EA|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:37:0:1:0:60:4:1:0:2	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1431. 

  1431. 3	189604160	189604160	T	C	intronic	TP63	.	.	.	0.79	0.7439	0.7564	0.5489	0.7152	0.5844	0.7131	0.7741	0.7179	rs1345186	rs1345186	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53208052;OCCURENCE=1(lung)	251060	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU15728135	LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.5	31	0	3	189604160	.	T	C	31	d5;v3;pSTD	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTCCCTTGCTCACCAT;RSEQ=ATTTCCATGTTTGTCTTCCT;CSQ=C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114978.2|protein_coding||10/12|NM_001114978.2:c.1350-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|downstream_gene_variant|MODIFIER|TP63|8626|Transcript|NM_001114979.2|protein_coding||||||||||rs1345186&COSV53208052|4868|1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114980.2|protein_coding||8/11|NM_001114980.2:c.1068-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001114981.2|protein_coding||8/10|NM_001114981.2:c.1068-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|downstream_gene_variant|MODIFIER|TP63|8626|Transcript|NM_001114982.2|protein_coding||||||||||rs1345186&COSV53208052|4868|1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329144.2|protein_coding||10/11|NM_001329144.2:c.1350-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329145.2|protein_coding||8/9|NM_001329145.2:c.1068-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329146.2|protein_coding||7/10|NM_001329146.2:c.813-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329148.2|protein_coding||10/13|NM_001329148.2:c.1338-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329149.2|protein_coding||8/9|NM_001329149.2:c.1056-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329150.2|protein_coding||7/8|NM_001329150.2:c.801-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_001329964.2|protein_coding||10/13|NM_001329964.2:c.1344-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1,C|intron_variant|MODIFIER|TP63|8626|Transcript|NM_003722.5|protein_coding||10/13|NM_003722.5:c.1350-23T>C|||||||rs1345186&COSV53208052||1||EntrezGene||YES||||3:g.189604160T>C|0.7107|0.7463|0.5013|0.6862|0.5979|0.6956|0.7893|0.7373|0.7179|0.7945|EA|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:31:1:1:0:60:4:1:0:2	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1432. 

  1432. 3	192126757	192126757	G	T	UTR5	FGF12	NM_021032:c.-745C>A	.	.	0.28	0.2246	0.1244	0.2428	0.2848	0.1691	0.2646	0.2740	0.2732	rs3109189	rs3109189	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	37	0	3	192126757	.	G	T	37	d5;v3	STATUS=SampleSpecific;SAMPLE=LibM078FTT;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=2;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCGCGAAGTGGGAGCG;RSEQ=TTACCCGGAGTCTGGGTAGG;CSQ=T|intron_variant|MODIFIER|FGF12|2257|Transcript|NM_001377292.1|protein_coding||2/4|NM_001377292.1:c.14-73504C>A|||||||rs3109189||-1||EntrezGene||||||3:g.192126757G>T||||||||||0.281|AMR|||,T|intron_variant|MODIFIER|FGF12|2257|Transcript|NM_001377293.1|protein_coding||1/4|NM_001377293.1:c.-59-48430C>A|||||||rs3109189||-1||EntrezGene||||||3:g.192126757G>T||||||||||0.281|AMR|||,T|intron_variant|MODIFIER|FGF12|2257|Transcript|NM_001377294.1|protein_coding||1/4|NM_001377294.1:c.-60+544C>A|||||||rs3109189||-1||EntrezGene||||||3:g.192126757G>T||||||||||0.281|AMR|||,T|intron_variant|MODIFIER|FGF12|2257|Transcript|NM_004113.6|protein_coding||2/5|NM_004113.6:c.14-48430C>A|||||||rs3109189||-1||EntrezGene||||||3:g.192126757G>T||||||||||0.281|AMR|||,T|5_prime_UTR_variant|MODIFIER|FGF12|2257|Transcript|NM_021032.5|protein_coding|1/5||NM_021032.5:c.-745C>A||630|||||rs3109189||-1||EntrezGene||YES||||3:g.192126757G>T||||||||||0.281|AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2:2:1,1:0,0:0,2:1:0,2:49:1:37:0:1:0:60:4:1:0:1	0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1433. 

  1433. 4	1801114	1801114	G	T	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon3:c.G243T:p.L81L,FGFR3:NM_001163213:exon3:c.G243T:p.L81L,FGFR3:NM_022965:exon3:c.G243T:p.L81L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	176	4	1801114	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1133;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01799;SOR=0;LSEQ=GTCAAGGATGGCACAGGGCT;RSEQ=GTGCCCTCGGAGCGTGTCCT;CSQ=T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|3/18||NM_000142.5:c.243G>T|NP_000133.1:p.Leu81%3D|518|243|81|L|ctG/ctT|rs1161718944||1||EntrezGene||||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|3/18||NM_001163213.2:c.243G>T|NP_001156685.1:p.Leu81%3D|518|243|81|L|ctG/ctT|rs1161718944||1||EntrezGene||YES||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|3/18||NM_001354809.2:c.243G>T|NP_001341738.1:p.Leu81%3D|518|243|81|L|ctG/ctT|rs1161718944||1||EntrezGene||||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|3/17||NM_001354810.2:c.243G>T|NP_001341739.1:p.Leu81%3D|518|243|81|L|ctG/ctT|rs1161718944||1||EntrezGene||||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|3/16||NM_022965.4:c.243G>T|NP_075254.1:p.Leu81%3D|518|243|81|L|ctG/ctT|rs1161718944||1||EntrezGene||||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|3/19||NR_148971.2:n.518G>T||518|||||rs1161718944||1||EntrezGene||||||4:g.1801114G>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1133:0:0,0:601,532:1133,0:0:2,0:34.1:1:36.6:1:1:0:60:160.857:1:0:0.1	0/1:176:2:1,1:91,83:174,2:0.0114:2,2:60:1:37:0:1:1.09581:60:4:0.0114:0:1
    1434. 

  1434. 4	1801158	1801158	T	C	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_000142:exon3:c.T287C:p.V96A,FGFR3:NM_001163213:exon3:c.T287C:p.V96A,FGFR3:NM_022965:exon3:c.T287C:p.V96A	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	0.504	0.647	P	0.458	0.641	P	0.000	0.454	D	0.874	0.281	N	2.665	0.782	M	1.79	0.255	T	-2.54	0.582	D	0.438	0.493	-1.033	0.194	T	0.132	0.445	T	0.147	0.829	D	4.837	0.649	24.8	0.997	0.787	0.824	0.413	D	c	0.391	0.315	1.000	0.500	0.696	0.567	0	2.39	0.284	2.641	0.460	0.932	0.445	0.282	0.249	0.811	0.340	6.159	0.194	Immunoglobulin subtype|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	199	4	1801158	.	T	C	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1219;VD=1;AF=0.0008;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.05337;SOR=0.08112;LSEQ=GGGGCCCCAGCGGCTGCAGG;RSEQ=GCTGAATGCCTCCCACGAGG;CSQ=C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|3/18||NM_000142.5:c.287T>C|NP_000133.1:p.Val96Ala|562|287|96|V/A|gTg/gCg|COSV53398297||1||EntrezGene||||||4:g.1801158T>C|||||||||||||1|1,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|3/18||NM_001163213.2:c.287T>C|NP_001156685.1:p.Val96Ala|562|287|96|V/A|gTg/gCg|COSV53398297||1||EntrezGene||YES||||4:g.1801158T>C|||||||||||||1|1,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|3/18||NM_001354809.2:c.287T>C|NP_001341738.1:p.Val96Ala|562|287|96|V/A|gTg/gCg|COSV53398297||1||EntrezGene||||||4:g.1801158T>C|||||||||||||1|1,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|3/17||NM_001354810.2:c.287T>C|NP_001341739.1:p.Val96Ala|562|287|96|V/A|gTg/gCg|COSV53398297||1||EntrezGene||||||4:g.1801158T>C|||||||||||||1|1,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|3/16||NM_022965.4:c.287T>C|NP_075254.1:p.Val96Ala|562|287|96|V/A|gTg/gCg|COSV53398297||1||EntrezGene||||||4:g.1801158T>C|||||||||||||1|1,C|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|3/19||NR_148971.2:n.562T>C||562|||||COSV53398297||1||EntrezGene||||||4:g.1801158T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1219:1:0,1:614,604:1218,1:0.0008:2,0:23:0:37:0:0.49631:0:60:2:0.0008:0:1	0/1:199:2:1,1:95,102:197,2:0.0101:2,2:39:1:37:0:1:1.07:60:4:0.0101:0:1.5
    1435. 

  1435. 4	1801219	1801219	C	T	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon3:c.C348T:p.R116R,FGFR3:NM_001163213:exon3:c.C348T:p.R116R,FGFR3:NM_022965:exon3:c.C348T:p.R116R	0.06	0.0160	0.0416	0.0120	0.0265	0.0203	0.0003	0.0050	0.0051	rs2305179	rs2305179	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53408813;OCCURENCE=5(meninges),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),4(prostate),1(thymus)	193381	Craniosynostosis_syndrome|not_specified|none_provided	Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	1	1	MU82303496	LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526	0.5	273	190	4	1801219	.	C	T	273	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1427;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=CGGCAGCGGCTCACGCAGCG;RSEQ=GTACTGTGCCACTTCAGTGT;CSQ=T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|3/18||NM_000142.5:c.348C>T|NP_000133.1:p.Arg116%3D|623|348|116|R|cgC/cgT|rs2305179&COSV53408813||1||EntrezGene||||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|3/18||NM_001163213.2:c.348C>T|NP_001156685.1:p.Arg116%3D|623|348|116|R|cgC/cgT|rs2305179&COSV53408813||1||EntrezGene||YES||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|3/18||NM_001354809.2:c.348C>T|NP_001341738.1:p.Arg116%3D|623|348|116|R|cgC/cgT|rs2305179&COSV53408813||1||EntrezGene||||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|3/17||NM_001354810.2:c.348C>T|NP_001341739.1:p.Arg116%3D|623|348|116|R|cgC/cgT|rs2305179&COSV53408813||1||EntrezGene||||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|3/16||NM_022965.4:c.348C>T|NP_075254.1:p.Arg116%3D|623|348|116|R|cgC/cgT|rs2305179&COSV53408813||1||EntrezGene||||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|3/19||NR_148971.2:n.623C>T||623|||||rs2305179&COSV53408813||1||EntrezGene||||||4:g.1801219C>T|0.01204|0.04067|0.008546|0.02683|0.02287|0.0004486|0.006717|0.01335|0.01636|0.04067|gnomAD_AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1427:0:0,0:707,719:1426,0:0:2,0:37.1:1:36.5:1:1:0:60:128.636:1:0:0.1	1/1:190:189:90,99:0,0:0,189:0.9947:0,2:38.1:1:36.2:1:1:0:60:62:1:0:1.1
    1436. 

  1436. 4	1801233	1801233	T	C	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_000142:exon3:c.T362C:p.F121S,FGFR3:NM_001163213:exon3:c.T362C:p.F121S,FGFR3:NM_022965:exon3:c.T362C:p.F121S	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.985	0.715	D	0.956	0.722	D	0.000	0.629	D	0.996	0.428	D	2.315	0.665	M	-1.3	0.796	T	-4.38	0.783	D	0.494	0.549	-0.206	0.775	T	0.623	0.867	D	0.823	0.986	D	5.635	0.768	26.6	0.998	0.872	0.396	0.260	N	c	0.115	0.013	1.000	0.467	0.696	0.567	0	3.45	0.384	2.603	0.457	0.932	0.445	1.000	0.715	0.901	0.381	9.960	0.407	Immunoglobulin subtype|Immunoglobulin-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	192	4	1801233	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1387;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.01472;SOR=0;LSEQ=GCAGCGCGTACTGTGCCACT;RSEQ=CAGTGTGCGGGTGACAGGTG;CSQ=C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|3/18||NM_000142.5:c.362T>C|NP_000133.1:p.Phe121Ser|637|362|121|F/S|tTc/tCc|||1||EntrezGene||||||4:g.1801233T>C||||||||||||||,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|3/18||NM_001163213.2:c.362T>C|NP_001156685.1:p.Phe121Ser|637|362|121|F/S|tTc/tCc|||1||EntrezGene||YES||||4:g.1801233T>C||||||||||||||,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|3/18||NM_001354809.2:c.362T>C|NP_001341738.1:p.Phe121Ser|637|362|121|F/S|tTc/tCc|||1||EntrezGene||||||4:g.1801233T>C||||||||||||||,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|3/17||NM_001354810.2:c.362T>C|NP_001341739.1:p.Phe121Ser|637|362|121|F/S|tTc/tCc|||1||EntrezGene||||||4:g.1801233T>C||||||||||||||,C|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|3/16||NM_022965.4:c.362T>C|NP_075254.1:p.Phe121Ser|637|362|121|F/S|tTc/tCc|||1||EntrezGene||||||4:g.1801233T>C||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|3/19||NR_148971.2:n.637T>C||637|||||||1||EntrezGene||||||4:g.1801233T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1387:0:0,0:674,711:1385,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:192:2:1,1:99,91:190,2:0.0104:2,2:38.5:1:37:0:1:1.08742:60:4:0.0106:0:2
    1437. 

  1437. 4	1801542	1801542	A	G	intronic	FGFR3	.	.	.	0.34	0.0914	0.3061	0.0227	0.0364	0.0204	0.0003	0.0056	0.0122	rs3135868	rs3135868	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53409724;OCCURENCE=12(meninges),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),10(prostate),1(lung)	251373	Craniosynostosis_syndrome|not_specified	Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU82303506	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.5	308	345	4	1801542	.	A	G	308	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2731;VD=0;AF=0;SHIFT3=3;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACAGGTGTGGACACAGGT;RSEQ=GGAGCAGGGTCCAGGGTTCA;CSQ=G|splice_donor_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding||4/17|NM_000142.5:c.445+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1,G|splice_donor_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||4/17|NM_001163213.2:c.445+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||YES||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1,G|splice_donor_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||4/17|NM_001354809.2:c.445+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1,G|splice_donor_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||4/16|NM_001354810.2:c.445+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1,G|splice_donor_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding||4/15|NM_022965.4:c.445+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1,G|splice_donor_region_variant&intron_variant&non_coding_transcript_variant|LOW|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||4/18|NR_148971.2:n.720+3A>G|||||||rs3135868&COSV53409724||1||EntrezGene||||||4:g.1801542A>G|0.03097|0.3057|0.0204|0.02652|0.02263|0.0003731|0.00717|0.02242|0.01633|0.3351|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2731:0:0,0:1234,1495:2729,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:345:343:160,183:0,0:0,343:0.9942:0,2:37.8:1:36.6:1:1:0:60:170.5:0.9942:0:1.1
    1438. 

  1438. 4	1803236	1803236	C	T	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon5:c.C588T:p.R196R,FGFR3:NM_001163213:exon5:c.C588T:p.R196R,FGFR3:NM_022965:exon5:c.C588T:p.R196R	0.13	0.0280	0.0841	0.0131	0.0265	0.0203	0.0003	0.0052	0.0031	rs2305180	rs2305180	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53400105;OCCURENCE=5(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(prostate)	194791	Craniosynostosis_syndrome|not_specified|none_provided	Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	1	1	MU118543	LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526	0.5	265	157	4	1803236	.	C	T	265	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1712;VD=2;AF=0.0012;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGAACGGCAGGGAGTTCCG;RSEQ=GGCGAGCACCGCATTGGAGG;CSQ=T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|5/18||NM_000142.5:c.588C>T|NP_000133.1:p.Arg196%3D|863|588|196|R|cgC/cgT|rs2305180&COSV53400105||1||EntrezGene||||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|5/18||NM_001163213.2:c.588C>T|NP_001156685.1:p.Arg196%3D|863|588|196|R|cgC/cgT|rs2305180&COSV53400105||1||EntrezGene||YES||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|5/18||NM_001354809.2:c.588C>T|NP_001341738.1:p.Arg196%3D|863|588|196|R|cgC/cgT|rs2305180&COSV53400105||1||EntrezGene||||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|5/17||NM_001354810.2:c.588C>T|NP_001341739.1:p.Arg196%3D|863|588|196|R|cgC/cgT|rs2305180&COSV53400105||1||EntrezGene||||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|5/16||NM_022965.4:c.588C>T|NP_075254.1:p.Arg196%3D|863|588|196|R|cgC/cgT|rs2305180&COSV53400105||1||EntrezGene||||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|5/19||NR_148971.2:n.863C>T||863|||||rs2305180&COSV53400105||1||EntrezGene||||||4:g.1803236C>T|0.01453|0.08611|0.01007|0.02651|0.02163|0.0003827|0.006558|0.01492|0.01638|0.08611|gnomAD_AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1712:2:2,0:1115,593:1708,2:0.0012:2,0:33:1:37:0:0.54669:0:60:4:0.0012:0:1	1/1:157:156:107,49:0,0:0,156:0.9936:0,2:37.3:1:36.5:1:1:0:60:77:1:0:2.6
    1439. 

  1439. 4	1803251	1803251	T	C	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon5:c.T603C:p.I201I,FGFR3:NM_001163213:exon5:c.T603C:p.I201I,FGFR3:NM_022965:exon5:c.T603C:p.I201I	0.39	0.0905	0.3030	0.0215	0.0364	0.0210	0.0003	0.0057	0.0133	rs2305181	rs2305181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53400123;OCCURENCE=10(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),2(prostate)	194789	not_specified	MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	1	MU118562	LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526	0.5	273	180	4	1803251	.	T	C	273	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1906;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCCGCGGCGAGCACCGCAT;RSEQ=GGAGGCATCAAGGTGGGCGC;CSQ=C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|5/18||NM_000142.5:c.603T>C|NP_000133.1:p.Ile201%3D|878|603|201|I|atT/atC|rs2305181&COSV53400123||1||EntrezGene||||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|5/18||NM_001163213.2:c.603T>C|NP_001156685.1:p.Ile201%3D|878|603|201|I|atT/atC|rs2305181&COSV53400123||1||EntrezGene||YES||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|5/18||NM_001354809.2:c.603T>C|NP_001341738.1:p.Ile201%3D|878|603|201|I|atT/atC|rs2305181&COSV53400123||1||EntrezGene||||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|5/17||NM_001354810.2:c.603T>C|NP_001341739.1:p.Ile201%3D|878|603|201|I|atT/atC|rs2305181&COSV53400123||1||EntrezGene||||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|5/16||NM_022965.4:c.603T>C|NP_075254.1:p.Ile201%3D|878|603|201|I|atT/atC|rs2305181&COSV53400123||1||EntrezGene||||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1,C|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|5/19||NR_148971.2:n.878T>C||878|||||rs2305181&COSV53400123||1||EntrezGene||||||4:g.1803251T>C|0.02771|0.295|0.01987|0.02673|0.02214|0.0004238|0.0071|0.02409|0.01641|0.3359|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1906:0:0,0:1197,704:1901,0:0:0:0:0:0:0:1:0:0:0:0:0:0	1/1:180:179:111,68:0,0:0,179:0.9944:0,2:36.3:1:36.6:1:1:0:60:178:1:0:2.6
    1440. 

  1440. 4	1803307	1803307	T	C	intronic	FGFR3	.	.	.	0.46	0.2092	0.4042	0.1148	0.2219	0.0415	0.1390	0.1398	0.1418	rs2305183	rs2305183	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53402151;OCCURENCE=1(breast),1(haematopoietic_and_lymphoid_tissue),19(prostate),4(meninges),1(upper_aerodigestive_tract)	251374	not_specified|not_provided	MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU67949081	SKCA-BR|1|100|0.01,LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526,BRCA-KR|1|50|0.02	0.5	295	259	4	1803307	.	T	C	295	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2745;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCTGGCAGGCGCGGTGGT;RSEQ=GCTGCCTCCGCTCACTCACC;CSQ=C|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_000142.5|protein_coding||5/17|NM_000142.5:c.616-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1,C|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||5/17|NM_001163213.2:c.616-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||YES||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1,C|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||5/17|NM_001354809.2:c.616-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1,C|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||5/16|NM_001354810.2:c.616-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1,C|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||5/15|NM_022965.4:c.616-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1,C|intron_variant&non_coding_transcript_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||5/18|NR_148971.2:n.891-40T>C|||||||rs2305183&COSV53402151||1||EntrezGene||||||4:g.1803307T>C|0.1602|0.4026|0.1254|0.2171|0.04252|0.1329|0.1428|0.1654|0.2119|0.4334|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2745:0:0,0:1496,1249:2745,0:0:2,0:38.5:1:36.4:1:1:0:60:108.8:1:0:0.1	1/1:259:259:129,130:0,0:0,259:1:0,2:36.2:1:36.9:1:1:0:60:518:1:0:2
    1441. 

  1441. 4	1803576	1803576	C	T	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_000142:exon7:c.C754T:p.R252W,FGFR3:NM_001163213:exon7:c.C754T:p.R252W,FGFR3:NM_022965:exon7:c.C754T:p.R252W	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.891	0.916	P	0.000	0.537	D	1	0.810	D	3.71	0.948	H	-1.56	0.818	D	-6.91	0.962	D	0.798	0.868	0.280	0.872	D	0.795	0.930	D	0.785	0.983	D	7.302	0.948	34	0.999	0.975	0.880	0.475	D	c	0.613	0.468	1.000	0.747	0.696	0.567	0	3.94	0.446	3.805	0.550	0.721	0.304	1.000	0.715	0.988	0.529	16.288	0.825	Immunoglobulin-like domain	.	.	ID=COSV53406990;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	4	1803576	.	C	T	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1901;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00663;SOR=0;LSEQ=CCACAGAGCGCTCCCCGCAC;RSEQ=GGCCCATCCTGCAGGCGGGG;CSQ=T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|7/18||NM_000142.5:c.754C>T|NP_000133.1:p.Arg252Trp|1029|754|252|R/W|Cgg/Tgg|COSV53406990||1||EntrezGene||||||4:g.1803576C>T|||||||||||||1|1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|7/18||NM_001163213.2:c.754C>T|NP_001156685.1:p.Arg252Trp|1029|754|252|R/W|Cgg/Tgg|COSV53406990||1||EntrezGene||YES||||4:g.1803576C>T|||||||||||||1|1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|7/18||NM_001354809.2:c.754C>T|NP_001341738.1:p.Arg252Trp|1029|754|252|R/W|Cgg/Tgg|COSV53406990||1||EntrezGene||||||4:g.1803576C>T|||||||||||||1|1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|7/17||NM_001354810.2:c.754C>T|NP_001341739.1:p.Arg252Trp|1029|754|252|R/W|Cgg/Tgg|COSV53406990||1||EntrezGene||||||4:g.1803576C>T|||||||||||||1|1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|7/16||NM_022965.4:c.754C>T|NP_075254.1:p.Arg252Trp|1029|754|252|R/W|Cgg/Tgg|COSV53406990||1||EntrezGene||||||4:g.1803576C>T|||||||||||||1|1,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|7/19||NR_148971.2:n.1029C>T||1029|||||COSV53406990||1||EntrezGene||||||4:g.1803576C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1901:0:0,0:1020,880:1900,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:169:2:1,1:85,82:167,2:0.0118:2,2:15:1:37:0:1:1.03638:60:4:0.0118:0:1.5
    1442. 

  1442. 4	1803704	1803704	T	C	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon7:c.T882C:p.N294N,FGFR3:NM_001163213:exon7:c.T882C:p.N294N,FGFR3:NM_022965:exon7:c.T882C:p.N294N	0.37	0.1948	0.3538	0.1100	0.2185	0.0469	0.1388	0.1397	0.1383	rs2234909	rs2234909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53401699;OCCURENCE=1(breast),5(meninges),1(large_intestine),1(haematopoietic_and_lymphoid_tissue),1(urinary_tract),2(skin),1(thyroid),5(upper_aerodigestive_tract)	251378	not_specified|none_provided|not_provided	MedGen:CN169374|MedGen:CN235283|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU153774	LAML-KR|1|205|0.00487805,COCA-CN|1|321|0.00311526,BRCA-KR|1|50|0.02	0.5	281	205	4	1803704	.	T	C	281	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2874;VD=1;AF=0.0003;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCAAGCACGTGGAGGTGAA;RSEQ=GGCAGCAAGGTGGGCCCGGA;CSQ=C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|7/18||NM_000142.5:c.882T>C|NP_000133.1:p.Asn294%3D|1157|882|294|N|aaT/aaC|rs2234909&COSV53401699||1||EntrezGene||||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|7/18||NM_001163213.2:c.882T>C|NP_001156685.1:p.Asn294%3D|1157|882|294|N|aaT/aaC|rs2234909&COSV53401699||1||EntrezGene||YES||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|7/18||NM_001354809.2:c.882T>C|NP_001341738.1:p.Asn294%3D|1157|882|294|N|aaT/aaC|rs2234909&COSV53401699||1||EntrezGene||||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|7/17||NM_001354810.2:c.882T>C|NP_001341739.1:p.Asn294%3D|1157|882|294|N|aaT/aaC|rs2234909&COSV53401699||1||EntrezGene||||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1,C|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|7/16||NM_022965.4:c.882T>C|NP_075254.1:p.Asn294%3D|1157|882|294|N|aaT/aaC|rs2234909&COSV53401699||1||EntrezGene||||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1,C|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|7/19||NR_148971.2:n.1157T>C||1157|||||rs2234909&COSV53401699||1||EntrezGene||||||4:g.1803704T>C|0.16|0.3553|0.1242|0.2183|0.04568|0.1337|0.1475|0.1674|0.2104|0.3707|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2874:1:0,1:1383,1486:2869,1:0.0003:2,0:1:0:37:0:1:0:60:2:0.0004:0:1	1/1:205:204:101,103:0,0:0,204:0.9951:0,2:38:1:36.7:1:1:0:60:203:0.9951:0:1.2
    1443. 

  1443. 4	1805513	1805513	G	A	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_000142:exon8:c.G1025A:p.G342D	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	0.587	0.637	P	0.542	0.620	P	0.057	0.225	N	1	0.810	D	-0.275	0.037	N	-0.2	0.661	T	-4.07	0.760	D	0.902	0.891	-0.441	0.707	T	0.270	0.642	T	0.143	0.826	D	2.106	0.314	16.89	0.999	0.937	0.953	0.641	D	c	0.437	0.497	1.000	0.747	0.696	0.567	0	4.29	0.502	9.747	0.981	0.953	0.551	1.000	0.715	1.000	0.888	17.093	0.864	Immunoglobulin I-set|Immunoglobulin subtype 2|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	147	4	1805513	.	G	A	37	v3;f0.01;pSTD	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2263;VD=1;AF=0.0004;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.01064;SOR=0.03218;LSEQ=GGAGTACACCTGCCTGGCGG;RSEQ=CAATTCTATTGGGTTTTCTC;CSQ=A|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|8/18||NM_000142.5:c.1025G>A|NP_000133.1:p.Gly342Asp|1300|1025|342|G/D|gGc/gAc|COSV53404328||1||EntrezGene||||||4:g.1805513G>A|||||||||||||1|1,A|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||8/17|NM_001163213.2:c.1082-544G>A|||||||COSV53404328||1||EntrezGene||YES||||4:g.1805513G>A|||||||||||||1|1,A|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|8/18||NM_001354809.2:c.1025G>A|NP_001341738.1:p.Gly342Asp|1300|1025|342|G/D|gGc/gAc|COSV53404328||1||EntrezGene||||||4:g.1805513G>A|||||||||||||1|1,A|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|8/17||NM_001354810.2:c.1025G>A|NP_001341739.1:p.Gly342Asp|1300|1025|342|G/D|gGc/gAc|COSV53404328||1||EntrezGene||||||4:g.1805513G>A|||||||||||||1|1,A|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||7/15|NM_022965.4:c.931-1038G>A|||||||COSV53404328||1||EntrezGene||||||4:g.1805513G>A|||||||||||||1|1,A|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|9/19||NR_148971.2:n.1451G>A||1451|||||COSV53404328||1||EntrezGene||||||4:g.1805513G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2263:1:1,0:1005,1255:2260,1:0.0004:2,0:31:0:37:0:0.44494:0:60:2:0.0004:0:1	0/1:147:2:1,1:70,75:145,2:0.0136:2,2:53.5:1:37:0:1:1.07:60:4:0.0142:0:1
    1444. 

  1444. 4	1805556	1805556	G	A	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon8:c.G1068A:p.V356V	0.001	3.232e-05	0	0	0	0	0	6.674e-05	0	rs201947443	rs201947443	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	MU129048711	PAAD-US|1|177|0.00564972	0.25	37	102	4	1805556	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1683;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.00324;SOR=0;LSEQ=CACTCTGCGTGGCTGGTGGT;RSEQ=CTGCCAGGTACCGGCTTCTG;CSQ=A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|8/18||NM_000142.5:c.1068G>A|NP_000133.1:p.Val356%3D|1343|1068|356|V|gtG/gtA|rs201947443||1||EntrezGene||||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||,A|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||8/17|NM_001163213.2:c.1082-501G>A|||||||rs201947443||1||EntrezGene||YES||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|8/18||NM_001354809.2:c.1068G>A|NP_001341738.1:p.Val356%3D|1343|1068|356|V|gtG/gtA|rs201947443||1||EntrezGene||||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|8/17||NM_001354810.2:c.1068G>A|NP_001341739.1:p.Val356%3D|1343|1068|356|V|gtG/gtA|rs201947443||1||EntrezGene||||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||,A|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||7/15|NM_022965.4:c.931-995G>A|||||||rs201947443||1||EntrezGene||||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||,A|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|9/19||NR_148971.2:n.1494G>A||1494|||||rs201947443||1||EntrezGene||||||4:g.1805556G>A|7.18e-05|0|0|0|0.0002176|4.641e-05|8.832e-05|0.0001634|6.533e-05|0.001|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1683:0:0,0:717,966:1683,0:0:2,0:36.9:1:36.5:1:1:0:60:186:1:0:0.1	0/1:102:2:1,1:35,65:100,2:0.0196:2,2:27:0:37:0:1:1.85:60:4:0.0198:0:2
    1445. 

  1445. 4	1805568	1805568	C	T	intronic	FGFR3	.	.	.	0.038	0.0146	0.0376	0.0131	0.0265	0.0117	0.0006	0.0053	0.0041	rs3135885	rs3135885	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV53409736;OCCURENCE=6(meninges),1(haematopoietic_and_lymphoid_tissue),1(soft_tissue),4(prostate)	251381	Craniosynostosis_syndrome|not_specified|none_provided	Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374|MedGen:CN235283	criteria_provided,_multiple_submitters,_no_conflicts	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU114239496	LAML-KR|1|205|0.00487805	0.25	201	93	4	1805568	.	C	T	201	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1499;VD=3;AF=0.002;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0.0016;LSEQ=CTGGTGGTGCTGCCAGGTAC;RSEQ=GGCTTCTGCTGCTGCTGCTG;CSQ=T|splice_donor_5th_base_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding||8/17|NM_000142.5:c.1075+5C>T|||||||rs3135885&COSV53409736||1||EntrezGene||||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||8/17|NM_001163213.2:c.1082-489C>T|||||||rs3135885&COSV53409736||1||EntrezGene||YES||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1,T|splice_donor_5th_base_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||8/17|NM_001354809.2:c.1075+5C>T|||||||rs3135885&COSV53409736||1||EntrezGene||||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1,T|splice_donor_5th_base_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||8/16|NM_001354810.2:c.1075+5C>T|||||||rs3135885&COSV53409736||1||EntrezGene||||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||7/15|NM_022965.4:c.931-983C>T|||||||rs3135885&COSV53409736||1||EntrezGene||||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1,T|splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant|LOW|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||9/18|NR_148971.2:n.1501+5C>T|||||||rs3135885&COSV53409736||1||EntrezGene||||||4:g.1805568C>T|0.01083|0.03661|0.00856|0.0269|0.01534|0.0004188|0.00641|0.01178|0.01525|0.0378|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1499:3:1,2:616,880:1496,3:0.002:2,2:50.3:1:29:1:1:1.3997:60:6:0.002:0:2.3	1/0:93:52:19,33:13,28:41,52:0.5591:2,2:38.8:1:35.3:1:0.66565:1.24:60:51:0.5604:0:1.2
    1446. 

  1446. 4	1806169	1806169	C	T	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_000142:exon9:c.C1188T:p.C396C,FGFR3:NM_001163213:exon9:c.C1194T:p.C398C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	58	206	4	1806169	.	C	T	58	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1524;VD=2;AF=0.0013;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01387;SOR=0.08913;LSEQ=GTGGCGGCTGTGACGCTCTG;RSEQ=CGCCTGCGCAGCCCCCCCAA;CSQ=T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|9/18||NM_000142.5:c.1188C>T|NP_000133.1:p.Cys396%3D|1463|1188|396|C|tgC/tgT|||1||EntrezGene||||||4:g.1806169C>T||||||||||||||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|9/18||NM_001163213.2:c.1194C>T|NP_001156685.1:p.Cys398%3D|1469|1194|398|C|tgC/tgT|||1||EntrezGene||YES||||4:g.1806169C>T||||||||||||||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|9/18||NM_001354809.2:c.1188C>T|NP_001341738.1:p.Cys396%3D|1463|1188|396|C|tgC/tgT|||1||EntrezGene||||||4:g.1806169C>T||||||||||||||,T|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|9/17||NM_001354810.2:c.1188C>T|NP_001341739.1:p.Cys396%3D|1463|1188|396|C|tgC/tgT|||1||EntrezGene||||||4:g.1806169C>T||||||||||||||,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||7/15|NM_022965.4:c.931-382C>T|||||||||1||EntrezGene||||||4:g.1806169C>T||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|10/19||NR_148971.2:n.1614C>T||1614|||||||1||EntrezGene||||||4:g.1806169C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1524:2:1,1:721,801:1522,2:0.0013:2,2:63:1:37:0:1:1.11:60:4:0.0013:0:1	0/1:206:3:1,2:84,119:203,3:0.0146:2,2:33.3:1:37:0:1:1.40949:60:6:0.0149:0:1
    1447. 

  1447. 4	1806522	1806522	C	T	intronic	FGFR3	.	.	.	0.0079	0.0005	0	0	0	0.0099	0	0	0	rs75514890	rs75514890	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	76	4	1806522	.	C	T	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=758;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.0082;SOR=0;LSEQ=ACGCCCTGTCGCCCACGCGG;RSEQ=GCCAACCTGCCCCTGCTGAC;CSQ=T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_000142.5|protein_coding||9/17|NM_000142.5:c.1267-29C>T|||||||rs75514890||1||EntrezGene||||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||9/17|NM_001163213.2:c.1273-29C>T|||||||rs75514890||1||EntrezGene||YES||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||9/17|NM_001354809.2:c.1267-26C>T|||||||rs75514890||1||EntrezGene||||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||9/16|NM_001354810.2:c.1267-26C>T|||||||rs75514890||1||EntrezGene||||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||,T|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||7/15|NM_022965.4:c.931-29C>T|||||||rs75514890||1||EntrezGene||||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||10/18|NR_148971.2:n.1693-29C>T|||||||rs75514890||1||EntrezGene||||||4:g.1806522C>T|0.0006313|0|8.081e-05|0|0.008333|0|1.674e-05|0.0002272|0|0.008333|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:758:0:0,0:434,324:758,0:0:2,0:39.8:1:36.5:1:1:0:60:251.667:1:0:0.1	0/1:76:2:1,1:45,29:74,2:0.0263:2,2:21.5:1:31:1:1:1.54245:60:4:0.027:0:1.5
    1448. 

  1448. 4	1806633	1806633	C	T	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_022965:exon8:c.C1013T:p.T338M,FGFR3:NM_000142:exon10:c.C1349T:p.T450M,FGFR3:NM_001163213:exon10:c.C1355T:p.T452M	0.018	0.0012	0.0015	0	0	0.0111	0	0.0003	0.0010	rs56240927	rs56240927	1.0	0.010	T	0.002	0.197	B	0.004	0.093	B	0.002	0.379	N	0.993	0.237	N	-1.585	0.004	N	-1.53	0.816	D	2.44	0.003	N	0.161	0.195	-0.868	0.507	T	0.046	0.198	T	.	.	.	0.003	0.094	2.619	0.077	0.000	0.654	0.325	D	c	-1.234	-1.086	0.994	0.334	0.696	0.567	0	0.613	0.167	1.649	0.367	0.075	0.182	0.876	0.307	0.014	0.122	6.807	0.228	Immunoglobulin I-set|Immunoglobulin subtype 2|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	ID=COSV53417024;OCCURENCE=1(skin)	138149	Craniosynostosis_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0001363,Human_Phenotype_Ontology:HP:0001365,Human_Phenotype_Ontology:HP:0004494,Human_Phenotype_Ontology:HP:0005448,Human_Phenotype_Ontology:HP:0005457,Human_Phenotype_Ontology:HP:0005467,Human_Phenotype_Ontology:HP:0008492,MONDO:MONDO:0015469,MeSH:D003398,MedGen:C0010278,OMIM:PS123100,Orphanet:ORPHA1531,SNOMED_CT:57219006|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	1	0	.	.	0.25	188	76	4	1806633	.	C	T	188	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=748;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCCTCAGGGGAGGGCCCCA;RSEQ=GCTGGCCAATGTCTCCGAGC;CSQ=T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|10/18||NM_000142.5:c.1349C>T|NP_000133.1:p.Thr450Met|1624|1349|450|T/M|aCg/aTg|rs56240927&COSV53417024||1||EntrezGene||||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|10/18||NM_001163213.2:c.1355C>T|NP_001156685.1:p.Thr452Met|1630|1355|452|T/M|aCg/aTg|rs56240927&COSV53417024||1||EntrezGene||YES||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|10/18||NM_001354809.2:c.1352C>T|NP_001341738.1:p.Thr451Met|1627|1352|451|T/M|aCg/aTg|rs56240927&COSV53417024||1||EntrezGene||||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|10/17||NM_001354810.2:c.1352C>T|NP_001341739.1:p.Thr451Met|1627|1352|451|T/M|aCg/aTg|rs56240927&COSV53417024||1||EntrezGene||||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1,T|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|8/16||NM_022965.4:c.1013C>T|NP_075254.1:p.Thr338Met|1288|1013|338|T/M|aCg/aTg|rs56240927&COSV53417024||1||EntrezGene||||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1,T|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|11/19||NR_148971.2:n.1775C>T||1775|||||rs56240927&COSV53417024||1||EntrezGene||||||4:g.1806633C>T|0.001288|0.001259|0.0004847|0|0.01446|0|0.0001164|0.0004535|0.0002195|0.01446|gnomAD_EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:748:0:0,0:342,406:748,0:0:2,0:38:1:36.7:1:1:0:60:186:1:0:0.1	1/0:76:42:17,25:16,18:34,42:0.5526:2,2:38.9:1:34.9:1:0.64432:1.30255:60:20:0.5405:0:1.3
    1449. 

  1449. 4	1807076	1807076	T	C	intronic	FGFR3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	160	4	1807076	.	T	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1290;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01211;SOR=0;LSEQ=CATGGTCCCTCTGCCTCCAC;RSEQ=GCCAGGCTGACCCTGGGCAA;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding||10/17|NM_000142.5:c.1413-6T>C|||||||||1||EntrezGene||||||4:g.1807076T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||10/17|NM_001163213.2:c.1419-6T>C|||||||||1||EntrezGene||YES||||4:g.1807076T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||10/17|NM_001354809.2:c.1416-6T>C|||||||||1||EntrezGene||||||4:g.1807076T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||10/16|NM_001354810.2:c.1416-6T>C|||||||||1||EntrezGene||||||4:g.1807076T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding||8/15|NM_022965.4:c.1077-6T>C|||||||||1||EntrezGene||||||4:g.1807076T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant&non_coding_transcript_variant|LOW|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||11/18|NR_148971.2:n.1839-6T>C|||||||||1||EntrezGene||||||4:g.1807076T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1290:0:0,0:784,505:1289,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:160:2:1,1:110,48:158,2:0.0125:2,2:39:1:37:0:0.52005:2.27848:60:4:0.0126:0:1
    1450. 

  1450. 4	1807591	1807591	A	G	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_022965:exon11:c.A1424G:p.E475G,FGFR3:NM_000142:exon13:c.A1760G:p.E587G,FGFR3:NM_001163213:exon13:c.A1766G:p.E589G	.	.	.	.	.	.	.	.	.	.	.	0.102	0.302	T	1.0	0.899	D	0.989	0.769	D	0.000	0.843	D	1	0.810	D	0.25	0.098	N	-1.71	0.832	D	-3.75	0.770	D	0.681	0.759	0.102	0.842	D	0.552	0.836	D	0.862	0.989	D	4.148	0.556	23.8	0.986	0.425	0.964	0.687	D	c	0.132	0.146	1.000	0.747	0.718	0.821	0	4.32	0.507	5.886	0.693	1.109	0.879	1.000	0.715	0.973	0.468	13.767	0.623	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain;Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	148	4	1807591	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1271;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.01081;SOR=0;LSEQ=CACCTGCAAGCCGCCCGAGG;RSEQ=GCAGCTCACCTTCAAGGACC;CSQ=G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|13/18||NM_000142.5:c.1760A>G|NP_000133.1:p.Glu587Gly|2035|1760|587|E/G|gAg/gGg|||1||EntrezGene||||||4:g.1807591A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|13/18||NM_001163213.2:c.1766A>G|NP_001156685.1:p.Glu589Gly|2041|1766|589|E/G|gAg/gGg|||1||EntrezGene||YES||||4:g.1807591A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|13/18||NM_001354809.2:c.1763A>G|NP_001341738.1:p.Glu588Gly|2038|1763|588|E/G|gAg/gGg|||1||EntrezGene||||||4:g.1807591A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|13/17||NM_001354810.2:c.1763A>G|NP_001341739.1:p.Glu588Gly|2038|1763|588|E/G|gAg/gGg|||1||EntrezGene||||||4:g.1807591A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|11/16||NM_022965.4:c.1424A>G|NP_075254.1:p.Glu475Gly|1699|1424|475|E/G|gAg/gGg|||1||EntrezGene||||||4:g.1807591A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|14/19||NR_148971.2:n.2186A>G||2186|||||||1||EntrezGene||||||4:g.1807591A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1271:0:0,0:631,640:1271,0:0:2,0:36.3:1:36.2:1:1:0:60:73.765:1:0:0.1	0/1:148:2:1,1:76,70:146,2:0.0135:2,2:39:1:31:1:1:1.0851:60:4:0.0136:0:2
    1451. 

  1451. 4	1807605	1807605	A	G	exonic	FGFR3	.	nonsynonymous SNV	FGFR3:NM_022965:exon11:c.A1438G:p.K480E,FGFR3:NM_000142:exon13:c.A1774G:p.K592E,FGFR3:NM_001163213:exon13:c.A1780G:p.K594E	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.985	0.715	D	0.901	0.701	P	0.000	0.843	D	1	0.810	D	0.58	0.154	N	-1.61	0.823	D	-2.66	0.623	D	0.76	0.817	0.218	0.862	D	0.573	0.846	D	0.817	0.986	D	5.450	0.739	26.1	0.991	0.519	0.964	0.687	D	c	0.413	0.390	1.000	0.747	0.718	0.821	0	4.32	0.507	7.121	0.766	1.109	0.879	1.000	0.715	1.000	0.888	13.767	0.623	Protein kinase domain|Protein kinase, ATP binding site|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain;Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain;Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	157	4	1807605	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1226;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01281;SOR=0;LSEQ=CCGAGGAGCAGCTCACCTTC;RSEQ=AGGACCTGGTGTCCTGTGCC;CSQ=G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_000142.5|protein_coding|13/18||NM_000142.5:c.1774A>G|NP_000133.1:p.Lys592Glu|2049|1774|592|K/E|Aag/Gag|||1||EntrezGene||||||4:g.1807605A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|13/18||NM_001163213.2:c.1780A>G|NP_001156685.1:p.Lys594Glu|2055|1780|594|K/E|Aag/Gag|||1||EntrezGene||YES||||4:g.1807605A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|13/18||NM_001354809.2:c.1777A>G|NP_001341738.1:p.Lys593Glu|2052|1777|593|K/E|Aag/Gag|||1||EntrezGene||||||4:g.1807605A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|13/17||NM_001354810.2:c.1777A>G|NP_001341739.1:p.Lys593Glu|2052|1777|593|K/E|Aag/Gag|||1||EntrezGene||||||4:g.1807605A>G||||||||||||||,G|missense_variant|MODERATE|FGFR3|2261|Transcript|NM_022965.4|protein_coding|11/16||NM_022965.4:c.1438A>G|NP_075254.1:p.Lys480Glu|1713|1438|480|K/E|Aag/Gag|||1||EntrezGene||||||4:g.1807605A>G||||||||||||||,G|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|14/19||NR_148971.2:n.2200A>G||2200|||||||1||EntrezGene||||||4:g.1807605A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1226:0:0,0:634,592:1226,0:0:2,0:34.5:1:35.4:1:1:0:60:28.19:1:0:0.1	0/1:157:2:1,1:79,76:155,2:0.0127:2,2:25:1:31:1:1:1.03923:60:4:0.0129:0:2
    1452. 

  1452. 4	1807894	1807894	G	A	exonic	FGFR3	.	synonymous SNV	FGFR3:NM_022965:exon12:c.G1617A:p.T539T,FGFR3:NM_000142:exon14:c.G1953A:p.T651T,FGFR3:NM_001163213:exon14:c.G1959A:p.T653T	1.	0.9604	0.8608	0.9988	1	1	1	0.9997	0.9929	rs7688609	rs7688609	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99600161;OCCURENCE=18(meninges),2(central_nervous_system),2(biliary_tract),1(soft_tissue),2(lung)	861287	Squamous_cell_lung_carcinoma	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782	no_assertion_criteria_provided	Likely_benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU81778057	COCA-CN|5|321|0.0155763	1	428	414	4	1807894	.	G	A	428	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=4007;VD=3987;AF=0.995;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.3668;SOR=1.45496;LSEQ=CTCGACTACTACAAGAAGAC;RSEQ=ACCAACGTGAGCCCGGCCCT;CSQ=A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_000142.5|protein_coding|14/18||NM_000142.5:c.1953G>A|NP_000133.1:p.Thr651%3D|2228|1953|651|T|acG/acA|rs7688609&COSV99600161||1||EntrezGene||||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001163213.2|protein_coding|14/18||NM_001163213.2:c.1959G>A|NP_001156685.1:p.Thr653%3D|2234|1959|653|T|acG/acA|rs7688609&COSV99600161||1||EntrezGene||YES||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354809.2|protein_coding|14/18||NM_001354809.2:c.1956G>A|NP_001341738.1:p.Thr652%3D|2231|1956|652|T|acG/acA|rs7688609&COSV99600161||1||EntrezGene||||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_001354810.2|protein_coding|14/17||NM_001354810.2:c.1956G>A|NP_001341739.1:p.Thr652%3D|2231|1956|652|T|acG/acA|rs7688609&COSV99600161||1||EntrezGene||||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1,A|synonymous_variant|LOW|FGFR3|2261|Transcript|NM_022965.4|protein_coding|12/16||NM_022965.4:c.1617G>A|NP_075254.1:p.Thr539%3D|1892|1617|539|T|acG/acA|rs7688609&COSV99600161||1||EntrezGene||||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1,A|non_coding_transcript_exon_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA|15/19||NR_148971.2:n.2379G>A||2379|||||rs7688609&COSV99600161||1||EntrezGene||||||4:g.1807894G>A|0.9897|0.8583|0.994|1|1|1|0.9996|0.9951|0.9997|1|EAS&EUR&SAS&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN|likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4007:3987:2052,1935:0,0:0,3987:0.995:0,2:37.4:1:35.8:1:1:0:60:40.968:0.9972:0:1.1	1/1:414:411:219,192:0,0:0,411:0.9928:0,2:37.7:1:36.8:1:1:0:60:204.5:0.9927:0:1.1
    1453. 

  1453. 4	1808450	1808450	T	G	intronic	FGFR3	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	63	77	4	1808450	.	T	G	63	q22.5;SN1.5;NM5.25;Bias	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=663;VD=24;AF=0.0362;SHIFT3=0;MSI=5;MSILEN=1;SSF=0.48002;SOR=1.40788;LSEQ=CTCCACTGGGTCCTCAGGGG;RSEQ=GGGGGTCCCTCCGGGGCTGG;CSQ=G|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_000142.5|protein_coding||16/17|NM_000142.5:c.2168+40T>G|||||||||1||EntrezGene||||||4:g.1808450T>G||||||||||||||,G|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001163213.2|protein_coding||16/17|NM_001163213.2:c.2174+40T>G|||||||||1||EntrezGene||YES||||4:g.1808450T>G||||||||||||||,G|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354809.2|protein_coding||16/17|NM_001354809.2:c.2171+40T>G|||||||||1||EntrezGene||||||4:g.1808450T>G||||||||||||||,G|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_001354810.2|protein_coding||15/16|NM_001354810.2:c.2100+40T>G|||||||||1||EntrezGene||||||4:g.1808450T>G||||||||||||||,G|downstream_gene_variant|MODIFIER|LETM1|3954|Transcript|NM_012318.3|protein_coding|||||||||||4756|-1||EntrezGene||YES||||4:g.1808450T>G||||||||||||||,G|intron_variant|MODIFIER|FGFR3|2261|Transcript|NM_022965.4|protein_coding||14/15|NM_022965.4:c.1832+40T>G|||||||||1||EntrezGene||||||4:g.1808450T>G||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|FGFR3|2261|Transcript|NR_148971.2|misc_RNA||17/18|NR_148971.2:n.2594+40T>G|||||||||1||EntrezGene||||||4:g.1808450T>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:663:24:1,23:435,204:639,24:0.0362:2,1:29.1:1:13.8:1:0:48.821:60:0.2:0.007:0:6.3	0/1:77:2:0,2:50,25:75,2:0.026:2,0:11:1:25:0:0.11996:0:60:4:0.0278:0:7
    1454. 

  1454. 4	20255543	20255543	G	A	exonic	SLIT2	.	synonymous SNV	SLIT2:NM_001289135:exon1:c.G105A:p.S35S,SLIT2:NM_001289136:exon1:c.G105A:p.S35S,SLIT2:NM_004787:exon1:c.G105A:p.S35S	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	127	4	20255543	.	G	A	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1498;VD=0;AF=0;SHIFT3=4;MSI=3;MSILEN=1;SSF=0.00606;SOR=0;LSEQ=CCGGCGCAGTGCTCTTGCTC;RSEQ=GGCAGCACAGTGGACTGTCA;CSQ=A|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|1/37||NM_001289135.3:c.105G>A|NP_001276064.1:p.Ser35%3D|2016|105|35|S|tcG/tcA|rs947415082&COSV99882444||1||EntrezGene||||||4:g.20255543G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,A|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|1/36||NM_001289136.3:c.105G>A|NP_001276065.1:p.Ser35%3D|2016|105|35|S|tcG/tcA|rs947415082&COSV99882444||1||EntrezGene||||||4:g.20255543G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1,A|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding|1/37||NM_004787.4:c.105G>A|NP_004778.1:p.Ser35%3D|2016|105|35|S|tcG/tcA|rs947415082&COSV99882444||1||EntrezGene||YES||||4:g.20255543G>A|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1498:0:0,0:754,743:1497,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:127:2:1,1:63,62:125,2:0.0157:2,2:45.5:1:37:0:1:1.016:60:4:0.0157:0:1
    1455. 

  1455. 4	20259480	20259480	T	A	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	123	4	20259480	.	T	A	31	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0.98387;SOR=0;LSEQ=ATTAAGAAGCATGTTATATT;RSEQ=TGCATTTCAGTCAGCTTATG;CSQ=A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||2/36|NM_001289135.3:c.252-11T>A|||||||||1||EntrezGene||||||4:g.20259480T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||2/35|NM_001289136.3:c.252-11T>A|||||||||1||EntrezGene||||||4:g.20259480T>A||||||||||||||,A|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||2/36|NM_004787.4:c.252-11T>A|||||||||1||EntrezGene||YES||||4:g.20259480T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:37:0:1:0:60:2:1:0:0	0/1:123:2:1,1:73,48:121,2:0.0163:2,2:71:1:31:1:1:1.51547:60:4:0.0167:0:1
    1456. 

  1456. 4	20270434	20270434	C	T	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon4:c.C325T:p.R109C,SLIT2:NM_001289136:exon4:c.C325T:p.R109C,SLIT2:NM_004787:exon4:c.C325T:p.R109C	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.969	0.719	D	0.000	0.843	D	1	0.810	D	1.65	0.424	L	0.36	0.579	T	-5.23	0.910	D	0.904	0.894	-0.531	0.675	T	0.305	0.676	T	0.034	0.554	D	7.630	0.954	35	0.999	0.999	0.992	0.930	D	c	0.773	0.790	1.000	0.747	0.626	0.397	0	5.96	0.967	5.432	0.660	0.935	0.490	1.000	0.715	1.000	0.888	18.581	0.911	Leucine-rich repeat domain, L domain-like	.	.	ID=COSV56578701;OCCURENCE=1(large_intestine),2(central_nervous_system),1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU51062083	COCA-CN|1|321|0.00311526,UCEC-US|1|531|0.00188324	0.25	37	142	4	20270434	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=23;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.73991;SOR=0;LSEQ=GTTTTTGTTTTCTCAAAAGG;RSEQ=GTTTAAACAGAAATCACCTT;CSQ=T|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|4/37||NM_001289135.3:c.325C>T|NP_001276064.1:p.Arg109Cys|2236|325|109|R/C|Cgt/Tgt|COSV56578701||1||EntrezGene||||||4:g.20270434C>T|||||||||||||1|1,T|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|4/36||NM_001289136.3:c.325C>T|NP_001276065.1:p.Arg109Cys|2236|325|109|R/C|Cgt/Tgt|COSV56578701||1||EntrezGene||||||4:g.20270434C>T|||||||||||||1|1,T|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|4/37||NM_004787.4:c.325C>T|NP_004778.1:p.Arg109Cys|2236|325|109|R/C|Cgt/Tgt|COSV56578701||1||EntrezGene||YES||||4:g.20270434C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:23:0:0,0:13,10:23,0:0:2,0:29.2:1:35.9:1:1:0:60:22:1:0:0.3	0/1:142:2:1,1:80,60:140,2:0.0141:2,2:53:1:37:0:1:1.33058:60:4:0.0145:0:1
    1457. 

  1457. 4	20270435	20270435	G	A	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon4:c.G326A:p.R109H,SLIT2:NM_001289136:exon4:c.G326A:p.R109H,SLIT2:NM_004787:exon4:c.G326A:p.R109H	.	.	.	.	.	.	.	.	.	.	.	0.003	0.784	D	0.999	0.764	D	0.955	0.695	D	0.000	0.843	D	1	0.810	D	0.665	0.163	N	0.39	0.574	T	-3.36	0.723	D	0.777	0.776	-0.691	0.609	T	0.203	0.560	T	0.023	0.463	T	7.013	0.938	33	0.999	0.995	0.995	0.965	D	c	0.651	0.726	1.000	0.747	0.626	0.397	0	5.96	0.967	6.887	0.752	1.048	0.713	1.000	0.715	1.000	0.888	18.581	0.911	Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	143	4	20270435	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=25;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.72377;SOR=0;LSEQ=TTTTTGTTTTCTCAAAAGGC;RSEQ=TTTAAACAGAAATCACCTTC;CSQ=A|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|4/37||NM_001289135.3:c.326G>A|NP_001276064.1:p.Arg109His|2237|326|109|R/H|cGt/cAt|rs369657409||1||EntrezGene||||||4:g.20270435G>A|7.971e-06|0|0|0|5.439e-05|0|8.816e-06|0|0|5.439e-05|gnomAD_EAS|||,A|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|4/36||NM_001289136.3:c.326G>A|NP_001276065.1:p.Arg109His|2237|326|109|R/H|cGt/cAt|rs369657409||1||EntrezGene||||||4:g.20270435G>A|7.971e-06|0|0|0|5.439e-05|0|8.816e-06|0|0|5.439e-05|gnomAD_EAS|||,A|missense_variant&splice_region_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|4/37||NM_004787.4:c.326G>A|NP_004778.1:p.Arg109His|2237|326|109|R/H|cGt/cAt|rs369657409||1||EntrezGene||YES||||4:g.20270435G>A|7.971e-06|0|0|0|5.439e-05|0|8.816e-06|0|0|5.439e-05|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:25:0:0,0:14,11:25,0:0:2,0:27.6:1:37:0:1:0:60:50:1:0:0.3	0/1:143:2:1,1:80,61:141,2:0.014:2,2:28:0:37:0:1:1.30895:60:4:0.014:0:1
    1458. 

  1458. 4	20482404	20482404	A	T	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon6:c.A533T:p.E178V,SLIT2:NM_001289136:exon6:c.A533T:p.E178V,SLIT2:NM_004787:exon6:c.A533T:p.E178V	.	.	.	.	.	.	.	.	.	.	.	0.001	0.912	D	1.0	0.899	D	0.997	0.971	D	0.000	0.843	N	1	0.810	D	1.755	0.458	L	0.22	0.838	T	-5.94	0.891	D	0.607	0.648	0.376	0.887	D	0.667	0.885	D	0.339	0.920	D	5.882	0.806	27.4	0.993	0.576	0.964	0.685	D	c	0.722	0.690	1.000	0.747	0.693	0.558	0	4.54	0.551	9.098	0.935	1.199	0.960	1.000	0.715	1.000	0.888	12.201	0.535	Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	374	4	20482404	.	A	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=188;VD=2;AF=0.0106;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.11151;SOR=inf;LSEQ=CAGGGCTCTCCGGGACCTGG;RSEQ=AGTGCTGTAAGTACTGCTAT;CSQ=T|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|6/37||NM_001289135.3:c.533A>T|NP_001276064.1:p.Glu178Val|2444|533|178|E/V|gAa/gTa|||1||EntrezGene||||||4:g.20482404A>T||||||||||||||,T|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|6/36||NM_001289136.3:c.533A>T|NP_001276065.1:p.Glu178Val|2444|533|178|E/V|gAa/gTa|||1||EntrezGene||||||4:g.20482404A>T||||||||||||||,T|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|6/37||NM_004787.4:c.533A>T|NP_004778.1:p.Glu178Val|2444|533|178|E/V|gAa/gTa|||1||EntrezGene||YES||||4:g.20482404A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:188:2:1,1:87,99:186,2:0.0106:2,2:27:1:37:0:1:1.14:60:4:0.0108:0:1	0/0:374:0:0,0:188,186:374,0:0:2,0:38.7:1:36.6:1:1:0:60:373:1:0:0.3
    1459. 

  1459. 4	20482408	20482408	G	A	exonic	SLIT2	.	synonymous SNV	SLIT2:NM_001289135:exon6:c.G537A:p.V179V,SLIT2:NM_001289136:exon6:c.G537A:p.V179V,SLIT2:NM_004787:exon6:c.G537A:p.V179V	0.0001	.	.	.	.	.	.	.	.	rs372549576	rs372549576	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	373	4	20482408	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=186;VD=2;AF=0.0108;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.11032;SOR=inf;LSEQ=GCTCTCCGGGACCTGGAAGT;RSEQ=CTGTAAGTACTGCTATTTCT;CSQ=A|splice_region_variant&synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|6/37||NM_001289135.3:c.537G>A|NP_001276064.1:p.Val179%3D|2448|537|179|V|gtG/gtA|rs372549576||1||EntrezGene||||||4:g.20482408G>A|7.962e-06|0|0|0|0|0|1.761e-05|0|0|0.0001163|EA|||,A|splice_region_variant&synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|6/36||NM_001289136.3:c.537G>A|NP_001276065.1:p.Val179%3D|2448|537|179|V|gtG/gtA|rs372549576||1||EntrezGene||||||4:g.20482408G>A|7.962e-06|0|0|0|0|0|1.761e-05|0|0|0.0001163|EA|||,A|splice_region_variant&synonymous_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding|6/37||NM_004787.4:c.537G>A|NP_004778.1:p.Val179%3D|2448|537|179|V|gtG/gtA|rs372549576||1||EntrezGene||YES||||4:g.20482408G>A|7.962e-06|0|0|0|0|0|1.761e-05|0|0|0.0001163|EA|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:186:2:1,1:85,99:184,2:0.0108:2,2:17:0:37:0:1:1.16:60:4:0.0108:0:1	0/0:373:0:0,0:183,190:373,0:0:2,0:38.8:1:36.4:1:1:0:60:372:1:0:0.4
    1460. 

  1460. 4	20490581	20490581	-	A	exonic	SLIT2	.	frameshift insertion	SLIT2:NM_001289135:exon8:c.752dupA:p.R253Tfs*8,SLIT2:NM_001289136:exon8:c.752dupA:p.R253Tfs*17,SLIT2:NM_004787:exon8:c.752dupA:p.R253Tfs*17	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	60	172	4	20490581	.	C	CA	60	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=273;VD=3;AF=0.011;SHIFT3=5;MSI=6;MSILEN=1;SSF=0.22991;SOR=inf;LSEQ=GCCATAATGTAGCCGAGGTT;RSEQ=AAAAACGAGAATTTGTCTGC;CSQ=A|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|8/37||NM_001289135.3:c.756dup|NP_001276064.1:p.Arg253ThrfsTer7|2662-2663|751-752|251|Q/QX|caa/cAaa|||1||EntrezGene|||||5|4:g.20490586dup||||||||||||||,A|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|8/36||NM_001289136.3:c.756dup|NP_001276065.1:p.Arg253ThrfsTer17|2662-2663|751-752|251|Q/QX|caa/cAaa|||1||EntrezGene|||||5|4:g.20490586dup||||||||||||||,A|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_004787.4|protein_coding|8/37||NM_004787.4:c.756dup|NP_004778.1:p.Arg253ThrfsTer17|2662-2663|751-752|251|Q/QX|caa/cAaa|||1||EntrezGene||YES|||5|4:g.20490586dup||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:273:3:1,2:114,149:263,3:0.011:2,2:28.1:1:38:0:1:1.52785:61.6:6:0.0115:0:0	0/0:172:0:0,0:74,98:172,0:0:2,0:36.7:1:36.4:1:1:0:60:171:1:0:0.1
    1461. 

  1461. 4	20492380	20492380	A	G	intronic	SLIT2	.	.	.	0.55	0.3211	0.1942	0.4868	0.4172	0.55	0.3715	0.3431	0.3857	rs485909	rs485909	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU13916011	LAML-KR|1|205|0.00487805,COCA-CN|3|321|0.00934579,PBCA-DE|1|499|0.00200401	0.25	179	46	4	20492380	.	A	G	179	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00267;SOR=0;LSEQ=GAAATGACTAACAGTTCGTT;RSEQ=CTAACCACTTTTTTCTCTCT;CSQ=G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||8/36|NM_001289135.3:c.776-46A>G|||||||rs485909||1||EntrezGene||||||4:g.20492380A>G|0.3857|0.195|0.4881|0.3576|0.5401|0.3713|0.3529|0.4007|0.3456|0.5401|gnomAD_EAS|||,G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||8/35|NM_001289136.3:c.776-1004A>G|||||||rs485909||1||EntrezGene||||||4:g.20492380A>G|0.3857|0.195|0.4881|0.3576|0.5401|0.3713|0.3529|0.4007|0.3456|0.5401|gnomAD_EAS|||,G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||8/36|NM_004787.4:c.776-1004A>G|||||||rs485909||1||EntrezGene||YES||||4:g.20492380A>G|0.3857|0.195|0.4881|0.3576|0.5401|0.3713|0.3529|0.4007|0.3456|0.5401|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:6:0:0,0:5,1:6,0:0:2,0:23.5:1:37:0:1:0:60:12:1:0:0.3	1/0:46:31:22,9:12,3:15,31:0.6739:2,2:31.8:1:36.2:1:0.72326:1.61965:60:62:0.6739:0:1
    1462. 

  1462. 4	20492417	20492417	G	T	intronic	SLIT2	.	.	.	0.41	0.2367	0.4083	0.1799	0.2167	0.2737	0.1553	0.1592	0.1748	rs7695303	rs7695303	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56573764;OCCURENCE=1(breast)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU17460982	LAML-KR|2|205|0.0097561,COCA-CN|1|321|0.00311526,BRCA-KR|1|50|0.02	0.5	166	77	4	20492417	.	G	T	166	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=12;VD=4;AF=0.3333;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.62614;SOR=0.98098;LSEQ=CTCTTCACTTTTTCCTTTCT;RSEQ=TTTTCTAGATGAGGAAGAAG;CSQ=T|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||8/36|NM_001289135.3:c.776-9G>T|||||||rs7695303&COSV56573764||1||EntrezGene||||||4:g.20492417G>T|0.1902|0.4218|0.1875|0.2421|0.2781|0.1598|0.1709|0.1753|0.1223|0.4218|gnomAD_AFR||0&1|0&1,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||8/35|NM_001289136.3:c.776-967G>T|||||||rs7695303&COSV56573764||1||EntrezGene||||||4:g.20492417G>T|0.1902|0.4218|0.1875|0.2421|0.2781|0.1598|0.1709|0.1753|0.1223|0.4218|gnomAD_AFR||0&1|0&1,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||8/36|NM_004787.4:c.776-967G>T|||||||rs7695303&COSV56573764||1||EntrezGene||YES||||4:g.20492417G>T|0.1902|0.4218|0.1875|0.2421|0.2781|0.1598|0.1709|0.1753|0.1223|0.4218|gnomAD_AFR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:12:4:3,1:4,4:8,4:0.3333:2,2:31.2:1:37:0:0.57576:2.74:60:8:0.3333:0:1.2	0/1:77:26:17,9:29,22:51,26:0.3377:2,2:37.2:1:35.5:1:0.62383:1.43:60:25:0.3289:0:1.2
    1463. 

  1463. 4	20493381	20493381	T	C	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	188	4	20493381	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=48;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.6339;SOR=0;LSEQ=ATTCCTGTTTATTTCTTTTT;RSEQ=AGGTCACCAGTCATTTATGG;CSQ=C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||9/36|NM_001289135.3:c.788-3T>C|||||||||1||EntrezGene||||||4:g.20493381T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||8/35|NM_001289136.3:c.776-3T>C|||||||||1||EntrezGene||||||4:g.20493381T>C||||||||||||||,C|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||8/36|NM_004787.4:c.776-3T>C|||||||||1||EntrezGene||YES||||4:g.20493381T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:48:0:0,0:33,15:48,0:0:2,0:26.8:1:36.2:1:1:0:60:47:1:0:0.1	0/1:188:2:1,1:127,59:186,2:0.0106:2,2:53.5:1:31:1:0.5376:2.14296:60:4:0.0107:0:2
    1464. 

  1464. 4	20493389	20493389	C	A	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon9:c.C793A:p.Q265K,SLIT2:NM_001289136:exon9:c.C781A:p.Q261K,SLIT2:NM_004787:exon9:c.C781A:p.Q261K	.	.	.	.	.	.	.	.	.	.	.	0.853	0.085	T	0.017	0.179	B	0.026	0.198	B	0.005	0.336	N	1	0.810	D	0.2	0.092	N	-1.34	0.800	T	-0.67	0.193	N	0.555	0.601	-0.642	0.631	T	0.340	0.706	T	0.025	0.480	T	2.560	0.369	19.85	0.973	0.329	0.997	0.985	D	c	0.042	0.271	1.000	0.747	0.706	0.609	0	5.63	0.861	7.539	0.808	0.935	0.490	1.000	0.715	0.995	0.604	20.057	0.976	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	212	4	20493389	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=52;VD=2;AF=0.0385;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.0382;SOR=inf;LSEQ=TTATTTCTTTTTTAGGTCAC;RSEQ=AGTCATTTATGGCTCCTTCT;CSQ=A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|10/37||NM_001289135.3:c.793C>A|NP_001276064.1:p.Gln265Lys|2704|793|265|Q/K|Cag/Aag|||1||EntrezGene||||||4:g.20493389C>A||||||||||||||,A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|9/36||NM_001289136.3:c.781C>A|NP_001276065.1:p.Gln261Lys|2692|781|261|Q/K|Cag/Aag|||1||EntrezGene||||||4:g.20493389C>A||||||||||||||,A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|9/37||NM_004787.4:c.781C>A|NP_004778.1:p.Gln261Lys|2692|781|261|Q/K|Cag/Aag|||1||EntrezGene||YES||||4:g.20493389C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:52:2:1,1:33,17:50,2:0.0385:2,2:22.5:1:37:0:1:1.91492:60:4:0.0408:0:1	0/0:212:0:0,0:141,71:212,0:0:2,0:32.9:1:36.2:1:1:0:60:52:1:0:0.1
    1465. 

  1465. 4	20493501	20493501	T	C	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon9:c.T905C:p.L302P,SLIT2:NM_001289136:exon9:c.T893C:p.L298P,SLIT2:NM_004787:exon9:c.T893C:p.L298P	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.984	0.588	D	0.886	0.633	P	0.000	0.843	D	1	0.810	D	3.135	0.884	M	-4.66	0.980	D	-6.0	0.895	D	0.912	0.902	1.093	0.993	D	0.967	0.990	D	0.558	0.960	D	6.268	0.865	29.0	0.999	0.986	0.984	0.826	D	c	0.930	0.869	1.000	0.747	0.706	0.609	0	5.63	0.861	7.674	0.830	1.061	0.807	1.000	0.715	0.997	0.653	16.148	0.813	Leucine-rich repeat N-terminal domain|Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	261	4	20493501	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=105;VD=2;AF=0.019;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.08174;SOR=inf;LSEQ=CACTGAGATCCCCACAAATC;RSEQ=TCCAGAGACCATCACAGAAA;CSQ=C|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|10/37||NM_001289135.3:c.905T>C|NP_001276064.1:p.Leu302Pro|2816|905|302|L/P|cTt/cCt|||1||EntrezGene||||||4:g.20493501T>C||||||||||||||,C|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|9/36||NM_001289136.3:c.893T>C|NP_001276065.1:p.Leu298Pro|2804|893|298|L/P|cTt/cCt|||1||EntrezGene||||||4:g.20493501T>C||||||||||||||,C|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|9/37||NM_004787.4:c.893T>C|NP_004778.1:p.Leu298Pro|2804|893|298|L/P|cTt/cCt|||1||EntrezGene||YES||||4:g.20493501T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:105:2:1,1:47,56:103,2:0.019:2,2:70:1:37:0:1:1.19:60:4:0.0192:0:2	0/0:261:0:0,0:112,149:261,0:0:2,0:37.9:1:35.9:1:1:0:60:42.5:1:0:0
    1466. 

  1466. 4	20493528	20493528	T	A	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	212	4	20493528	.	T	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=2;AF=0.0244;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.07711;SOR=inf;LSEQ=GACCATCACAGAAATGTATG;RSEQ=GCCTGAAATTCTTTCTTATC;CSQ=A|splice_donor_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||10/36|NM_001289135.3:c.926+6T>A|||||||||1||EntrezGene||||||4:g.20493528T>A||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||9/35|NM_001289136.3:c.914+6T>A|||||||||1||EntrezGene||||||4:g.20493528T>A||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||9/36|NM_004787.4:c.914+6T>A|||||||||1||EntrezGene||YES||||4:g.20493528T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:82:2:1,1:32,48:80,2:0.0244:2,2:47.5:1:37:0:1:1.49:60:4:0.0247:0:2	0/0:212:0:0,0:73,139:212,0:0:2,0:33.8:1:36.1:1:1:0:60:52:1:0:0
    1467. 

  1467. 4	20512710	20512710	C	T	exonic	SLIT2	.	synonymous SNV	SLIT2:NM_001289135:exon11:c.C1020T:p.I340I,SLIT2:NM_001289136:exon11:c.C1008T:p.I336I,SLIT2:NM_004787:exon11:c.C1008T:p.I336I	0.001	.	.	.	.	.	.	.	.	rs556066872	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	226	4	20512710	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=35;VD=2;AF=0.0571;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.01754;SOR=inf;LSEQ=GACCTGAGCAATAATCAGAT;RSEQ=TCTGAACTTGCACCAGATGC;CSQ=T|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|12/37||NM_001289135.3:c.1020C>T|NP_001276064.1:p.Ile340%3D|2931|1020|340|I|atC/atT|rs556066872&COSV56593603||1||EntrezGene||||||4:g.20512710C>T|7.965e-06|0|0|0|0|0|8.798e-06|0|3.267e-05|0.001|SAS||0&1|0&1,T|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|11/36||NM_001289136.3:c.1008C>T|NP_001276065.1:p.Ile336%3D|2919|1008|336|I|atC/atT|rs556066872&COSV56593603||1||EntrezGene||||||4:g.20512710C>T|7.965e-06|0|0|0|0|0|8.798e-06|0|3.267e-05|0.001|SAS||0&1|0&1,T|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding|11/37||NM_004787.4:c.1008C>T|NP_004778.1:p.Ile336%3D|2919|1008|336|I|atC/atT|rs556066872&COSV56593603||1||EntrezGene||YES||||4:g.20512710C>T|7.965e-06|0|0|0|0|0|8.798e-06|0|3.267e-05|0.001|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:35:2:1,1:18,15:33,2:0.0571:2,2:13:1:37:0:1:1.19373:60:4:0.0571:0:1	0/0:226:0:0,0:116,110:226,0:0:2,0:37.3:1:36.5:1:1:0:60:112:1:0:0.1
    1468. 

  1468. 4	20520993	20520993	T	C	intronic	SLIT2	.	.	.	0.99	0.8804	0.8843	0.9368	0.9172	0.9876	0.9006	0.8573	0.8900	rs519813	rs519813	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81781571	COCA-CN|5|321|0.0155763	1	174	27	4	20520993	.	T	C	174	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=6;VD=6;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTTTTTTCATTTAAAA;RSEQ=ATTTTTTTCAGTGTCCTCTA;CSQ=C|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||12/36|NM_001289135.3:c.1071-12T>C|||||||rs519813||1||EntrezGene||||||4:g.20520993T>C|0.9032|0.8872|0.9442|0.9298|0.9891|0.8973|0.8692|0.8986|0.9362|0.9911|EAS|||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||11/35|NM_001289136.3:c.1059-12T>C|||||||rs519813||1||EntrezGene||||||4:g.20520993T>C|0.9032|0.8872|0.9442|0.9298|0.9891|0.8973|0.8692|0.8986|0.9362|0.9911|EAS|||,C|splice_polypyrimidine_tract_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||11/36|NM_004787.4:c.1059-12T>C|||||||rs519813||1||EntrezGene||YES||||4:g.20520993T>C|0.9032|0.8872|0.9442|0.9298|0.9891|0.8973|0.8692|0.8986|0.9362|0.9911|EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:6:6:4,2:0,0:0,6:1:0,2:26:1:37:0:1:0:60:12:1:0:1	1/1:27:27:20,7:0,0:0,27:1:0,2:31.8:1:36.6:1:1:0:60:54:1:0:1
    1469. 

  1469. 4	20525378	20525378	A	G	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	218	4	20525378	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=77;VD=2;AF=0.026;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.06747;SOR=inf;LSEQ=ATTCTACAACTATTTAATCA;RSEQ=ACAGATTATTGAATGCCAAC;CSQ=G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||13/36|NM_001289135.3:c.1143-5A>G|||||||rs1560499708||1||EntrezGene||||||4:g.20525378A>G|3.981e-06|0|0|0|0|0|8.799e-06|0|0|8.799e-06|gnomAD_NFE|||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||12/35|NM_001289136.3:c.1131-5A>G|||||||rs1560499708||1||EntrezGene||||||4:g.20525378A>G|3.981e-06|0|0|0|0|0|8.799e-06|0|0|8.799e-06|gnomAD_NFE|||,G|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||12/36|NM_004787.4:c.1131-5A>G|||||||rs1560499708||1||EntrezGene||YES||||4:g.20525378A>G|3.981e-06|0|0|0|0|0|8.799e-06|0|0|8.799e-06|gnomAD_NFE|||,G|upstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA||||||||||rs1560499708|4520|1||EntrezGene||YES||||4:g.20525378A>G|3.981e-06|0|0|0|0|0|8.799e-06|0|0|8.799e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:77:2:1,1:57,18:75,2:0.026:2,2:26:0:37:0:0.43506:3.1093:60:4:0.0263:0:1	0/0:218:0:0,0:149,69:218,0:0:2,0:38:1:36.1:1:1:0:60:71.667:1:0:0.1
    1470. 

  1470. 4	20525414	20525414	C	-	exonic	SLIT2	.	frameshift deletion	SLIT2:NM_001289135:exon13:c.1174delC:p.R392Gfs*2,SLIT2:NM_001289136:exon13:c.1162delC:p.R388Gfs*2,SLIT2:NM_004787:exon13:c.1162delC:p.R388Gfs*2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	299	4	20525413	.	TC	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=186;VD=2;AF=0.0108;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.14659;SOR=inf;LSEQ=GCCAACAAGATAAACTGCCT;RSEQ=GGGTAGATGCTTTTCAGGAT;CSQ=-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|14/37||NM_001289135.3:c.1174del|NP_001276064.1:p.Arg392GlyfsTer2|3085|1174|392|R/X|Cgg/gg|COSV56564001||1||EntrezGene||||||4:g.20525414del|||||||||||||1|1,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|13/36||NM_001289136.3:c.1162del|NP_001276065.1:p.Arg388GlyfsTer2|3073|1162|388|R/X|Cgg/gg|COSV56564001||1||EntrezGene||||||4:g.20525414del|||||||||||||1|1,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_004787.4|protein_coding|13/37||NM_004787.4:c.1162del|NP_004778.1:p.Arg388GlyfsTer2|3073|1162|388|R/X|Cgg/gg|COSV56564001||1||EntrezGene||YES||||4:g.20525414del|||||||||||||1|1,-|upstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA||||||||||COSV56564001|4484|1||EntrezGene||YES||||4:g.20525414del|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:186:2:1,1:119,65:184,2:0.0108:2,2:42.5:1:37:0:1:1.82436:60:4:0.0108:0:0	0/0:299:0:0,0:179,120:299,0:0:2,0:38.2:1:36.3:1:1:0:60:98.667:1:0:0.1
    1471. 

  1471. 4	20525537	20525537	G	A	intronic	SLIT2	.	.	.	0.072	0.0185	0.0265	0.0203	0.0132	0.0604	0.0146	0.0099	0.0234	rs2292438	rs2292438	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56589531;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU11966218	ESAD-UK|1|409|0.00244499,COCA-CN|2|321|0.00623053	0.25	258	303	4	20525537	.	G	A	258	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=238;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCAAACTATGTATGTATAA;RSEQ=TGATTTGGATCACTTTTGAT;CSQ=A|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||14/36|NM_001289135.3:c.1286+11G>A|||||||rs2292438&COSV56589531||1||EntrezGene||||||4:g.20525537G>A|0.01856|0.02522|0.02352|0.01699|0.07221|0.01767|0.007087|0.01731|0.02114|0.07221|gnomAD_EAS||0&1|0&1,A|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||13/35|NM_001289136.3:c.1274+11G>A|||||||rs2292438&COSV56589531||1||EntrezGene||||||4:g.20525537G>A|0.01856|0.02522|0.02352|0.01699|0.07221|0.01767|0.007087|0.01731|0.02114|0.07221|gnomAD_EAS||0&1|0&1,A|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||13/36|NM_004787.4:c.1274+11G>A|||||||rs2292438&COSV56589531||1||EntrezGene||YES||||4:g.20525537G>A|0.01856|0.02522|0.02352|0.01699|0.07221|0.01767|0.007087|0.01731|0.02114|0.07221|gnomAD_EAS||0&1|0&1,A|upstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA||||||||||rs2292438&COSV56589531|4361|1||EntrezGene||YES||||4:g.20525537G>A|0.01856|0.02522|0.02352|0.01699|0.07221|0.01767|0.007087|0.01731|0.02114|0.07221|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:238:0:0,0:122,116:238,0:0:2,0:34:1:35.7:1:1:0:60:46.6:1:0:0.1	0/1:303:138:66,72:79,85:164,138:0.4554:2,2:36.3:1:36.3:1:1:1.01386:60:68:0.4579:0:1.1
    1472. 

  1472. 4	20530564	20530564	C	A	intronic	SLIT2	.	.	.	0.	.	.	.	.	.	.	.	.	rs772089647	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	141	4	20530564	.	C	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.41961;SOR=0;LSEQ=TCTTTTTTTTGGTTTGAATT;RSEQ=TCAATAGGTACAGAAGATTA;CSQ=A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||15/36|NM_001289135.3:c.1451-8C>A|||||||rs772089647||1||EntrezGene||||||4:g.20530564C>A|1.221e-05|0|0|0|0|0|2.682e-05|0|0|2.682e-05|gnomAD_NFE|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||14/35|NM_001289136.3:c.1439-8C>A|||||||rs772089647||1||EntrezGene||||||4:g.20530564C>A|1.221e-05|0|0|0|0|0|2.682e-05|0|0|2.682e-05|gnomAD_NFE|||,A|splice_polypyrimidine_tract_variant&splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||15/36|NM_004787.4:c.1463-8C>A|||||||rs772089647||1||EntrezGene||YES||||4:g.20530564C>A|1.221e-05|0|0|0|0|0|2.682e-05|0|0|2.682e-05|gnomAD_NFE|||,A|downstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA||||||||||rs772089647|557|1||EntrezGene||YES||||4:g.20530564C>A|1.221e-05|0|0|0|0|0|2.682e-05|0|0|2.682e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:47:0:0,0:34,13:47,0:0:2,0:32.5:1:35.7:1:1:0:60:94:1:0:0.1	0/1:141:3:2,1:99,39:138,3:0.0213:2,2:38.3:1:37:0:1:1.26702:60:6:0.0216:0:2
    1473. 

  1473. 4	20530733	20530734	CC	-	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	221	4	20530732	.	TCC	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=123;VD=2;AF=0.0163;SHIFT3=3;MSI=5;MSILEN=1;SSF=0.12718;SOR=inf;LSEQ=ACTGCAGAGTTGTAAGTTCA;RSEQ=CCCAACAAAATTCTGGTTGG;CSQ=-|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||16/36|NM_001289135.3:c.1601+14_1601+15del|||||||||1||EntrezGene||||||4:g.20530736_20530737del||||||||||||||,-|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||15/35|NM_001289136.3:c.1589+14_1589+15del|||||||||1||EntrezGene||||||4:g.20530736_20530737del||||||||||||||,-|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||16/36|NM_004787.4:c.1613+14_1613+15del|||||||||1||EntrezGene||YES||||4:g.20530736_20530737del||||||||||||||,-|downstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA|||||||||||726|1||EntrezGene||YES||||4:g.20530736_20530737del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:123:2:1,1:47,74:121,2:0.0163:2,2:15.5:1:37:0:1:1.57:60:4:0.0164:0:0	0/0:221:0:0,0:79,142:221,0:0:2,0:38.6:1:36:1:1:0:60:54.25:1:0:0.1
    1474. 

  1474. 4	20533700	20533700	-	T	intronic	SLIT2	.	.	.	0.39	0.3331	0.2931	0.3656	0.42	0.3766	0.3683	0.3386	0.3567	rs5856564	rs5856564	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	174	44	4	20533700	.	A	AT	174	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=4;VD=4;AF=1;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.14084;SOR=inf;LSEQ=ATGTAAGTCACTTGTTAGCT;RSEQ=TTTTTTTTATTTCTGTAGCA;CSQ=T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||17/36|NM_001289135.3:c.1676+27dup|||||||rs3215198||1||EntrezGene||||||4:g.20533708dup|0.3316|0.2788|0.3634|0.384|0.3708|0.3519|0.3421|0.34|0.2342|0.384|gnomAD_ASJ|||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||16/35|NM_001289136.3:c.1664+27dup|||||||rs3215198||1||EntrezGene||||||4:g.20533708dup|0.3316|0.2788|0.3634|0.384|0.3708|0.3519|0.3421|0.34|0.2342|0.384|gnomAD_ASJ|||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||17/36|NM_004787.4:c.1688+27dup|||||||rs3215198||1||EntrezGene||YES||||4:g.20533708dup|0.3316|0.2788|0.3634|0.384|0.3708|0.3519|0.3421|0.34|0.2342|0.384|gnomAD_ASJ|||,T|downstream_gene_variant|MODIFIER|MIR218-1|407000|Transcript|NR_029631.1|miRNA||||||||||rs3215198|3693|1||EntrezGene||YES||||4:g.20533708dup|0.3316|0.2788|0.3634|0.384|0.3708|0.3519|0.3421|0.34|0.2342|0.384|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:4:4:2,2:0,0:0,4:1:0,2:25.6:1:38.7:0:1:0:62.8:8:1:0:0	1/0:44:26:10,15:1,1:2,26:0.5909:2,2:40.2:1:37.2:0:1:1.47706:60.4:52:0.5778:0:0
    1475. 

  1475. 4	20541038	20541038	T	C	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	125	4	20541038	.	T	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=25;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.69351;SOR=0;LSEQ=TGCCTGATGCTTTGTCTCCA;RSEQ=AACAATGTCCTTTTTTTCCC;CSQ=C|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||18/36|NM_001289135.3:c.1821-26T>C|||||||||1||EntrezGene||||||4:g.20541038T>C||||||||||||||,C|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||17/35|NM_001289136.3:c.1809-26T>C|||||||||1||EntrezGene||||||4:g.20541038T>C||||||||||||||,C|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||18/36|NM_004787.4:c.1833-26T>C|||||||||1||EntrezGene||YES||||4:g.20541038T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:25:0:0,0:15,10:25,0:0:2,0:32:1:36:1:1:0:60:50:1:0:0	0/1:125:2:1,1:77,46:123,2:0.016:2,2:39:1:37:0:1:1.66666:60:4:0.016:0:1
    1476. 

  1476. 4	20541201	20541201	C	A	exonic	SLIT2	.	nonsynonymous SNV	SLIT2:NM_001289135:exon18:c.C1958A:p.S653Y,SLIT2:NM_001289136:exon18:c.C1946A:p.S649Y,SLIT2:NM_004787:exon19:c.C1970A:p.S657Y	.	.	.	.	.	.	.	.	.	.	.	0.003	0.721	D	1.0	0.899	D	0.99	0.782	D	0.000	0.843	D	1	0.810	D	1.405	0.356	L	0.34	0.582	T	-3.75	0.711	D	0.942	0.937	-0.551	0.668	T	0.279	0.651	T	0.058	0.674	D	6.963	0.935	33	0.996	0.723	0.988	0.865	D	c	0.761	0.789	1.000	0.747	0.693	0.558	0	5.69	0.883	7.894	0.858	0.852	0.362	1.000	0.715	0.820	0.343	19.817	0.966	Leucine-rich repeat domain, L domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU88277858	ESAD-UK|1|409|0.00244499	0.25	37	140	4	20541201	.	C	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=7;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.90672;SOR=0;LSEQ=TGATACTCTCCATTCTTTAT;RSEQ=TACTCTGTAAGTATGAAAAA;CSQ=A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|19/37||NM_001289135.3:c.1958C>A|NP_001276064.1:p.Ser653Tyr|3869|1958|653|S/Y|tCt/tAt|||1||EntrezGene||||||4:g.20541201C>A||||||||||||||,A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|18/36||NM_001289136.3:c.1946C>A|NP_001276065.1:p.Ser649Tyr|3857|1946|649|S/Y|tCt/tAt|||1||EntrezGene||||||4:g.20541201C>A||||||||||||||,A|missense_variant|MODERATE|SLIT2|9353|Transcript|NM_004787.4|protein_coding|19/37||NM_004787.4:c.1970C>A|NP_004778.1:p.Ser657Tyr|3881|1970|657|S/Y|tCt/tAt|||1||EntrezGene||YES||||4:g.20541201C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:7:0:0,0:2,5:7,0:0:2,0:39:1:37:0:1:0:60:14:1:0:0	0/1:140:2:1,1:52,86:138,2:0.0143:2,2:11:1:37:0:1:1.65:60:4:0.0143:0:1
    1477. 

  1477. 4	20555394	20555394	A	G	intronic	SLIT2	.	.	.	0.0098	9.808e-05	0	0.0012	0	0	0	0.0001	0	rs773531041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	58	145	4	20555394	.	A	G	58	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=194;VD=3;AF=0.0155;SHIFT3=9;MSI=1;MSILEN=1;SSF=0.18617;SOR=inf;LSEQ=GTGTGTATGTGTGTGTGTGT;RSEQ=TGTGTGTGTGCTTCTGTGGT;CSQ=G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||25/36|NM_001289135.3:c.2550-34A>G|||||||rs773531041||1||EntrezGene||||||4:g.20555394A>G|0.0007721|0.00319|0.0003467|0.0002418|0.0006072|0.001298|0.0004708|0.0007622|0.0005501|0.00319|gnomAD_AFR|||,G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||24/35|NM_001289136.3:c.2538-34A>G|||||||rs773531041||1||EntrezGene||||||4:g.20555394A>G|0.0007721|0.00319|0.0003467|0.0002418|0.0006072|0.001298|0.0004708|0.0007622|0.0005501|0.00319|gnomAD_AFR|||,G|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||25/36|NM_004787.4:c.2562-34A>G|||||||rs773531041||1||EntrezGene||YES||||4:g.20555394A>G|0.0007721|0.00319|0.0003467|0.0002418|0.0006072|0.001298|0.0004708|0.0007622|0.0005501|0.00319|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:194:3:1,2:121,70:191,3:0.0155:2,2:31.3:1:37:0:0.55645:3.43419:60:6:0.0162:0:2.3	0/0:145:0:0,0:94,51:145,0:0:2,0:10:0:11:0:1:0:60:0:0:0:3
    1478. 

  1478. 4	20569189	20569189	A	-	exonic	SLIT2	.	frameshift deletion	SLIT2:NM_001289135:exon27:c.2887delA:p.K963Nfs*8,SLIT2:NM_001289136:exon27:c.2875delA:p.K959Nfs*8,SLIT2:NM_004787:exon28:c.2899delA:p.K967Nfs*8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	213	4	20569188	.	TA	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=37;VD=2;AF=0.0541;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.0214;SOR=inf;LSEQ=GCCTGCATCAGTAACCCATG;RSEQ=AACATGGAGGAACTTGCCAC;CSQ=-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|28/37||NM_001289135.3:c.2889del|NP_001276064.1:p.Lys963AsnfsTer8|4798|2887|963|K/X|Aaa/aa|||1||EntrezGene|||||2|4:g.20569191del||||||||||||||,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|27/36||NM_001289136.3:c.2877del|NP_001276065.1:p.Lys959AsnfsTer8|4786|2875|959|K/X|Aaa/aa|||1||EntrezGene|||||2|4:g.20569191del||||||||||||||,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_004787.4|protein_coding|28/37||NM_004787.4:c.2901del|NP_004778.1:p.Lys967AsnfsTer8|4810|2899|967|K/X|Aaa/aa|||1||EntrezGene||YES|||2|4:g.20569191del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:37:2:1,1:11,24:35,2:0.0541:2,2:26.5:1:37:0:1:2.13:60:4:0.0541:0:1	0/0:213:0:0,0:103,110:213,0:0:2,0:40.4:1:36:1:1:0:60:70:1:0:0.1
    1479. 

  1479. 4	20569210	20569210	T	C	exonic	SLIT2	.	synonymous SNV	SLIT2:NM_001289135:exon27:c.T2908C:p.L970L,SLIT2:NM_001289136:exon27:c.T2896C:p.L966L,SLIT2:NM_004787:exon28:c.T2920C:p.L974L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	214	4	20569210	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=2;AF=0.0714;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.01296;SOR=inf;LSEQ=AACATGGAGGAACTTGCCAC;RSEQ=TAAAGGAAGGAGAAGAAGAT;CSQ=C|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|28/37||NM_001289135.3:c.2908T>C|NP_001276064.1:p.Leu970%3D|4819|2908|970|L|Tta/Cta|||1||EntrezGene||||||4:g.20569210T>C||||||||||||||,C|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|27/36||NM_001289136.3:c.2896T>C|NP_001276065.1:p.Leu966%3D|4807|2896|966|L|Tta/Cta|||1||EntrezGene||||||4:g.20569210T>C||||||||||||||,C|synonymous_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding|28/37||NM_004787.4:c.2920T>C|NP_004778.1:p.Leu974%3D|4831|2920|974|L|Tta/Cta|||1||EntrezGene||YES||||4:g.20569210T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:28:2:1,1:8,18:26,2:0.0714:2,2:52:1:37:0:1:2.18:60:4:0.0714:0:1	0/0:214:0:0,0:98,116:214,0:0:2,0:41:1:36.1:1:1:0:60:106:1:0:0.1
    1480. 

  1480. 4	20597261	20597261	C	T	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	271	4	20597261	.	C	T	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=138;VD=4;AF=0.029;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.01259;SOR=inf;LSEQ=CATTGTGTCTAGATAAAATG;RSEQ=ATTGTTTACTTATTTTGGCT;CSQ=T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||30/36|NM_001289135.3:c.3171-59C>T|||||||||1||EntrezGene||||||4:g.20597261C>T||||||||||||||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||29/35|NM_001289136.3:c.3159-59C>T|||||||||1||EntrezGene||||||4:g.20597261C>T||||||||||||||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||30/36|NM_004787.4:c.3183-59C>T|||||||||1||EntrezGene||YES||||4:g.20597261C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:138:4:3,1:97,37:134,4:0.029:2,2:25.5:1:37:0:1:1.14:60:8:0.0292:0:1	0/0:271:0:0,0:187,84:271,0:0:2,0:37.4:1:35.8:1:1:0:60:44.167:1:0:0.1
    1481. 

  1481. 4	20597464	20597464	G	A	intronic	SLIT2	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	271	4	20597464	.	G	A	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=2;AF=0.0135;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.12422;SOR=inf;LSEQ=CCCGAAGGTTACAGGTAAAA;RSEQ=CAGAAATGAATAAGACCTAG;CSQ=A|splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||31/36|NM_001289135.3:c.3308+7G>A|||||||||1||EntrezGene||||||4:g.20597464G>A||||||||||||||,A|splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||30/35|NM_001289136.3:c.3296+7G>A|||||||||1||EntrezGene||||||4:g.20597464G>A||||||||||||||,A|splice_region_variant&intron_variant|LOW|SLIT2|9353|Transcript|NM_004787.4|protein_coding||31/36|NM_004787.4:c.3320+7G>A|||||||||1||EntrezGene||YES||||4:g.20597464G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:148:2:1,1:36,110:146,2:0.0135:2,2:7:0:37:0:0.43878:3.03:60:4:0.0138:0:1	0/0:271:0:0,0:91,178:269,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1482. 

  1482. 4	20598244	20598244	C	-	exonic	SLIT2	.	frameshift deletion	SLIT2:NM_001289135:exon31:c.3515delC:p.K1173Rfs*8,SLIT2:NM_001289136:exon31:c.3503delC:p.K1169Rfs*8,SLIT2:NM_004787:exon32:c.3527delC:p.K1177Rfs*8	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	220	4	20598243	.	GC	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=53;VD=2;AF=0.0377;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.03711;SOR=inf;LSEQ=CTTATCTTCAGATTCCTTCA;RSEQ=CAAGGTTCGGCCTCAGACGA;CSQ=-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|32/37||NM_001289135.3:c.3516del|NP_001276064.1:p.Lys1173ArgfsTer8|5426|3515|1172|A/X|gCc/gc|||1||EntrezGene|||||1|4:g.20598245del||||||||||||||,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|31/36||NM_001289136.3:c.3504del|NP_001276065.1:p.Lys1169ArgfsTer8|5414|3503|1168|A/X|gCc/gc|||1||EntrezGene|||||1|4:g.20598245del||||||||||||||,-|frameshift_variant|HIGH|SLIT2|9353|Transcript|NM_004787.4|protein_coding|32/37||NM_004787.4:c.3528del|NP_004778.1:p.Lys1177ArgfsTer8|5438|3527|1176|A/X|gCc/gc|||1||EntrezGene||YES|||1|4:g.20598245del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:53:2:1,1:12,39:51,2:0.0377:2,2:38.5:1:37:0:0.43396:3.16:60:4:0.0377:0:0	0/0:220:0:0,0:81,139:220,0:0:2,0:37.9:1:36.4:1:1:0:60:109:1:0:0.1
    1483. 

  1483. 4	20611617	20611617	-	T	intronic	SLIT2	.	.	.	0.036	0.0100	0.0338	0.0037	0	0	0	0.0005	0.0010	rs374661023	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5	61	159	4	20611617	.	A	AT	61	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Insertion;DP=24;VD=2;AF=0.0833;SHIFT3=9;MSI=10;MSILEN=1;SSF=0.12887;SOR=4.66399;LSEQ=AGAAAATGGAAGAATCAGCC;RSEQ=TTTTTTTTTCCGTTGTAGTG;CSQ=T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||33/36|NM_001289135.3:c.3681-10dup|||||||rs374661023||1||EntrezGene||||||4:g.20611626dup|0.005162|0.04166|0.004868|0.004215|0.002979|0.0006049|0.001807|0.005327|0.001953|0.04166|gnomAD_AFR|||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||32/35|NM_001289136.3:c.3669-10dup|||||||rs374661023||1||EntrezGene||||||4:g.20611626dup|0.005162|0.04166|0.004868|0.004215|0.002979|0.0006049|0.001807|0.005327|0.001953|0.04166|gnomAD_AFR|||,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||33/36|NM_004787.4:c.3693-10dup|||||||rs374661023||1||EntrezGene||YES||||4:g.20611626dup|0.005162|0.04166|0.004868|0.004215|0.002979|0.0006049|0.001807|0.005327|0.001953|0.04166|gnomAD_AFR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:24:2:1,1:16,6:22,2:0.0833:2,2:59:1:39:0:0.50725:2.54484:63.2:4:0.0909:0:0	0/1:159:3:3,0:106,43:149,3:0.0189:2,0:32.7:1:39:0:0.55891:0:63.2:6:0.0207:0:0.4
    1484. 

  1484. 4	20611818	20611818	C	T	intronic	SLIT2	.	.	.	0.36	0.1115	0.0380	0.3026	0.0861	0.3531	0.1325	0.1114	0.1426	rs35891001	rs35891001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56594744;OCCURENCE=1(haematopoietic_and_lymphoid_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU778803	COCA-CN|3|321|0.00934579	0.5	238	93	4	20611818	.	C	T	238	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=46;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTTCCAAATTCAGGTGGT;RSEQ=CTGAAACCCTGTGATTCTCA;CSQ=T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding||34/36|NM_001289135.3:c.3835+28C>T|||||||rs35891001&COSV56594744||1||EntrezGene||||||4:g.20611818C>T|0.1572|0.03741|0.3074|0.1412|0.3529|0.1328|0.1086|0.1562|0.1416|0.3591|EAS||0&1|0&1,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding||33/35|NM_001289136.3:c.3823+28C>T|||||||rs35891001&COSV56594744||1||EntrezGene||||||4:g.20611818C>T|0.1572|0.03741|0.3074|0.1412|0.3529|0.1328|0.1086|0.1562|0.1416|0.3591|EAS||0&1|0&1,T|intron_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding||34/36|NM_004787.4:c.3847+28C>T|||||||rs35891001&COSV56594744||1||EntrezGene||YES||||4:g.20611818C>T|0.1572|0.03741|0.3074|0.1412|0.3529|0.1328|0.1086|0.1562|0.1416|0.3591|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:46:0:0,0:15,31:46,0:0:2,0:32.4:1:36.2:1:1:0:60:45:1:0:0.2	1/1:93:93:17,76:0,0:0,93:1:0,2:33:1:36.5:1:1:0:60:186:1:0:1.1
    1485. 

  1485. 4	20620683	20620683	G	A	UTR3	SLIT2	NM_004787:c.*51G>A;NM_001289136:c.*51G>A;NM_001289135:c.*51G>A	.	.	0.99	0.8601	0.9603	0.9007	0.8344	0.8410	0.8137	0.8160	0.8092	rs1379659	rs1379659	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU26842522	COCA-CN|5|321|0.0155763	0.75	256	145	4	20620683	.	G	A	256	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=234;VD=88;AF=0.3761;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=0;LSEQ=AGGTTGTATACTTCTTGACC;RSEQ=TGTGGGACTAATGAATGCTT;CSQ=A|3_prime_UTR_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289135.3|protein_coding|37/37||NM_001289135.3:c.*51G>A||6540|||||rs1379659||1||EntrezGene||||||4:g.20620683G>A|0.8461|0.9681|0.9137|0.8411|0.8329|0.8167|0.8067|0.8343|0.8828|0.9924|AFR|||1,A|3_prime_UTR_variant|MODIFIER|SLIT2|9353|Transcript|NM_001289136.3|protein_coding|36/36||NM_001289136.3:c.*51G>A||6528|||||rs1379659||1||EntrezGene||||||4:g.20620683G>A|0.8461|0.9681|0.9137|0.8411|0.8329|0.8167|0.8067|0.8343|0.8828|0.9924|AFR|||1,A|3_prime_UTR_variant|MODIFIER|SLIT2|9353|Transcript|NM_004787.4|protein_coding|37/37||NM_004787.4:c.*51G>A||6552|||||rs1379659||1||EntrezGene||YES||||4:g.20620683G>A|0.8461|0.9681|0.9137|0.8411|0.8329|0.8167|0.8067|0.8343|0.8828|0.9924|AFR|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:234:88:17,71:33,113:146,88:0.3761:2,2:24.1:1:36.3:1:0.62295:1.21866:60:176:0.381:0:1.2	1/1:145:145:42,103:0,0:0,145:1:0,2:33.2:1:35.7:1:1:0:60:71.5:1:0:1.1
    1486. 

  1486. 4	41747792	41747794	CGC	-	UTR3	PHOX2B	NM_003924:c.*32_*30delGCG	.	.	0.042	3.269e-05	0	0	0	0	0.0003	0	0	rs763380864	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU76678351	GACA-JP|2|585|0.0034188	0.5	157	182	4	41747791	.	TCGC	T	157	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=1792;VD=19;AF=0.0106;SHIFT3=18;MSI=7;MSILEN=3;SSF=0.33107;SOR=0.63958;LSEQ=GGGCCCTGGCTCGCCCGCTG;RSEQ=CGCCGCCGCCGCCGCCGCAG;CSQ=-|3_prime_UTR_variant|MODIFIER|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.*30_*32del||1090-1092|||||rs763380864||-1||EntrezGene||YES||||4:g.41747810_41747812del|0.001263|0.003313|0.00119|0.000615|0.002175|0.0004739|0.001232|0.001145|0.000981|0.04243|EA|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:1792:19:11,8:1033,734:1767,19:0.0106:2,2:39.3:1:37:1:1:1.02353:60:38:0.0107:0.0006:0.2	0/1:182:3:2,1:119,60:179,3:0.0165:2,2:61.3:1:37:0:1:1.01:60:6:0.0168:0:0
    1487. 

  1487. 4	41747966	41747966	C	-	exonic	PHOX2B	.	frameshift deletion	PHOX2B:NM_003924:exon3:c.803delG:p.G268Afs*41	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	180	4	41747965	.	GC	G	74	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Deletion;DP=873;VD=1;AF=0.0011;SHIFT3=4;MSI=5;MSILEN=1;SSF=0.00359;SOR=0.05068;LSEQ=GGAGCCCAGCCTTGTCCAGG;RSEQ=CCCCAGCCGCAGCCAGGCCT;CSQ=-|frameshift_variant|HIGH|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.803del|NP_003915.2:p.Gly268AlafsTer41|918|803|268|G/X|gGc/gc|||-1||EntrezGene||YES||||4:g.41747970del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:873:1:0,1:308,564:872,1:0.0011:2,0:39:0:37:0:1:0:60:2:0.0012:0:0	0/1:180:4:2,2:58,118:176,4:0.0222:2,2:39.5:1:37:0:0.60162:2.03:60:8:0.0222:0:0
    1488. 

  1488. 4	41748007	41748007	T	G	exonic	PHOX2B	.	synonymous SNV	PHOX2B:NM_003924:exon3:c.A762C:p.A254A	0.099	0.0356	0.0749	0.0092	0.0085	0.0917	0.0032	0.0107	0.0169	rs17884724	rs17884724	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99891459;OCCURENCE=1(stomach)	173810	Congenital_central_hypoventilation|Neuroblastoma_2|Hereditary_cancer-predisposing_syndrome|not_specified|none_provided|not_provided	MONDO:MONDO:0008852,MedGen:C1275808,OMIM:209880,Orphanet:ORPHA661,SNOMED_CT:399040002|MONDO:MONDO:0013082,MedGen:C2751682,OMIM:613013,Orphanet:ORPHA2151|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN235283|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	1	1	MU114340806	LAML-KR|1|205|0.00487805,GACA-JP|1|585|0.0017094	0.25	210	110	4	41748007	.	T	G	210	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=279;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=6;SSF=0;SOR=0;LSEQ=CCAGCTGCCGCCGCTGCCGC;RSEQ=GCCGCCGCCGCCGCTGCCGC;CSQ=G|synonymous_variant|LOW|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.762A>C|NP_003915.2:p.Ala254%3D|877|762|254|A|gcA/gcC|rs17884724&COSV99891459||-1||EntrezGene||YES||||4:g.41748007T>G|0.005721|0.01309|0.007853|0.004513|0.02304|0.002475|0.004764|0.006098|0.009081|0.0992|EAS|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:279:0:0,0:39,240:279,0:0:2,0:27.4:1:35.5:1:1:0:60:45.5:1:0:0.2	0/1:110:53:9,44:14,43:57,53:0.4818:2,2:36.2:1:36.8:1:0.35772:1.58504:60:106:0.4862:0:1.2
    1489. 

  1489. 4	41748108	41748108	C	T	exonic	PHOX2B	.	nonsynonymous SNV	PHOX2B:NM_003924:exon3:c.G661A:p.A221T	0.	.	.	.	.	.	.	.	.	rs746684161	.	0.345	0.125	T	0.001	0.067	B	0.001	0.040	B	0.209	0.164	N	1	0.090	N	-0.345	0.033	N	-1.15	0.780	T	0.3	0.041	N	0.277	0.335	-1.025	0.221	T	0.151	0.479	T	0.185	0.858	D	-0.055	0.088	2.088	0.830	0.140	0.213	0.211	N	c	-1.299	-1.298	0.774	0.237	0.598	0.340	0	0.302	0.150	0.376	0.201	-0.172	0.105	0.246	0.246	0.133	0.200	0.977	0.013	.	.	.	.	632218	Hereditary_cancer-predisposing_syndrome|Haddad_syndrome	MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MONDO:MONDO:0020493,MedGen:C1859049,Orphanet:ORPHA99803	criteria_provided,_multiple_submitters,_no_conflicts	Uncertain_significance	Uncertain significance	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	31	28	4	41748108	.	C	T	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=2;AF=0.0267;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.52827;SOR=inf;LSEQ=CGCCGCCCCCGGAGCTCCAG;RSEQ=CGGGCTGGGCCCGCCGCCGC;CSQ=T|missense_variant|MODERATE|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.661G>A|NP_003915.2:p.Ala221Thr|776|661|221|A/T|Gct/Act|rs746684161||-1||EntrezGene||YES||||4:g.41748108C>T|1.063e-05|0|0|0|0|0|2.272e-05|0|0|2.272e-05|gnomAD_NFE|uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:75:2:1,1:53,20:73,2:0.0267:2,2:45:1:31:1:0.48432:2.61042:60:4:0.0267:0:1	0/0:28:0:0,0:10,18:28,0:0:2,0:32.6:1:35.2:1:1:0:60:27:1:0:0.5
    1490. 

  1490. 4	41748119	41748121	CCG	-	exonic	PHOX2B	.	nonframeshift deletion	PHOX2B:NM_003924:exon3:c.648_650del:p.G217del	0.0072	3.513e-05	0	0	0	0	0	7.045e-05	0	rs760638643	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	95	27	4	41748118	.	CCCG	C	95	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=98;VD=6;AF=0.0612;SHIFT3=11;MSI=4;MSILEN=3;SSF=0.22441;SOR=inf;LSEQ=GGAGCTCCAGCCGGGCTGGG;RSEQ=CCGCCGCCGCCTCCATTCGC;CSQ=-|inframe_deletion|MODERATE|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.648_650del|NP_003915.2:p.Gly217del|763-765|648-650|216-217|GG/G|ggCGGg/ggg|rs760638643||-1||EntrezGene||YES||||4:g.41748130_41748132del|0.0003539|0.0004653|0.0005771|0.0002314|0.0005757|7.338e-05|0.0002921|0.0008288|0.0002597|0.007225|AA|||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:98:6:4,2:60,32:92,6:0.0612:2,2:25.5:1:37:1:1:1.07:60:12:0.0612:0.0102:0	0/0:27:0:0,0:11,16:27,0:0:2,0:34.1:1:36.6:1:1:0:60:54:1:0:0.5
    1491. 

  1491. 4	41748147	41748147	A	C	exonic	PHOX2B	.	nonsynonymous SNV	PHOX2B:NM_003924:exon3:c.T622G:p.C208G	.	.	.	.	.	.	.	.	.	.	.	0.072	0.349	T	0.0	0.026	B	0.0	0.013	B	0.000	0.629	D	1.000	0.494	D	0.975	0.246	L	1.51	0.309	T	-1.13	0.291	N	0.332	0.393	-1.080	0.074	T	0.038	0.165	T	0.018	0.407	T	-0.233	0.073	0.934	0.385	0.026	0.977	0.766	D	c	-0.607	-0.535	0.940	0.274	0.598	0.340	0	3.19	0.356	1.148	0.310	1.002	0.622	1.000	0.715	0.943	0.417	7.936	0.289	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	28	4	41748147	.	A	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=2;AF=0.0127;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.71951;SOR=inf;LSEQ=GCCGCCTCCATTCGCCCCGC;RSEQ=GCTGGGGGTGGGGTTGGGAT;CSQ=C|missense_variant|MODERATE|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|3/3||NM_003924.4:c.622T>G|NP_003915.2:p.Cys208Gly|737|622|208|C/G|Tgc/Ggc|||-1||EntrezGene||YES||||4:g.41748147A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:157:2:1,1:104,51:155,2:0.0127:2,2:37.5:1:37:0:1:2.02926:60:4:0.0132:0:1	0/0:28:0:0,0:13,15:28,0:0:2,0:36.2:1:34.4:1:1:0:60:27:1:0:0.4
    1492. 

  1492. 4	41749438	41749438	C	A	exonic	PHOX2B	.	nonsynonymous SNV	PHOX2B:NM_003924:exon2:c.G357T:p.E119D	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	0.999	0.764	D	0.992	0.790	D	0.000	0.843	D	1	0.810	D	1.26	0.320	L	-3.99	0.963	D	-2.78	0.589	D	0.317	0.555	-0.901	0.479	T	0.173	0.516	T	0.147	0.830	D	4.857	0.652	24.9	0.997	0.808	0.970	0.721	D	c	-0.023	0.073	1.000	0.402	0.598	0.340	0	4.56	0.555	2.019	0.404	0.061	0.167	1.000	0.715	0.989	0.536	14.470	0.669	Homeobox domain|Homeodomain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	129	4	41749438	.	C	A	37	v3;f0.01;pSTD;q22.5;SN1.5	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1672;VD=1;AF=0.0006;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.01456;SOR=0.0382;LSEQ=TAGATGTCGGGGTAGTGAGT;RSEQ=TCCGCGAAGACCCTTTCCAG;CSQ=A|missense_variant|MODERATE|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|2/3||NM_003924.4:c.357G>T|NP_003915.2:p.Glu119Asp|472|357|119|E/D|gaG/gaT|COSV99891713||-1||EntrezGene||YES||||4:g.41749438C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1672:1:1,0:972,699:1671,1:0.0006:2,0:25:0:11:0:1:0:60:0:0:0:4	0/1:129:2:1,1:71,56:127,2:0.0155:2,2:25.5:1:37:0:1:1.2655:60:4:0.0156:0:1
    1493. 

  1493. 4	41749457	41749457	A	G	exonic	PHOX2B	.	nonsynonymous SNV	PHOX2B:NM_003924:exon2:c.T338C:p.L113P	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.843	D	1	0.810	D	4.995	0.999	H	-6.23	0.996	D	-6.61	0.921	D	0.894	0.982	0.833	0.948	D	0.733	0.909	D	0.753	0.980	D	5.303	0.717	25.8	0.997	0.813	0.990	0.901	D	c	0.773	0.727	1.000	0.747	0.598	0.340	0	5.4	0.779	9.319	0.954	1.199	0.960	1.000	0.715	0.994	0.587	15.590	0.762	Homeobox domain|Homeodomain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	152	4	41749457	.	A	G	37	v3;f0.01	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1937;VD=2;AF=0.001;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02863;SOR=0.07776;LSEQ=TCTCCGCGAAGACCCTTTCC;RSEQ=GCTCTTTGAGCTGGGCACTG;CSQ=G|missense_variant|MODERATE|PHOX2B|8929|Transcript|NM_003924.4|protein_coding|2/3||NM_003924.4:c.338T>C|NP_003915.2:p.Leu113Pro|453|338|113|L/P|cTg/cCg|||-1||EntrezGene||YES||||4:g.41749457A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1937:2:1,1:1131,800:1931,2:0.001:2,2:43.5:1:37:0:1:1.41347:60:4:0.0011:0:1	0/1:152:2:1,1:81,69:150,2:0.0132:2,2:30.5:1:37:0:1:1.17267:60:4:0.0139:0:1
    1494. 

  1494. 4	55130078	55130078	T	C	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347827:exon4:c.T612C:p.N204N,PDGFRA:NM_001347829:exon4:c.T612C:p.N204N,PDGFRA:NM_001347830:exon4:c.T651C:p.N217N,PDGFRA:NM_006206:exon4:c.T612C:p.N204N,PDGFRA:NM_001347828:exon5:c.T687C:p.N229N	0.43	0.1677	0.2562	0.3759	0.07	0.1780	0.1216	0.1175	0.1487	rs2229307	rs2229307	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57264195;OCCURENCE=2(meninges),3(large_intestine),1(haematopoietic_and_lymphoid_tissue),6(soft_tissue)	251492	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU12032527	LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.25	235	198	4	55130078	.	T	C	235	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCCAGACCATCCCATTTAA;RSEQ=GTTTATGCTTTAAAAGGTAC;CSQ=C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|4/17||NM_001347827.2:c.612T>C|NP_001334756.1:p.Asn204%3D|747|612|204|N|aaT/aaC|rs2229307&COSV57264195||1||EntrezGene||||||4:g.55130078T>C|0.1862|0.2596|0.4138|0.07124|0.1787|0.1246|0.1215|0.1476|0.2236|0.4138|gnomAD_AMR|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|5/24||NM_001347828.2:c.687T>C|NP_001334757.1:p.Asn229%3D|825|687|229|N|aaT/aaC|rs2229307&COSV57264195||1||EntrezGene||YES||||4:g.55130078T>C|0.1862|0.2596|0.4138|0.07124|0.1787|0.1246|0.1215|0.1476|0.2236|0.4138|gnomAD_AMR|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|4/23||NM_001347829.2:c.612T>C|NP_001334758.1:p.Asn204%3D|968|612|204|N|aaT/aaC|rs2229307&COSV57264195||1||EntrezGene||||||4:g.55130078T>C|0.1862|0.2596|0.4138|0.07124|0.1787|0.1246|0.1215|0.1476|0.2236|0.4138|gnomAD_AMR|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|4/23||NM_001347830.2:c.651T>C|NP_001334759.1:p.Asn217%3D|1163|651|217|N|aaT/aaC|rs2229307&COSV57264195||1||EntrezGene||||||4:g.55130078T>C|0.1862|0.2596|0.4138|0.07124|0.1787|0.1246|0.1215|0.1476|0.2236|0.4138|gnomAD_AMR|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|4/23||NM_006206.6:c.612T>C|NP_006197.1:p.Asn204%3D|747|612|204|N|aaT/aaC|rs2229307&COSV57264195||1||EntrezGene||||||4:g.55130078T>C|0.1862|0.2596|0.4138|0.07124|0.1787|0.1246|0.1215|0.1476|0.2236|0.4138|gnomAD_AMR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:82:0:0,0:27,55:82,0:0:2,0:25.2:1:36.6:1:1:0:60:164:1:0:0.2	1/0:198:100:31,69:37,61:98,100:0.5051:2,2:32.3:1:35.5:1:0.36977:1.34801:60:32.333:0.4974:0:1.4
    1495. 

  1495. 4	55130108	55130108	C	A	intronic	PDGFRA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	137	4	55130108	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=28;VD=2;AF=0.0714;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02794;SOR=inf;LSEQ=TTAAAAGGTACTTGTATCAT;RSEQ=TCCTTCCTTCTTTAAATAAG;CSQ=A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||4/16|NM_001347827.2:c.628+14C>A|||||||||1||EntrezGene||||||4:g.55130108C>A||||||||||||||,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||5/23|NM_001347828.2:c.703+14C>A|||||||||1||EntrezGene||YES||||4:g.55130108C>A||||||||||||||,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||4/22|NM_001347829.2:c.628+14C>A|||||||||1||EntrezGene||||||4:g.55130108C>A||||||||||||||,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||4/22|NM_001347830.2:c.667+14C>A|||||||||1||EntrezGene||||||4:g.55130108C>A||||||||||||||,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||4/22|NM_006206.6:c.628+14C>A|||||||||1||EntrezGene||||||4:g.55130108C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:28:2:1,1:11,15:26,2:0.0714:2,2:8.5:1:37:0:1:1.35:60:4:0.0741:0:1	0/0:137:0:0,0:33,104:137,0:0:2,0:34.6:1:35.7:1:1:0:60:33.25:1:0:0.9
    1496. 

  1496. 4	55131039	55131039	G	-	intronic	PDGFRA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	130	4	55131038	.	TG	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=55;VD=2;AF=0.0364;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.08725;SOR=inf;LSEQ=ACCCAAACTTTATAAGATCC;RSEQ=GCTATCCTGTGGATTTTTAG;CSQ=-|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||4/16|NM_001347827.2:c.629-46del|||||||||1||EntrezGene||||||4:g.55131040del||||||||||||||,-|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||5/23|NM_001347828.2:c.704-46del|||||||||1||EntrezGene||YES||||4:g.55131040del||||||||||||||,-|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||4/22|NM_001347829.2:c.629-46del|||||||||1||EntrezGene||||||4:g.55131040del||||||||||||||,-|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||4/22|NM_001347830.2:c.668-46del|||||||||1||EntrezGene||||||4:g.55131040del||||||||||||||,-|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||4/22|NM_006206.6:c.629-46del|||||||||1||EntrezGene||||||4:g.55131040del||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:55:2:1,1:40,13:53,2:0.0364:2,2:15:0:37:0:0.44781:3.00181:60:4:0.0377:0:0	0/0:130:0:0,0:98,32:130,0:0:2,0:28.6:1:34.3:1:1:0:60:17.571:1:0:0.6
    1497. 

  1497. 4	55131088	55131088	A	G	exonic	PDGFRA	.	nonsynonymous SNV	PDGFRA:NM_001347827:exon5:c.A631G:p.T211A,PDGFRA:NM_001347829:exon5:c.A631G:p.T211A,PDGFRA:NM_001347830:exon5:c.A670G:p.T224A,PDGFRA:NM_006206:exon5:c.A631G:p.T211A,PDGFRA:NM_001347828:exon6:c.A706G:p.T236A	.	.	.	.	.	.	.	.	.	.	.	0.285	0.152	T	0.0	0.067	B	0.003	0.080	B	0.005	0.328	U	1	0.810	D	1.78	0.463	L	-0.86	0.745	T	0.21	0.048	N	0.065	0.056	-0.929	0.442	T	0.220	0.583	T	0.010	0.267	T	0.955	0.185	10.40	0.930	0.221	0.844	0.432	D	c	-0.414	-0.255	0.998	0.367	0.598	0.340	0	2.85	0.322	3.183	0.504	0.196	0.251	0.993	0.376	0.079	0.180	9.125	0.358	Immunoglobulin-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	201	4	55131088	.	A	G	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=124;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.38177;SOR=0;LSEQ=ATTTGTTCTTTTTTATAGCA;RSEQ=CATCAGAGCTGGATCTAGAA;CSQ=G|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|5/17||NM_001347827.2:c.631A>G|NP_001334756.1:p.Thr211Ala|766|631|211|T/A|Aca/Gca|rs1170188252||1||EntrezGene||||||4:g.55131088A>G|3.978e-06|0|0|0|0|0|8.794e-06|0|0|8.794e-06|gnomAD_NFE|||,G|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|6/24||NM_001347828.2:c.706A>G|NP_001334757.1:p.Thr236Ala|844|706|236|T/A|Aca/Gca|rs1170188252||1||EntrezGene||YES||||4:g.55131088A>G|3.978e-06|0|0|0|0|0|8.794e-06|0|0|8.794e-06|gnomAD_NFE|||,G|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|5/23||NM_001347829.2:c.631A>G|NP_001334758.1:p.Thr211Ala|987|631|211|T/A|Aca/Gca|rs1170188252||1||EntrezGene||||||4:g.55131088A>G|3.978e-06|0|0|0|0|0|8.794e-06|0|0|8.794e-06|gnomAD_NFE|||,G|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|5/23||NM_001347830.2:c.670A>G|NP_001334759.1:p.Thr224Ala|1182|670|224|T/A|Aca/Gca|rs1170188252||1||EntrezGene||||||4:g.55131088A>G|3.978e-06|0|0|0|0|0|8.794e-06|0|0|8.794e-06|gnomAD_NFE|||,G|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|5/23||NM_006206.6:c.631A>G|NP_006197.1:p.Thr211Ala|766|631|211|T/A|Aca/Gca|rs1170188252||1||EntrezGene||||||4:g.55131088A>G|3.978e-06|0|0|0|0|0|8.794e-06|0|0|8.794e-06|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:124:0:0,0:87,37:124,0:0:2,0:36.8:1:36.2:1:1:0:60:61:1:0:0.4	0/1:201:2:1,1:119,79:198,2:0.01:2,2:17:1:31:1:1:1.50312:60:4:0.0103:0:1
    1498. 

  1498. 4	55133726	55133726	T	G	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347827:exon7:c.T939G:p.G313G,PDGFRA:NM_001347829:exon7:c.T939G:p.G313G,PDGFRA:NM_001347830:exon7:c.T978G:p.G326G,PDGFRA:NM_006206:exon7:c.T939G:p.G313G,PDGFRA:NM_001347828:exon8:c.T1014G:p.G338G	0.43	0.1669	0.2557	0.3747	0.0662	0.1782	0.1219	0.1162	0.1472	rs4358459	rs4358459	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57264201;OCCURENCE=1(oesophagus),2(meninges),3(large_intestine),1(central_nervous_system),1(haematopoietic_and_lymphoid_tissue),6(soft_tissue),1(pancreas)	251493	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU12032533	LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526,ESCA-CN|1|332|0.00301205	0.25	242	222	4	55133726	.	T	G	242	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=511;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCCCTGTACAGAGAAAGG;RSEQ=TTCATTGAAATCAAACCCAC;CSQ=G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|7/17||NM_001347827.2:c.939T>G|NP_001334756.1:p.Gly313%3D|1074|939|313|G|ggT/ggG|rs4358459&COSV57264201||1||EntrezGene||||||4:g.55133726T>G|0.1848|0.2572|0.4114|0.06651|0.1793|0.1246|0.12|0.1451|0.2238|0.4114|gnomAD_AMR|benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|8/24||NM_001347828.2:c.1014T>G|NP_001334757.1:p.Gly338%3D|1152|1014|338|G|ggT/ggG|rs4358459&COSV57264201||1||EntrezGene||YES||||4:g.55133726T>G|0.1848|0.2572|0.4114|0.06651|0.1793|0.1246|0.12|0.1451|0.2238|0.4114|gnomAD_AMR|benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|7/23||NM_001347829.2:c.939T>G|NP_001334758.1:p.Gly313%3D|1295|939|313|G|ggT/ggG|rs4358459&COSV57264201||1||EntrezGene||||||4:g.55133726T>G|0.1848|0.2572|0.4114|0.06651|0.1793|0.1246|0.12|0.1451|0.2238|0.4114|gnomAD_AMR|benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|7/23||NM_001347830.2:c.978T>G|NP_001334759.1:p.Gly326%3D|1490|978|326|G|ggT/ggG|rs4358459&COSV57264201||1||EntrezGene||||||4:g.55133726T>G|0.1848|0.2572|0.4114|0.06651|0.1793|0.1246|0.12|0.1451|0.2238|0.4114|gnomAD_AMR|benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|7/23||NM_006206.6:c.939T>G|NP_006197.1:p.Gly313%3D|1074|939|313|G|ggT/ggG|rs4358459&COSV57264201||1||EntrezGene||||||4:g.55133726T>G|0.1848|0.2572|0.4114|0.06651|0.1793|0.1246|0.12|0.1451|0.2238|0.4114|gnomAD_AMR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:511:0:0,0:253,257:510,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:222:103:61,42:58,61:119,103:0.464:2,2:32.8:1:36.3:1:0.13821:1.52:60:50.5:0.4591:0:1.1
    1499. 

  1499. 4	55133936	55133936	C	TT	intronic	PDGFRA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	85	93	4	55133936	.	C	TT	85	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Complex;DP=289;VD=0;AF=0;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00079;SOR=0;LSEQ=AACTCTCTGCCCAAGTATGC;RSEQ=TTTTTTTAGTGTGCATCAGA;CSQ=TT|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||7/16|NM_001347827.2:c.1121+28delinsTT|||||||COSV99956060||1||EntrezGene||||||4:g.55133936delinsTT|||||||||||||1|1,TT|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||8/23|NM_001347828.2:c.1196+28delinsTT|||||||COSV99956060||1||EntrezGene||YES||||4:g.55133936delinsTT|||||||||||||1|1,TT|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||7/22|NM_001347829.2:c.1121+28delinsTT|||||||COSV99956060||1||EntrezGene||||||4:g.55133936delinsTT|||||||||||||1|1,TT|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||7/22|NM_001347830.2:c.1160+28delinsTT|||||||COSV99956060||1||EntrezGene||||||4:g.55133936delinsTT|||||||||||||1|1,TT|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||7/22|NM_006206.6:c.1121+28delinsTT|||||||COSV99956060||1||EntrezGene||||||4:g.55133936delinsTT|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:289:0:0,0:76,213:289,0:0:2,0:37.6:1:35.6:1:1:0:60:47.167:1:0:0.1	0/1:93:5:2,3:25,63:88,5:0.0538:2,2:28.6:1:37:1:0.62557:1.67:60:10:0.0549:0.0323:1.2
    1500. 

  1500. 4	55133959	55133959	C	T	intronic	PDGFRA	.	.	.	0.43	0.1625	0.2515	0.3696	0.0662	0.1702	0.1122	0.1138	0.1370	rs28650939	rs28650939	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57264774;OCCURENCE=2(meninges),2(large_intestine)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU24769283	LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	189	73	4	55133959	.	C	T	189	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=207;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTTTAGTGTGCATCAGAGG;RSEQ=GGACTGAGGTTTGTGTGTGT;CSQ=T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||7/16|NM_001347827.2:c.1121+51C>T|||||||rs28650939&COSV57264774||1||EntrezGene||||||4:g.55133959C>T|0.1831|0.2535|0.4067|0.06599|0.1737|0.1153|0.1187|0.1429|0.2233|0.4067|gnomAD_AMR||0&1|0&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||8/23|NM_001347828.2:c.1196+51C>T|||||||rs28650939&COSV57264774||1||EntrezGene||YES||||4:g.55133959C>T|0.1831|0.2535|0.4067|0.06599|0.1737|0.1153|0.1187|0.1429|0.2233|0.4067|gnomAD_AMR||0&1|0&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||7/22|NM_001347829.2:c.1121+51C>T|||||||rs28650939&COSV57264774||1||EntrezGene||||||4:g.55133959C>T|0.1831|0.2535|0.4067|0.06599|0.1737|0.1153|0.1187|0.1429|0.2233|0.4067|gnomAD_AMR||0&1|0&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||7/22|NM_001347830.2:c.1160+51C>T|||||||rs28650939&COSV57264774||1||EntrezGene||||||4:g.55133959C>T|0.1831|0.2535|0.4067|0.06599|0.1737|0.1153|0.1187|0.1429|0.2233|0.4067|gnomAD_AMR||0&1|0&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||7/22|NM_006206.6:c.1121+51C>T|||||||rs28650939&COSV57264774||1||EntrezGene||||||4:g.55133959C>T|0.1831|0.2535|0.4067|0.06599|0.1737|0.1153|0.1187|0.1429|0.2233|0.4067|gnomAD_AMR||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:207:0:0,0:38,169:207,0:0:2,0:31:1:36.6:1:1:0:60:206:1:0:0.1	0/1:73:36:8,28:9,28:37,36:0.4932:2,2:34.1:1:36.7:1:1:1.12319:60:72:0.4932:0:2.1
    1501. 

  1501. 4	55133997	55133997	A	G	intronic	PDGFRA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	41	4	55133997	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=0;AF=0;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.12294;SOR=0;LSEQ=TGTCTTACAACCCAGACCCA;RSEQ=AGTCAGTCTAGAAAATGTAA;CSQ=G|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||7/16|NM_001347827.2:c.1121+89A>G|||||||||1||EntrezGene||||||4:g.55133997A>G||||||||||||||,G|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||8/23|NM_001347828.2:c.1196+89A>G|||||||||1||EntrezGene||YES||||4:g.55133997A>G||||||||||||||,G|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||7/22|NM_001347829.2:c.1121+89A>G|||||||||1||EntrezGene||||||4:g.55133997A>G||||||||||||||,G|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||7/22|NM_001347830.2:c.1160+89A>G|||||||||1||EntrezGene||||||4:g.55133997A>G||||||||||||||,G|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||7/22|NM_006206.6:c.1121+89A>G|||||||||1||EntrezGene||||||4:g.55133997A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:75:0:0,0:7,68:75,0:0:2,0:25.6:1:34.6:1:1:0:60:14:1:0:0	0/1:41:2:1,1:6,33:39,2:0.0488:2,2:39.5:1:37:0:0.31585:5.17:60:4:0.0488:0:1
    1502. 

  1502. 4	55138508	55138508	A	C	intronic	PDGFRA	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	68	189	4	55138508	.	A	C	68	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=636;VD=8;AF=0.0126;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.12349;SOR=inf;LSEQ=ATATTCCACTTTGTAGTCTC;RSEQ=TATGTTCTGGGACACGAGCT;CSQ=C|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||8/16|NM_001347827.2:c.1238-53A>C|||||||||1||EntrezGene||||||4:g.55138508A>C||||||||||||||,C|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||9/23|NM_001347828.2:c.1313-53A>C|||||||||1||EntrezGene||YES||||4:g.55138508A>C||||||||||||||,C|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||8/22|NM_001347829.2:c.1238-53A>C|||||||||1||EntrezGene||||||4:g.55138508A>C||||||||||||||,C|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||8/22|NM_001347830.2:c.1277-53A>C|||||||||1||EntrezGene||||||4:g.55138508A>C||||||||||||||,C|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||8/22|NM_006206.6:c.1238-53A>C|||||||||1||EntrezGene||||||4:g.55138508A>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:636:8:0,8:412,216:628,8:0.0126:2,0:24.5:1:22.8:1:0.00022:0:60:1.667:0.0085:0:1.4	0/0:189:0:0,0:146,43:189,0:0:2,0:33.8:1:36.7:1:1:0:60:188:1:0:0.1
    1503. 

  1503. 4	55139771	55139771	T	C	exonic	PDGFRA	.	nonsynonymous SNV	PDGFRA:NM_001347827:exon10:c.T1432C:p.S478P,PDGFRA:NM_001347829:exon10:c.T1432C:p.S478P,PDGFRA:NM_001347830:exon10:c.T1471C:p.S491P,PDGFRA:NM_006206:exon10:c.T1432C:p.S478P,PDGFRA:NM_001347828:exon11:c.T1507C:p.S503P	0.3	0.1473	0.2301	0.2596	0.0497	0.1338	0.1224	0.1024	0.1424	rs35597368	rs35597368	0.305	0.142	T	0.0	0.026	B	0.0	0.013	B	0.234	0.035	N	1	0.090	P	-0.345	0.033	N	-0.95	0.754	T	-0.16	0.095	N	0.092	0.091	-1.098	0.043	T	0.000	0.000	T	.	.	.	-0.578	0.051	0.142	0.658	0.077	0.007	0.030	N	c	-1.510	-1.466	1.000	0.409	0.447	0.083	0	0.811	0.178	-1.151	0.033	-0.364	0.068	0.000	0.063	0.000	0.016	6.025	0.188	.	.	.	ID=COSV57266881;OCCURENCE=5(soft_tissue),2(meninges),2(large_intestine)	50233	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified|not_provided	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374|MedGen:CN517202	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	1	0	MU26845387	LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.25	236	202	4	55139771	.	T	C	236	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1031;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0;LSEQ=ACATCATCACGGAGATCCAC;RSEQ=CCCGAGACAGGAGTACCGTG;CSQ=C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|10/17||NM_001347827.2:c.1432T>C|NP_001334756.1:p.Ser478Pro|1567|1432|478|S/P|Tcc/Ccc|rs35597368&COSV57266881&COSV57268625||1||EntrezGene||||||4:g.55139771T>C|0.1543|0.2359|0.2855|0.05792|0.1434|0.1235|0.1058|0.1251|0.2081|0.2855|gnomAD_AMR|benign|0&1&1|1&1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|11/24||NM_001347828.2:c.1507T>C|NP_001334757.1:p.Ser503Pro|1645|1507|503|S/P|Tcc/Ccc|rs35597368&COSV57266881&COSV57268625||1||EntrezGene||YES||||4:g.55139771T>C|0.1543|0.2359|0.2855|0.05792|0.1434|0.1235|0.1058|0.1251|0.2081|0.2855|gnomAD_AMR|benign|0&1&1|1&1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|10/23||NM_001347829.2:c.1432T>C|NP_001334758.1:p.Ser478Pro|1788|1432|478|S/P|Tcc/Ccc|rs35597368&COSV57266881&COSV57268625||1||EntrezGene||||||4:g.55139771T>C|0.1543|0.2359|0.2855|0.05792|0.1434|0.1235|0.1058|0.1251|0.2081|0.2855|gnomAD_AMR|benign|0&1&1|1&1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|10/23||NM_001347830.2:c.1471T>C|NP_001334759.1:p.Ser491Pro|1983|1471|491|S/P|Tcc/Ccc|rs35597368&COSV57266881&COSV57268625||1||EntrezGene||||||4:g.55139771T>C|0.1543|0.2359|0.2855|0.05792|0.1434|0.1235|0.1058|0.1251|0.2081|0.2855|gnomAD_AMR|benign|0&1&1|1&1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|10/23||NM_006206.6:c.1432T>C|NP_006197.1:p.Ser478Pro|1567|1432|478|S/P|Tcc/Ccc|rs35597368&COSV57266881&COSV57268625||1||EntrezGene||||||4:g.55139771T>C|0.1543|0.2359|0.2855|0.05792|0.1434|0.1235|0.1058|0.1251|0.2081|0.2855|gnomAD_AMR|benign|0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1031:0:0,0:629,402:1031,0:0:2,0:35.8:1:36.2:1:1:0:60:67.733:1:0:0.1	0/1:202:98:58,40:61,43:104,98:0.4851:2,2:34.6:1:35.7:1:1:1.02:60:31.667:0.4822:0:1.1
    1504. 

  1504. 4	55141055	55141055	A	G	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347827:exon12:c.A1701G:p.P567P,PDGFRA:NM_001347829:exon12:c.A1701G:p.P567P,PDGFRA:NM_001347830:exon12:c.A1740G:p.P580P,PDGFRA:NM_006206:exon12:c.A1701G:p.P567P,PDGFRA:NM_001347828:exon13:c.A1776G:p.P592P	1.	0.9677	0.8906	0.9881	0.9834	0.9994	1	0.9986	0.9908	rs1873778	rs1873778	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99955338;OCCURENCE=2(liver),18(meninges),2(central_nervous_system),2(biliary_tract),1(soft_tissue),2(lung)	251495	Squamous_cell_lung_carcinoma|Gastrointestinal_stromal_tumor|Carcinoma_of_colon|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0002032,MedGen:C0699790,SNOMED_CT:269533000|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	1	0	0	1	MU81783993	COCA-CN|5|321|0.0155763	1	346	264	4	55141055	.	A	G	346	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=744;VD=744;AF=1;SHIFT3=0;MSI=1;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATTGAATCAATCAGCCC;RSEQ=GATGGACATGAATATATTTA;CSQ=G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|12/17||NM_001347827.2:c.1701A>G|NP_001334756.1:p.Pro567%3D|1836|1701|567|P|ccA/ccG|rs1873778&COSV99955338||1||EntrezGene||||||4:g.55141055A>G|0.99|0.8851|0.9914|0.9942|0.9999|1|0.9981|0.9922|0.9997|1|EAS&SAS&gnomAD_FIN|benign&likely_benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|13/24||NM_001347828.2:c.1776A>G|NP_001334757.1:p.Pro592%3D|1914|1776|592|P|ccA/ccG|rs1873778&COSV99955338||1||EntrezGene||YES||||4:g.55141055A>G|0.99|0.8851|0.9914|0.9942|0.9999|1|0.9981|0.9922|0.9997|1|EAS&SAS&gnomAD_FIN|benign&likely_benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|12/23||NM_001347829.2:c.1701A>G|NP_001334758.1:p.Pro567%3D|2057|1701|567|P|ccA/ccG|rs1873778&COSV99955338||1||EntrezGene||||||4:g.55141055A>G|0.99|0.8851|0.9914|0.9942|0.9999|1|0.9981|0.9922|0.9997|1|EAS&SAS&gnomAD_FIN|benign&likely_benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|12/23||NM_001347830.2:c.1740A>G|NP_001334759.1:p.Pro580%3D|2252|1740|580|P|ccA/ccG|rs1873778&COSV99955338||1||EntrezGene||||||4:g.55141055A>G|0.99|0.8851|0.9914|0.9942|0.9999|1|0.9981|0.9922|0.9997|1|EAS&SAS&gnomAD_FIN|benign&likely_benign|0&1|1&1,G|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|12/23||NM_006206.6:c.1701A>G|NP_006197.1:p.Pro567%3D|1836|1701|567|P|ccA/ccG|rs1873778&COSV99955338||1||EntrezGene||||||4:g.55141055A>G|0.99|0.8851|0.9914|0.9942|0.9999|1|0.9981|0.9922|0.9997|1|EAS&SAS&gnomAD_FIN|benign&likely_benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:744:744:344,400:0,0:0,744:1:0,2:37.3:1:36.3:1:1:0:60:81.667:1:0:1.1	1/1:264:264:155,109:0,0:0,264:1:0,2:37.7:1:36.6:1:1:0:60:263:1:0:1.1
    1505. 

  1505. 4	55143577	55143577	G	A	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347827:exon13:c.G1809A:p.A603A,PDGFRA:NM_001347829:exon13:c.G1809A:p.A603A,PDGFRA:NM_001347830:exon13:c.G1848A:p.A616A,PDGFRA:NM_006206:exon13:c.G1809A:p.A603A,PDGFRA:NM_001347828:exon14:c.G1884A:p.A628A	0.34	0.1664	0.3054	0.2763	0.0497	0.1379	0.1125	0.0999	0.1337	rs10028020	rs10028020	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57265177;OCCURENCE=1(haematopoietic_and_lymphoid_tissue),5(soft_tissue),1(skin),2(meninges),2(large_intestine)	251496	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU12032552	LUSC-KR|1|170|0.00588235,COCA-CN|1|321|0.00311526	0.25	265	359	4	55143577	.	G	A	265	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1976;VD=3;AF=0.0015;SHIFT3=0;MSI=3;MSILEN=1;SSF=0;SOR=0.00155;LSEQ=CGGGTCTTGGGGTCTGGAGC;RSEQ=TTTGGGAAGGTGGTTGAAGG;CSQ=A|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|13/17||NM_001347827.2:c.1809G>A|NP_001334756.1:p.Ala603%3D|1944|1809|603|A|gcG/gcA|rs10028020&COSV57265177||1||EntrezGene||||||4:g.55143577G>A|0.1595|0.3124|0.3016|0.05834|0.1454|0.1128|0.1024|0.1245|0.2115|0.3366|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|14/24||NM_001347828.2:c.1884G>A|NP_001334757.1:p.Ala628%3D|2022|1884|628|A|gcG/gcA|rs10028020&COSV57265177||1||EntrezGene||YES||||4:g.55143577G>A|0.1595|0.3124|0.3016|0.05834|0.1454|0.1128|0.1024|0.1245|0.2115|0.3366|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|13/23||NM_001347829.2:c.1809G>A|NP_001334758.1:p.Ala603%3D|2165|1809|603|A|gcG/gcA|rs10028020&COSV57265177||1||EntrezGene||||||4:g.55143577G>A|0.1595|0.3124|0.3016|0.05834|0.1454|0.1128|0.1024|0.1245|0.2115|0.3366|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|13/23||NM_001347830.2:c.1848G>A|NP_001334759.1:p.Ala616%3D|2360|1848|616|A|gcG/gcA|rs10028020&COSV57265177||1||EntrezGene||||||4:g.55143577G>A|0.1595|0.3124|0.3016|0.05834|0.1454|0.1128|0.1024|0.1245|0.2115|0.3366|AFR|benign|0&1|1&1,A|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|13/23||NM_006206.6:c.1809G>A|NP_006197.1:p.Ala603%3D|1944|1809|603|A|gcG/gcA|rs10028020&COSV57265177||1||EntrezGene||||||4:g.55143577G>A|0.1595|0.3124|0.3016|0.05834|0.1454|0.1128|0.1024|0.1245|0.2115|0.3366|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1976:3:1,2:968,1004:1972,3:0.0015:2,2:36.3:1:37:0:1:1.92766:60:6:0.0015:0:1	0/1:359:179:87,92:92,88:180,179:0.4986:2,2:38.1:1:35.5:1:0.67335:1.10523:60:34.8:0.4929:0:1.1
    1506. 

  1506. 4	55144549	55144549	G	C	exonic	PDGFRA	.	nonsynonymous SNV	PDGFRA:NM_001347827:exon15:c.G2023C:p.E675Q,PDGFRA:NM_001347829:exon15:c.G2023C:p.E675Q,PDGFRA:NM_001347830:exon15:c.G2062C:p.E688Q,PDGFRA:NM_006206:exon15:c.G2023C:p.E675Q,PDGFRA:NM_001347828:exon16:c.G2098C:p.E700Q	.	.	.	.	.	.	.	.	.	.	.	0.02	0.784	D	1.0	0.899	D	1.0	0.971	D	0.006	0.321	U	0.966	0.810	D	2.19	0.618	M	-3.59	0.950	D	-2.08	0.590	N	0.976	0.978	1.000	0.972	D	0.918	0.973	D	0.182	0.856	D	6.188	0.854	28.6	0.998	0.919	0.994	0.958	D	c	0.978	0.963	1.0	0.983	0.560	0.301	0	6.06	0.983	9.923	0.988	1.048	0.713	1.000	0.715	0.760	0.324	20.621	0.995	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV57267782;OCCURENCE=1(urinary_tract)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU4981504	BLCA-US|1|411|0.00243309	0.25	37	181	4	55144549	.	G	C	37	v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=541;VD=0;AF=0;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.06259;SOR=0;LSEQ=GCCCCATTTACATCATCACA;RSEQ=AGTATTGCTTCTATGGAGAT;CSQ=C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|15/17||NM_001347827.2:c.2023G>C|NP_001334756.1:p.Glu675Gln|2158|2023|675|E/Q|Gag/Cag|COSV57267782&COSV99070921||1||EntrezGene||||||4:g.55144549G>C|||||||||||||1&1|1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|16/24||NM_001347828.2:c.2098G>C|NP_001334757.1:p.Glu700Gln|2236|2098|700|E/Q|Gag/Cag|COSV57267782&COSV99070921||1||EntrezGene||YES||||4:g.55144549G>C|||||||||||||1&1|1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|15/23||NM_001347829.2:c.2023G>C|NP_001334758.1:p.Glu675Gln|2379|2023|675|E/Q|Gag/Cag|COSV57267782&COSV99070921||1||EntrezGene||||||4:g.55144549G>C|||||||||||||1&1|1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|15/23||NM_001347830.2:c.2062G>C|NP_001334759.1:p.Glu688Gln|2574|2062|688|E/Q|Gag/Cag|COSV57267782&COSV99070921||1||EntrezGene||||||4:g.55144549G>C|||||||||||||1&1|1&1,C|missense_variant|MODERATE|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|15/23||NM_006206.6:c.2023G>C|NP_006197.1:p.Glu675Gln|2158|2023|675|E/Q|Gag/Cag|COSV57267782&COSV99070921||1||EntrezGene||||||4:g.55144549G>C|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:541:0:0,0:332,207:539,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:181:2:1,1:114,65:179,2:0.011:2,2:24:1:37:0:1:1.74804:60:4:0.0114:0:1.5
    1507. 

  1507. 4	55146484	55146484	T	C	exonic	PDGFRA	.	nonsynonymous SNV	PDGFRA:NM_001347827:exon16:c.T2158C:p.Y720H,PDGFRA:NM_001347829:exon16:c.T2158C:p.Y720H,PDGFRA:NM_001347830:exon16:c.T2197C:p.Y733H,PDGFRA:NM_006206:exon16:c.T2158C:p.Y720H,PDGFRA:NM_001347828:exon17:c.T2233C:p.Y745H	.	.	.	.	.	.	.	.	.	.	.	0.561	0.073	T	1.0	0.899	D	0.997	0.850	D	0.011	0.295	U	0.545	0.810	N	0.695	0.181	N	-1.31	0.797	T	-0.48	0.154	N	0.809	0.822	-0.252	0.763	T	0.482	0.802	T	0.075	0.722	D	4.466	0.598	24.2	0.998	0.868	0.997	0.985	D	c	0.472	0.531	1.000	0.747	0.615	0.372	0	5.54	0.828	5.956	0.698	1.061	0.807	1.000	0.715	0.888	0.373	15.691	0.771	Protein kinase domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	143	4	55146484	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=2;AF=0.0741;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.02443;SOR=inf;LSEQ=TCTCTTTCTGTTTTTACAGC;RSEQ=ATGTTATTTTATCTTTTGAA;CSQ=C|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding|16/17||NM_001347827.2:c.2158T>C|NP_001334756.1:p.Tyr720His|2293|2158|720|Y/H|Tat/Cat|||1||EntrezGene||||||4:g.55146484T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|17/24||NM_001347828.2:c.2233T>C|NP_001334757.1:p.Tyr745His|2371|2233|745|Y/H|Tat/Cat|||1||EntrezGene||YES||||4:g.55146484T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|16/23||NM_001347829.2:c.2158T>C|NP_001334758.1:p.Tyr720His|2514|2158|720|Y/H|Tat/Cat|||1||EntrezGene||||||4:g.55146484T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|16/23||NM_001347830.2:c.2197T>C|NP_001334759.1:p.Tyr733His|2709|2197|733|Y/H|Tat/Cat|||1||EntrezGene||||||4:g.55146484T>C||||||||||||||,C|missense_variant&splice_region_variant|MODERATE|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|16/23||NM_006206.6:c.2158T>C|NP_006197.1:p.Tyr720His|2293|2158|720|Y/H|Tat/Cat|||1||EntrezGene||||||4:g.55146484T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:27:2:1,1:13,12:25,2:0.0741:2,2:33.5:1:37:0:1:1.0801:60:4:0.0741:0:1	0/0:143:0:0,0:91,52:143,0:0:2,0:36.4:1:36.1:1:1:0:59.9:142:1:0:0.3
    1508. 

  1508. 4	55151958	55151958	-	A	intronic	PDGFRA	.	.	.	0.87	0.7650	0.5355	0.6850	0.9362	0.8600	0.8726	0.8597	0.8279	rs3830355	rs3830355	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99955341;OCCURENCE=10(meninges)	861306	Squamous_cell_lung_carcinoma	Human_Phenotype_Ontology:HP:0030359,MONDO:MONDO:0005097,MedGen:C0149782	no_assertion_criteria_provided	Uncertain_significance	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.75	378	160	4	55151958	.	T	TA	378	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=1403;VD=1401;AF=0.9986;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=474.567;LSEQ=GTCTTGCAGGGGTGATGCTA;RSEQ=TCAGCTACAGATGGCTTGAT;CSQ=A|downstream_gene_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||||||||||rs3830355&COSV99955341|3813|1||EntrezGene||||||4:g.55151958_55151959insA|0.8045|0.5245|0.6772|0.925|0.8498|0.8742|0.857|0.8398|0.782|0.925|gnomAD_ASJ||0&1|0&1,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||18/23|NM_001347828.2:c.2515-50_2515-49insA|||||||rs3830355&COSV99955341||1||EntrezGene||YES||||4:g.55151958_55151959insA|0.8045|0.5245|0.6772|0.925|0.8498|0.8742|0.857|0.8398|0.782|0.925|gnomAD_ASJ||0&1|0&1,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||17/22|NM_001347829.2:c.2440-50_2440-49insA|||||||rs3830355&COSV99955341||1||EntrezGene||||||4:g.55151958_55151959insA|0.8045|0.5245|0.6772|0.925|0.8498|0.8742|0.857|0.8398|0.782|0.925|gnomAD_ASJ||0&1|0&1,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||17/22|NM_001347830.2:c.2479-50_2479-49insA|||||||rs3830355&COSV99955341||1||EntrezGene||||||4:g.55151958_55151959insA|0.8045|0.5245|0.6772|0.925|0.8498|0.8742|0.857|0.8398|0.782|0.925|gnomAD_ASJ||0&1|0&1,A|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||17/22|NM_006206.6:c.2440-50_2440-49insA|||||||rs3830355&COSV99955341||1||EntrezGene||||||4:g.55151958_55151959insA|0.8045|0.5245|0.6772|0.925|0.8498|0.8742|0.857|0.8398|0.782|0.925|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1403:1401:847,554:0,0:0,1401:0.9986:0,2:36.8:1:36.2:1:1:0:60:86.562:1:0.1468:0.1	1/0:160:95:59,36:37,28:65,95:0.5938:2,2:34.5:1:36.4:1:0.51655:1.24:60:94:0.5912:0.0938:0
    1509. 

  1509. 4	55152040	55152040	C	T	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347829:exon18:c.C2472T:p.V824V,PDGFRA:NM_001347830:exon18:c.C2511T:p.V837V,PDGFRA:NM_006206:exon18:c.C2472T:p.V824V,PDGFRA:NM_001347828:exon19:c.C2547T:p.V849V	0.34	0.1941	0.3254	0.3026	0.0633	0.1316	0.1271	0.1392	0.1582	rs2228230	rs2228230	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV57264143;OCCURENCE=2(breast),4(meninges),2(large_intestine),3(central_nervous_system),2(biliary_tract),12(haematopoietic_and_lymphoid_tissue),1(urinary_tract),17(soft_tissue),2(skin),1(endometrium)	251497	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU797701	COCA-CN|2|321|0.00623053	0.25	251	253	4	55152040	.	C	T	251	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=2173;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GATCTGGCTGCTCGCAACGT;RSEQ=CTCCTGGCACAAGGAAAAAT;CSQ=T|downstream_gene_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347827.2|protein_coding||||||||||rs2228230&COSV57264143|3895|1||EntrezGene||||||4:g.55152040C>T|0.1831|0.3294|0.3142|0.07404|0.1407|0.127|0.1419|0.154|0.2174|0.3449|AFR|benign|0&1|1&1,T|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|19/24||NM_001347828.2:c.2547C>T|NP_001334757.1:p.Val849%3D|2685|2547|849|V|gtC/gtT|rs2228230&COSV57264143||1||EntrezGene||YES||||4:g.55152040C>T|0.1831|0.3294|0.3142|0.07404|0.1407|0.127|0.1419|0.154|0.2174|0.3449|AFR|benign|0&1|1&1,T|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|18/23||NM_001347829.2:c.2472C>T|NP_001334758.1:p.Val824%3D|2828|2472|824|V|gtC/gtT|rs2228230&COSV57264143||1||EntrezGene||||||4:g.55152040C>T|0.1831|0.3294|0.3142|0.07404|0.1407|0.127|0.1419|0.154|0.2174|0.3449|AFR|benign|0&1|1&1,T|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|18/23||NM_001347830.2:c.2511C>T|NP_001334759.1:p.Val837%3D|3023|2511|837|V|gtC/gtT|rs2228230&COSV57264143||1||EntrezGene||||||4:g.55152040C>T|0.1831|0.3294|0.3142|0.07404|0.1407|0.127|0.1419|0.154|0.2174|0.3449|AFR|benign|0&1|1&1,T|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|18/23||NM_006206.6:c.2472C>T|NP_006197.1:p.Val824%3D|2607|2472|824|V|gtC/gtT|rs2228230&COSV57264143||1||EntrezGene||||||4:g.55152040C>T|0.1831|0.3294|0.3142|0.07404|0.1407|0.127|0.1419|0.154|0.2174|0.3449|AFR|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:2173:0:0,0:1052,1120:2172,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:253:112:61,51:75,66:141,112:0.4427:2,2:38.6:1:36.9:1:0.89917:1.05:60:224:0.4462:0:1.1
    1510. 

  1510. 4	55161254	55161254	C	T	intronic	PDGFRA	.	.	.	0.87	0.7539	0.4871	0.6802	0.9205	0.8671	0.8726	0.8649	0.8262	rs3733540	rs3733540	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99955593;OCCURENCE=2(meninges)	251498	not_specified	MedGen:CN169374	criteria_provided,_single_submitter	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU26313221	COCA-CN|5|321|0.0155763	0.75	368	117	4	55161254	.	C	T	368	PASS	STATUS=LikelyLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1431;VD=1425;AF=0.9958;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=255.04;LSEQ=AGTCTAGGTCTAGTTCTGTG;RSEQ=AGGAGTTGTAATATTTGCTC;CSQ=T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding||23/23|NM_001347828.2:c.3198-38C>T|||||||rs3733540&COSV99955593||1||EntrezGene||YES||||4:g.55161254C>T|0.8035|0.477|0.6735|0.921|0.8585|0.8738|0.8613|0.8401|0.7824|0.921|gnomAD_ASJ|benign|0&1|1&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding||22/22|NM_001347829.2:c.3123-38C>T|||||||rs3733540&COSV99955593||1||EntrezGene||||||4:g.55161254C>T|0.8035|0.477|0.6735|0.921|0.8585|0.8738|0.8613|0.8401|0.7824|0.921|gnomAD_ASJ|benign|0&1|1&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding||22/22|NM_001347830.2:c.3162-38C>T|||||||rs3733540&COSV99955593||1||EntrezGene||||||4:g.55161254C>T|0.8035|0.477|0.6735|0.921|0.8585|0.8738|0.8613|0.8401|0.7824|0.921|gnomAD_ASJ|benign|0&1|1&1,T|intron_variant|MODIFIER|PDGFRA|5156|Transcript|NM_006206.6|protein_coding||22/22|NM_006206.6:c.3123-38C>T|||||||rs3733540&COSV99955593||1||EntrezGene||||||4:g.55161254C>T|0.8035|0.477|0.6735|0.921|0.8585|0.8738|0.8613|0.8401|0.7824|0.921|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:1431:1425:861,564:0,0:0,1425:0.9958:0,2:37.9:1:35.2:1:1:0:60:28.082:0.9978:0:1.2	0/1:117:56:32,24:39,22:61,56:0.4786:2,2:34:1:36.4:1:0.57006:1.32628:60:112:0.487:0:1.2
    1511. 

  1511. 4	55161391	55161391	T	C	exonic	PDGFRA	.	synonymous SNV	PDGFRA:NM_001347829:exon23:c.T3222C:p.D1074D,PDGFRA:NM_001347830:exon23:c.T3261C:p.D1087D,PDGFRA:NM_006206:exon23:c.T3222C:p.D1074D,PDGFRA:NM_001347828:exon24:c.T3297C:p.D1099D	1.	0.9980	0.9929	1	1	1	1	1	1	rs7685117	rs7685117	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99955343;OCCURENCE=18(meninges)	251499	Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|Idiopathic_hypereosinophilic_syndrome|not_specified	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:C0206141,OMIM:607685,SNOMED_CT:423294001|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU81784009	COCA-CN|5|321|0.0155763	1	411	279	4	55161391	.	T	C	411	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=2428;VD=2417;AF=0.9955;SHIFT3=0;MSI=2;MSILEN=4;SSF=0.30154;SOR=0;LSEQ=GAAGACATCGACATGATGGA;RSEQ=GACATCGGCATAGACTCTTC;CSQ=C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347828.2|protein_coding|24/24||NM_001347828.2:c.3297T>C|NP_001334757.1:p.Asp1099%3D|3435|3297|1099|D|gaT/gaC|rs7685117&COSV99955343||1||EntrezGene||YES||||4:g.55161391T>C|0.9992|0.9902|0.9997|1|0.9999|1|0.9999|1|0.9995|1|AMR&EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347829.2|protein_coding|23/23||NM_001347829.2:c.3222T>C|NP_001334758.1:p.Asp1074%3D|3578|3222|1074|D|gaT/gaC|rs7685117&COSV99955343||1||EntrezGene||||||4:g.55161391T>C|0.9992|0.9902|0.9997|1|0.9999|1|0.9999|1|0.9995|1|AMR&EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_001347830.2|protein_coding|23/23||NM_001347830.2:c.3261T>C|NP_001334759.1:p.Asp1087%3D|3773|3261|1087|D|gaT/gaC|rs7685117&COSV99955343||1||EntrezGene||||||4:g.55161391T>C|0.9992|0.9902|0.9997|1|0.9999|1|0.9999|1|0.9995|1|AMR&EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|benign|0&1|1&1,C|synonymous_variant|LOW|PDGFRA|5156|Transcript|NM_006206.6|protein_coding|23/23||NM_006206.6:c.3222T>C|NP_006197.1:p.Asp1074%3D|3357|3222|1074|D|gaT/gaC|rs7685117&COSV99955343||1||EntrezGene||||||4:g.55161391T>C|0.9992|0.9902|0.9997|1|0.9999|1|0.9999|1|0.9995|1|AMR&EAS&EUR&SAS&EA&gnomAD_ASJ&gnomAD_FIN&gnomAD_OTH|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:2428:2417:1232,1185:2,1:3,2417:0.9955:2,2:35.3:1:36.6:1:1:1.92319:60:141.176:0.9963:0:1.2	1/1:279:279:142,137:0,0:0,279:1:0,2:40:1:36.7:1:1:0:60:138.5:1:0:1.1
    1512. 

  1512. 4	55564414	55564414	C	T	intronic	KIT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	63	4	55564414	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=133;VD=2;AF=0.015;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.45934;SOR=inf;LSEQ=TTTTCAGTGTCTGTGACCAG;RSEQ=CATTCCAACTACTGATTTTG;CSQ=T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_000222.3|protein_coding||2/20|NM_000222.3:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001093772.2|protein_coding||2/20|NM_001093772.2:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385284.1|protein_coding||2/20|NM_001385284.1:c.338-36C>T|||||||||1||EntrezGene||YES||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385285.1|protein_coding||2/20|NM_001385285.1:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385286.1|protein_coding||2/20|NM_001385286.1:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385288.1|protein_coding||2/20|NM_001385288.1:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385290.1|protein_coding||2/20|NM_001385290.1:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||,T|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385292.1|protein_coding||2/20|NM_001385292.1:c.338-36C>T|||||||||1||EntrezGene||||||4:g.55564414C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:133:2:1,1:104,26:130,2:0.015:2,2:57:1:37:0:0.36849:3.94405:60:4:0.0152:0:1	0/0:63:0:0,0:52,11:63,0:0:2,0:31.5:1:36.2:1:1:0:60:62:1:0:0.1
    1513. 

  1513. 4	55593472	55593472	G	A	exonic	KIT	.	synonymous SNV	KIT:NM_000222:exon10:c.G1629A:p.L543L,KIT:NM_001093772:exon10:c.G1617A:p.L539L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	248	4	55593472	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=130;VD=2;AF=0.0154;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.11768;SOR=inf;LSEQ=TGCATTATTGTGATGATTCT;RSEQ=ACCTACAAATATTTACAGGT;CSQ=A|synonymous_variant|LOW|KIT|3815|Transcript|NM_000222.3|protein_coding|10/21||NM_000222.3:c.1629G>A|NP_000213.1:p.Leu543%3D|1687|1629|543|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001093772.2|protein_coding|10/21||NM_001093772.2:c.1617G>A|NP_001087241.1:p.Leu539%3D|1675|1617|539|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385284.1|protein_coding|10/21||NM_001385284.1:c.1632G>A|NP_001372213.1:p.Leu544%3D|1690|1632|544|L|ctG/ctA|COSV55395814||1||EntrezGene||YES||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385285.1|protein_coding|10/21||NM_001385285.1:c.1629G>A|NP_001372214.1:p.Leu543%3D|1687|1629|543|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385286.1|protein_coding|10/21||NM_001385286.1:c.1617G>A|NP_001372215.1:p.Leu539%3D|1675|1617|539|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385288.1|protein_coding|10/21||NM_001385288.1:c.1620G>A|NP_001372217.1:p.Leu540%3D|1678|1620|540|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385290.1|protein_coding|10/21||NM_001385290.1:c.1632G>A|NP_001372219.1:p.Leu544%3D|1690|1632|544|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1,A|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385292.1|protein_coding|10/21||NM_001385292.1:c.1620G>A|NP_001372221.1:p.Leu540%3D|1678|1620|540|L|ctG/ctA|COSV55395814||1||EntrezGene||||||4:g.55593472G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:130:2:1,1:36,92:128,2:0.0154:2,2:14.5:1:37:0:0.4898:2.53:60:4:0.0154:0:1	0/0:248:0:0,0:131,117:248,0:0:2,0:40.5:1:36.7:1:1:0:60:123:1:0:0.1
    1514. 

  1514. 4	55593481	55593481	A	G	exonic	KIT	.	synonymous SNV	KIT:NM_000222:exon10:c.A1638G:p.K546K,KIT:NM_001093772:exon10:c.A1626G:p.K542K	0.048	0.0257	0.0062	0.0048	0.0596	0.0567	0.0146	0.0365	0.0285	rs55986963	rs55986963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55391099;OCCURENCE=1(breast),1(meninges),2(bone),2(haematopoietic_and_lymphoid_tissue),3(soft_tissue),3(lung)	251502	Partial_albinism|Mastocytosis|Gastrointestinal_stromal_tumor|Hereditary_cancer-predisposing_syndrome|not_specified	Human_Phenotype_Ontology:HP:0001044,Human_Phenotype_Ontology:HP:0007443,Human_Phenotype_Ontology:HP:0007544,MONDO:MONDO:0008244,MedGen:C0080024,OMIM:172800,Orphanet:ORPHA2884,SNOMED_CT:6479008|Human_Phenotype_Ontology:HP:0100495,MONDO:MONDO:0007950,MedGen:C0024899,OMIM:154800,Orphanet:ORPHA98292|Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374	criteria_provided,_multiple_submitters,_no_conflicts	Benign	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	1	MU12034439	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|2|321|0.00623053	0.25	210	242	4	55593481	.	A	G	210	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=104;VD=54;AF=0.5192;SHIFT3=0;MSI=2;MSILEN=2;SSF=0;SOR=inf;LSEQ=GTGATGATTCTGACCTACAA;RSEQ=TATTTACAGGTAACCATTTA;CSQ=G|synonymous_variant|LOW|KIT|3815|Transcript|NM_000222.3|protein_coding|10/21||NM_000222.3:c.1638A>G|NP_000213.1:p.Lys546%3D|1696|1638|546|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001093772.2|protein_coding|10/21||NM_001093772.2:c.1626A>G|NP_001087241.1:p.Lys542%3D|1684|1626|542|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385284.1|protein_coding|10/21||NM_001385284.1:c.1641A>G|NP_001372213.1:p.Lys547%3D|1699|1641|547|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||YES||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385285.1|protein_coding|10/21||NM_001385285.1:c.1638A>G|NP_001372214.1:p.Lys546%3D|1696|1638|546|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385286.1|protein_coding|10/21||NM_001385286.1:c.1626A>G|NP_001372215.1:p.Lys542%3D|1684|1626|542|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385288.1|protein_coding|10/21||NM_001385288.1:c.1629A>G|NP_001372217.1:p.Lys543%3D|1687|1629|543|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385290.1|protein_coding|10/21||NM_001385290.1:c.1641A>G|NP_001372219.1:p.Lys547%3D|1699|1641|547|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1,G|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385292.1|protein_coding|10/21||NM_001385292.1:c.1629A>G|NP_001372221.1:p.Lys543%3D|1687|1629|543|K|aaA/aaG|rs55986963&COSV55391099||1||EntrezGene||||||4:g.55593481A>G|0.02745|0.005475|0.008996|0.0669|0.04917|0.01807|0.02951|0.02826|0.03276|0.0669|gnomAD_ASJ|benign|0&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/0:104:54:21,33:11,39:50,54:0.5192:2,2:32.2:1:36.6:1:0.08854:2.24:60:108:0.5192:0:1.1	0/0:242:0:0,0:127,115:242,0:0:2,0:39.4:1:36.1:1:1:0:60:47.4:1:0:0.1
    1515. 

  1515. 4	55593645	55593645	A	T	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon11:c.A1711T:p.I571L,KIT:NM_001093772:exon11:c.A1699T:p.I567L	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.95	0.577	P	0.98	0.732	D	0.000	0.629	D	1	0.810	D	2.21	0.624	M	-3.51	0.947	D	-1.78	0.420	N	0.72	0.720	0.991	0.970	D	0.898	0.966	D	0.395	0.933	D	6.402	0.884	29.6	0.995	0.664	0.977	0.760	D	c	0.816	0.823	1.000	0.747	0.706	0.609	0	6.06	0.983	9.137	0.937	1.199	0.960	1.000	0.715	0.999	0.750	16.600	0.846	Protein kinase-like domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	221	4	55593645	.	A	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=139;VD=2;AF=0.0144;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14842;SOR=inf;LSEQ=ATGGAAACAATTATGTTTAC;RSEQ=TAGACCCAACACAACTTCCT;CSQ=T|missense_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|11/21||NM_000222.3:c.1711A>T|NP_000213.1:p.Ile571Leu|1769|1711|571|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|11/21||NM_001093772.2:c.1699A>T|NP_001087241.1:p.Ile567Leu|1757|1699|567|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|11/21||NM_001385284.1:c.1714A>T|NP_001372213.1:p.Ile572Leu|1772|1714|572|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||YES||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385285.1|protein_coding|11/21||NM_001385285.1:c.1711A>T|NP_001372214.1:p.Ile571Leu|1769|1711|571|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385286.1|protein_coding|11/21||NM_001385286.1:c.1699A>T|NP_001372215.1:p.Ile567Leu|1757|1699|567|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|11/21||NM_001385288.1:c.1702A>T|NP_001372217.1:p.Ile568Leu|1760|1702|568|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385290.1|protein_coding|11/21||NM_001385290.1:c.1714A>T|NP_001372219.1:p.Ile572Leu|1772|1714|572|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385292.1|protein_coding|11/21||NM_001385292.1:c.1702A>T|NP_001372221.1:p.Ile568Leu|1760|1702|568|I/L|Ata/Tta|COSV55415288&COSV99078448||1||EntrezGene||||||4:g.55593645A>T|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:139:2:1,1:94,43:137,2:0.0144:2,2:11:0:37:0:0.53446:2.17257:60:4:0.0144:0:1	0/0:221:0:0,0:106,115:221,0:0:2,0:38.6:1:36.8:1:1:0:60:442:1:0:0.1
    1516. 

  1516. 4	55593667	55593667	A	-	exonic	KIT	.	frameshift deletion	KIT:NM_000222:exon11:c.1733delA:p.Y578Lfs*12,KIT:NM_001093772:exon11:c.1721delA:p.Y574Lfs*12	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	35	223	4	55593666	.	TA	T	35	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=193;VD=2;AF=0.0104;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.21464;SOR=inf;LSEQ=TAGACCCAACACAACTTCCT;RSEQ=TGATCACAAATGGGAGTTTC;CSQ=-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_000222.3|protein_coding|11/21||NM_000222.3:c.1733del|NP_000213.1:p.Tyr578LeufsTer12|1791|1733|578|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001093772.2|protein_coding|11/21||NM_001093772.2:c.1721del|NP_001087241.1:p.Tyr574LeufsTer12|1779|1721|574|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385284.1|protein_coding|11/21||NM_001385284.1:c.1736del|NP_001372213.1:p.Tyr579LeufsTer12|1794|1736|579|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||YES||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385285.1|protein_coding|11/21||NM_001385285.1:c.1733del|NP_001372214.1:p.Tyr578LeufsTer12|1791|1733|578|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385286.1|protein_coding|11/21||NM_001385286.1:c.1721del|NP_001372215.1:p.Tyr574LeufsTer12|1779|1721|574|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385288.1|protein_coding|11/21||NM_001385288.1:c.1724del|NP_001372217.1:p.Tyr575LeufsTer12|1782|1724|575|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385290.1|protein_coding|11/21||NM_001385290.1:c.1736del|NP_001372219.1:p.Tyr579LeufsTer12|1794|1736|579|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1,-|frameshift_variant|HIGH|KIT|3815|Transcript|NM_001385292.1|protein_coding|11/21||NM_001385292.1:c.1724del|NP_001372221.1:p.Tyr575LeufsTer12|1782|1724|575|Y/X|tAt/tt|COSV55393841&COSV55414237||1||EntrezGene||||||4:g.55593667del|||||||||||||1&1|1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:193:2:1,1:131,60:191,2:0.0104:2,2:17:1:35.1:1:0.53335:2.17365:60:4:0.0106:0.0052:0	0/0:223:0:0,0:107,116:223,0:0:2,0:36.2:1:35.8:1:1:0:60:43.6:1:0:0
    1517. 

  1517. 4	55593669	55593669	G	T	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon11:c.G1735T:p.D579Y,KIT:NM_001093772:exon11:c.G1723T:p.D575Y	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.968	0.742	D	0.000	0.629	D	1	0.810	D	2.885	0.838	M	-3.51	0.947	D	-6.02	0.897	D	0.894	0.883	1.004	0.973	D	0.920	0.973	D	0.306	0.911	D	6.679	0.915	32	0.996	0.715	0.966	0.699	D	c	0.929	0.910	1.000	0.747	0.706	0.609	0	6.06	0.983	7.569	0.816	1.048	0.713	1.000	0.715	0.999	0.750	20.613	0.995	Protein kinase-like domain	.	.	ID=COSV55411200;OCCURENCE=1(lung)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	225	4	55593669	.	G	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=199;VD=2;AF=0.0101;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.21969;SOR=inf;LSEQ=ACCCAACACAACTTCCTTAT;RSEQ=ATCACAAATGGGAGTTTCCC;CSQ=T|missense_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|11/21||NM_000222.3:c.1735G>T|NP_000213.1:p.Asp579Tyr|1793|1735|579|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|11/21||NM_001093772.2:c.1723G>T|NP_001087241.1:p.Asp575Tyr|1781|1723|575|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|11/21||NM_001385284.1:c.1738G>T|NP_001372213.1:p.Asp580Tyr|1796|1738|580|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||YES||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385285.1|protein_coding|11/21||NM_001385285.1:c.1735G>T|NP_001372214.1:p.Asp579Tyr|1793|1735|579|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385286.1|protein_coding|11/21||NM_001385286.1:c.1723G>T|NP_001372215.1:p.Asp575Tyr|1781|1723|575|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|11/21||NM_001385288.1:c.1726G>T|NP_001372217.1:p.Asp576Tyr|1784|1726|576|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385290.1|protein_coding|11/21||NM_001385290.1:c.1738G>T|NP_001372219.1:p.Asp580Tyr|1796|1738|580|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385292.1|protein_coding|11/21||NM_001385292.1:c.1726G>T|NP_001372221.1:p.Asp576Tyr|1784|1726|576|D/Y|Gat/Tat|CD057857&COSV55411200&COSV55412946||1||EntrezGene||||||4:g.55593669G>T|||||||||||||0&1&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:199:2:1,1:133,64:197,2:0.0101:2,2:38.5:1:37:0:0.54769:2.06987:60:4:0.0101:0:1	0/0:225:0:0,0:110,115:225,0:0:2,0:35.7:1:36.6:1:1:0:60:111.5:1:0:0
    1518. 

  1518. 4	55597496	55597496	G	A	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon15:c.G2144A:p.S715N,KIT:NM_001093772:exon15:c.G2132A:p.S711N	.	6.459e-05	0	0	0	0	0	0.0001	0	rs56094246	rs56094246	0.591	0.079	T	0.002	0.090	B	0.006	0.112	B	0.809	0.093	N	1	0.090	N	0.665	0.163	N	-1.24	0.790	T	-0.35	0.129	N	0.04	0.020	-0.904	0.475	T	0.270	0.642	T	0.028	0.506	D	-0.416	0.061	0.354	0.688	0.085	0.752	0.365	D	c	-0.965	-0.945	0.118	0.168	0.651	0.465	0	-1.17	0.091	1.475	0.348	0.064	0.169	0.997	0.399	0.129	0.199	11.158	0.475	Protein kinase domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	632414	Gastrointestinal_stromal_tumor	Human_Phenotype_Ontology:HP:0100723,MONDO:MONDO:0011719,MeSH:D046152,MedGen:C0238198,OMIM:606764,Orphanet:ORPHA44890	criteria_provided,_single_submitter	Uncertain_significance	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	220	4	55597496	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=183;VD=2;AF=0.0109;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.20558;SOR=inf;LSEQ=TTGTTTCATCTCTCCCAGCA;RSEQ=CGATAGTACTAATGAGTACA;CSQ=A|missense_variant&splice_region_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|15/21||NM_000222.3:c.2144G>A|NP_000213.1:p.Ser715Asn|2202|2144|715|S/N|aGc/aAc|rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|missense_variant&splice_region_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|15/21||NM_001093772.2:c.2132G>A|NP_001087241.1:p.Ser711Asn|2190|2132|711|S/N|aGc/aAc|rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|missense_variant&splice_region_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|15/21||NM_001385284.1:c.2147G>A|NP_001372213.1:p.Ser716Asn|2205|2147|716|S/N|aGc/aAc|rs56094246||1||EntrezGene||YES||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|splice_acceptor_variant|HIGH|KIT|3815|Transcript|NM_001385285.1|protein_coding||14/20|NM_001385285.1:c.2142-1G>A|||||||rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|splice_acceptor_variant|HIGH|KIT|3815|Transcript|NM_001385286.1|protein_coding||14/20|NM_001385286.1:c.2130-1G>A|||||||rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|missense_variant&splice_region_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|15/21||NM_001385288.1:c.2135G>A|NP_001372217.1:p.Ser712Asn|2193|2135|712|S/N|aGc/aAc|rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|splice_acceptor_variant|HIGH|KIT|3815|Transcript|NM_001385290.1|protein_coding||14/20|NM_001385290.1:c.2145-1G>A|||||||rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1,A|splice_acceptor_variant|HIGH|KIT|3815|Transcript|NM_001385292.1|protein_coding||14/20|NM_001385292.1:c.2133-1G>A|||||||rs56094246||1||EntrezGene||||||4:g.55597496G>A||||||||||||uncertain_significance||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:183:2:1,1:92,89:181,2:0.0109:2,2:27:1:37:0:1:1.03353:60:4:0.0113:0:1	0/0:220:0:0,0:121,99:220,0:0:2,0:38.1:1:36.5:1:1:0:60:109:1:0:0
    1519. 

  1519. 4	55597521	55597521	C	T	exonic	KIT	.	synonymous SNV	KIT:NM_000222:exon15:c.C2169T:p.D723D,KIT:NM_001093772:exon15:c.C2157T:p.D719D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	256	4	55597521	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=184;VD=2;AF=0.0109;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.17432;SOR=inf;LSEQ=AGTACTAATGAGTACATGGA;RSEQ=ATGAAACCTGGAGTTTCTTA;CSQ=T|synonymous_variant|LOW|KIT|3815|Transcript|NM_000222.3|protein_coding|15/21||NM_000222.3:c.2169C>T|NP_000213.1:p.Asp723%3D|2227|2169|723|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001093772.2|protein_coding|15/21||NM_001093772.2:c.2157C>T|NP_001087241.1:p.Asp719%3D|2215|2157|719|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385284.1|protein_coding|15/21||NM_001385284.1:c.2172C>T|NP_001372213.1:p.Asp724%3D|2230|2172|724|D|gaC/gaT|||1||EntrezGene||YES||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385285.1|protein_coding|15/21||NM_001385285.1:c.2166C>T|NP_001372214.1:p.Asp722%3D|2224|2166|722|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385286.1|protein_coding|15/21||NM_001385286.1:c.2154C>T|NP_001372215.1:p.Asp718%3D|2212|2154|718|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385288.1|protein_coding|15/21||NM_001385288.1:c.2160C>T|NP_001372217.1:p.Asp720%3D|2218|2160|720|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385290.1|protein_coding|15/21||NM_001385290.1:c.2169C>T|NP_001372219.1:p.Asp723%3D|2227|2169|723|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||,T|synonymous_variant|LOW|KIT|3815|Transcript|NM_001385292.1|protein_coding|15/21||NM_001385292.1:c.2157C>T|NP_001372221.1:p.Asp719%3D|2215|2157|719|D|gaC/gaT|||1||EntrezGene||||||4:g.55597521C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:184:2:1,1:85,97:182,2:0.0109:2,2:38:1:37:0:1:1.14:60:4:0.0109:0:1	0/0:256:0:0,0:132,124:256,0:0:2,0:36:1:36.4:1:1:0:60:84.333:1:0:0
    1520. 

  1520. 4	55598156	55598156	T	A	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon16:c.T2353A:p.S785T,KIT:NM_001093772:exon16:c.T2341A:p.S781T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.997	0.850	D	0.000	0.559	D	1	0.810	D	1.62	0.416	L	-2.68	0.904	D	-2.26	0.505	N	0.517	0.559	0.766	0.940	D	0.803	0.933	D	0.110	0.788	D	3.543	0.483	23.1	0.996	0.741	0.963	0.683	D	c	0.640	0.643	1.000	0.480	0.707	0.730	0	5.82	0.927	3.153	0.501	1.061	0.807	1.000	0.715	0.996	0.625	16.184	0.817	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	295	4	55598156	.	T	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=238;VD=3;AF=0.0126;SHIFT3=2;MSI=2;MSILEN=1;SSF=0.08841;SOR=inf;LSEQ=AGGGCATGGCTTTCCTCGCC;RSEQ=CCAAGAATGTAAGTGGGAGT;CSQ=A|missense_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|16/21||NM_000222.3:c.2353T>A|NP_000213.1:p.Ser785Thr|2411|2353|785|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|16/21||NM_001093772.2:c.2341T>A|NP_001087241.1:p.Ser781Thr|2399|2341|781|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|16/21||NM_001385284.1:c.2356T>A|NP_001372213.1:p.Ser786Thr|2414|2356|786|S/T|Tcc/Acc|||1||EntrezGene||YES||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385285.1|protein_coding|16/21||NM_001385285.1:c.2350T>A|NP_001372214.1:p.Ser784Thr|2408|2350|784|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385286.1|protein_coding|16/21||NM_001385286.1:c.2338T>A|NP_001372215.1:p.Ser780Thr|2396|2338|780|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|16/21||NM_001385288.1:c.2344T>A|NP_001372217.1:p.Ser782Thr|2402|2344|782|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385290.1|protein_coding|16/21||NM_001385290.1:c.2353T>A|NP_001372219.1:p.Ser785Thr|2411|2353|785|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385292.1|protein_coding|16/21||NM_001385292.1:c.2341T>A|NP_001372221.1:p.Ser781Thr|2399|2341|781|S/T|Tcc/Acc|||1||EntrezGene||||||4:g.55598156T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:238:3:1,2:87,147:234,3:0.0126:2,2:14.3:1:28.3:1:1:1.18289:60:2:0.0085:0:3	0/0:295:0:0,0:124,171:295,0:0:2,0:37.4:1:34.2:1:1:0:60:9.536:1:0:0.5
    1521. 

  1521. 4	55598173	55598173	G	A	intronic	KIT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	260	4	55598173	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=163;VD=2;AF=0.0123;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.14793;SOR=inf;LSEQ=GCCTCCAAGAATGTAAGTGG;RSEQ=AGTGATTCTCTAAAGAGTTT;CSQ=A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_000222.3|protein_coding||16/20|NM_000222.3:c.2361+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001093772.2|protein_coding||16/20|NM_001093772.2:c.2349+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385284.1|protein_coding||16/20|NM_001385284.1:c.2364+9G>A|||||||||1||EntrezGene||YES||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385285.1|protein_coding||16/20|NM_001385285.1:c.2358+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385286.1|protein_coding||16/20|NM_001385286.1:c.2346+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385288.1|protein_coding||16/20|NM_001385288.1:c.2352+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385290.1|protein_coding||16/20|NM_001385290.1:c.2361+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||,A|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385292.1|protein_coding||16/20|NM_001385292.1:c.2349+9G>A|||||||||1||EntrezGene||||||4:g.55598173G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:163:2:1,1:57,103:160,2:0.0123:2,2:40:0:37:0:1:1.8:60:4:0.0129:0:1	0/0:260:0:0,0:98,162:260,0:0:2,0:32.6:1:34.9:1:1:0:60:17.571:1:0:0.7
    1522. 

  1522. 4	55599381	55599381	A	G	intronic	KIT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	204	4	55599381	.	A	G	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=17;VD=2;AF=0.1176;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.00559;SOR=inf;LSEQ=GAGTACCCATTCTCTGCTTG;RSEQ=CAGTCCTGCAAAGGATTTTT;CSQ=G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_000222.3|protein_coding||17/20|NM_000222.3:c.2484+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001093772.2|protein_coding||17/20|NM_001093772.2:c.2472+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385284.1|protein_coding||17/20|NM_001385284.1:c.2487+23A>G|||||||||1||EntrezGene||YES||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385285.1|protein_coding||17/20|NM_001385285.1:c.2481+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385286.1|protein_coding||17/20|NM_001385286.1:c.2469+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385288.1|protein_coding||17/20|NM_001385288.1:c.2475+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385290.1|protein_coding||17/20|NM_001385290.1:c.2484+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||,G|intron_variant|MODIFIER|KIT|3815|Transcript|NM_001385292.1|protein_coding||17/20|NM_001385292.1:c.2472+23A>G|||||||||1||EntrezGene||||||4:g.55599381A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:17:2:1,1:4,11:15,2:0.1176:2,2:9:1:37:0:0.51471:2.57:60:4:0.1176:0:1	0/0:204:0:0,0:75,129:204,0:0:2,0:36.8:1:36.6:1:1:0:60:203:1:0:0.6
    1523. 

  1523. 4	55602910	55602910	C	T	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon19:c.C2620T:p.P874S,KIT:NM_001093772:exon19:c.C2608T:p.P870S	.	.	.	.	.	.	.	.	.	.	.	0.128	0.373	T	0.686	0.431	P	0.485	0.535	P	0.000	0.629	D	1	0.810	D	0.025	0.080	N	-2.28	0.875	D	-3.25	0.652	D	0.492	0.539	-0.076	0.807	T	0.510	0.816	D	0.119	0.800	D	4.741	0.636	24.7	0.997	0.797	0.896	0.499	D	c	-0.194	-0.115	0.999	0.383	0.732	0.924	0	4.74	0.596	3.968	0.563	0.935	0.490	1.000	0.715	0.781	0.330	16.473	0.839	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV105160567;OCCURENCE=1(skin)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	292	4	55602910	.	C	T	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=854;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.01642;SOR=0;LSEQ=GCAGCCCCTATCCTGGAATG;RSEQ=CGGTCGATTCTAAGTTCTAC;CSQ=T|missense_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|19/21||NM_000222.3:c.2620C>T|NP_000213.1:p.Pro874Ser|2678|2620|874|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|19/21||NM_001093772.2:c.2608C>T|NP_001087241.1:p.Pro870Ser|2666|2608|870|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|19/21||NM_001385284.1:c.2623C>T|NP_001372213.1:p.Pro875Ser|2681|2623|875|P/S|Ccg/Tcg|||1||EntrezGene||YES||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385285.1|protein_coding|19/21||NM_001385285.1:c.2617C>T|NP_001372214.1:p.Pro873Ser|2675|2617|873|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385286.1|protein_coding|19/21||NM_001385286.1:c.2605C>T|NP_001372215.1:p.Pro869Ser|2663|2605|869|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|19/21||NM_001385288.1:c.2611C>T|NP_001372217.1:p.Pro871Ser|2669|2611|871|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385290.1|protein_coding|19/21||NM_001385290.1:c.2620C>T|NP_001372219.1:p.Pro874Ser|2678|2620|874|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||,T|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385292.1|protein_coding|19/21||NM_001385292.1:c.2608C>T|NP_001372221.1:p.Pro870Ser|2666|2608|870|P/S|Ccg/Tcg|||1||EntrezGene||||||4:g.55602910C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:854:0:0,0:382,472:854,0:0:2,0:41.4:1:36.2:1:1:0:60:70.167:1:0:0.1	0/1:292:3:1,2:124,164:288,3:0.0103:2,2:32.3:1:37:0:1:1.51013:60:6:0.0104:0:1
    1524. 

  1524. 4	55604674	55604674	G	A	exonic	KIT	.	nonsynonymous SNV	KIT:NM_000222:exon21:c.G2882A:p.G961D,KIT:NM_001093772:exon21:c.G2870A:p.G957D	.	.	.	.	.	.	.	.	.	.	.	0.017	0.599	D	1.0	0.899	D	0.994	0.971	D	0.000	0.629	D	1	0.810	D	2.045	0.562	M	-1.09	0.772	T	-2.27	0.506	N	0.384	0.444	0.119	0.845	D	0.614	0.864	D	0.106	0.783	D	4.987	0.671	25.1	0.998	0.894	0.992	0.926	D	c	0.729	0.689	1.000	0.747	0.732	0.924	0	5.72	0.893	8.645	0.907	1.048	0.713	1.000	0.715	0.880	0.369	17.674	0.881	.	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	58	248	4	55604674	.	G	A	58	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1267;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.00434;SOR=0;LSEQ=TGTGCGGATCAATTCTGTCG;RSEQ=CAGCACCGCTTCCTCCTCCC;CSQ=A|missense_variant|MODERATE|KIT|3815|Transcript|NM_000222.3|protein_coding|21/21||NM_000222.3:c.2882G>A|NP_000213.1:p.Gly961Asp|2940|2882|961|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001093772.2|protein_coding|21/21||NM_001093772.2:c.2870G>A|NP_001087241.1:p.Gly957Asp|2928|2870|957|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385284.1|protein_coding|21/21||NM_001385284.1:c.2885G>A|NP_001372213.1:p.Gly962Asp|2943|2885|962|G/D|gGc/gAc|rs1334133798||1||EntrezGene||YES||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385285.1|protein_coding|21/21||NM_001385285.1:c.2879G>A|NP_001372214.1:p.Gly960Asp|2937|2879|960|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385286.1|protein_coding|21/21||NM_001385286.1:c.2867G>A|NP_001372215.1:p.Gly956Asp|2925|2867|956|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385288.1|protein_coding|21/21||NM_001385288.1:c.2873G>A|NP_001372217.1:p.Gly958Asp|2931|2873|958|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385290.1|protein_coding|21/21||NM_001385290.1:c.2882G>A|NP_001372219.1:p.Gly961Asp|2940|2882|961|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||,A|missense_variant|MODERATE|KIT|3815|Transcript|NM_001385292.1|protein_coding|21/21||NM_001385292.1:c.2870G>A|NP_001372221.1:p.Gly957Asp|2928|2870|957|G/D|gGc/gAc|rs1334133798||1||EntrezGene||||||4:g.55604674G>A|7.959e-06|0|5.782e-05|0|0|0|0|0|0|5.782e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1267:0:0,0:655,611:1266,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:248:3:1,2:116,129:245,3:0.0121:2,2:40.3:1:37:0:1:1.79437:60:6:0.0122:0:1
    1525. 

  1525. 4	55948108	55948108	A	G	intronic	KDR	.	.	.	1.	0.9975	0.9923	1	0.9967	1	1	0.9995	0.9980	rs2412617	rs2412617	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	508794	Hemangioma,_capillary_infantile	MONDO:MONDO:0011191,MedGen:C1865871,OMIM:602089	no_assertion_criteria_provided	Benign	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81784046	COCA-CN|5|321|0.0155763	1	189	35	4	55948108	.	A	G	189	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=0;MSI=2;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAAATTTGTCTTTTTAAT;RSEQ=TGGCTGAGTCTTACCCAAAA;CSQ=G|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||29/29|NM_002253.3:c.3848+15T>C|||||||rs2412617||-1||EntrezGene||YES||||4:g.55948108A>G|0.9986|0.9916|0.9974|0.9951|1|1|0.9994|0.9962|1|1|EAS&SAS&gnomAD_EAS&gnomAD_FIN&gnomAD_SAS|benign||1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	1/1:9:9:5,4:0,0:0,9:1:0,2:48.2:1:37:0:1:0:60:18:1:0:1	1/1:35:35:23,12:0,0:0,35:1:0,2:37.8:1:37:0:1:0:60:70:1:0:1
    1526. 

  1526. 4	55953947	55953947	A	G	intronic	KDR	.	.	.	.	3.229e-05	0	0	0	0.0006	0	0	0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	226	189	4	55953947	.	A	G	226	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=324;VD=0;AF=0;SHIFT3=1;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=TGAAACAATAAACACAGAAG;RSEQ=CTGTTGTTATGGCTTCAGTT;CSQ=G|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||26/29|NM_002253.3:c.3511-22T>C|||||||rs902453458||-1||EntrezGene||YES||||4:g.55953947A>G|3.984e-06|0|0|0|5.438e-05|0|0|0|0|5.438e-05|gnomAD_EAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:324:0:0,0:107,217:324,0:0:2,0:35.6:1:35.1:1:1:0:60:31.4:1:0:0.1	0/1:189:79:23,56:44,66:110,79:0.418:2,2:34.2:1:35.9:1:0.16509:1.61903:60:78:0.4171:0:1.1
    1527. 

  1527. 4	55955608	55955608	C	T	exonic	KDR	.	nonsynonymous SNV	KDR:NM_002253:exon25:c.G3337A:p.E1113K	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	0.995	0.818	D	0.000	0.629	D	1	0.810	D	1.1	0.281	L	-2.62	0.900	D	-3.64	0.698	D	0.923	0.915	0.666	0.927	D	0.776	0.924	D	0.324	0.916	D	7.466	0.952	34	0.999	0.993	0.990	0.892	D	c	0.637	0.653	1.000	0.747	0.722	0.854	0	5.57	0.840	7.905	0.864	0.892	0.403	1.000	0.715	1.000	0.888	19.529	0.952	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	279	4	55955608	.	C	T	37	v3;p8;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=51;VD=2;AF=0.0392;SHIFT3=1;MSI=2;MSILEN=3;SSF=0.02349;SOR=inf;LSEQ=CAATCGCCTACAAAATTCTT;RSEQ=ATCAATCTTTACCCCAGGAT;CSQ=T|missense_variant|MODERATE|KDR|3791|Transcript|NM_002253.3|protein_coding|25/30||NM_002253.3:c.3337G>A|NP_002244.1:p.Glu1113Lys|3639|3337|1113|E/K|Gaa/Aaa|||-1||EntrezGene||YES||||4:g.55955608C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:51:2:1,1:24,25:49,2:0.0392:2,2:7:0:37:0:1:1.04:60:4:0.04:0:1	0/0:279:0:0,0:128,151:279,0:0:2,0:38.2:1:36:1:1:0:60:38.857:1:0:0.1
    1528. 

  1528. 4	55956114	55956114	G	C	intronic	KDR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	180	4	55956114	.	G	C	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=157;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.28455;SOR=0;LSEQ=CAAGCACTGGGTTCATATTT;RSEQ=AAACTTACATCTCCTTTTCT;CSQ=C|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||23/29|NM_002253.3:c.3192+9C>G|||||||||-1||EntrezGene||YES||||4:g.55956114G>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:157:0:0,0:92,65:157,0:0:2,0:30.7:1:36.6:1:1:0:60:77.5:1:0:0.2	0/1:180:2:1,1:96,82:178,2:0.0111:2,2:52:1:37:0:1:1.1697:60:4:0.0112:0:1
    1529. 

  1529. 4	55961159	55961159	T	C	intronic	KDR	.	.	.	0.46	0.2344	0.1383	0.1265	0.2067	0.4825	0.2936	0.2565	0.2363	rs2219471	rs2219471	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55764437;OCCURENCE=8(meninges),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU779058	LAML-KR|1|205|0.00487805,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.5	193	97	4	55961159	.	T	C	193	PASS	STATUS=Germline;SAMPLE=LibM078FTT;TYPE=SNV;DP=148;VD=2;AF=0.0135;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0.02069;LSEQ=GAACAAACAAACTCCTTGAA;RSEQ=ACAAAATGAGTCTTTAAAAG;CSQ=C|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||20/29|NM_002253.3:c.2818-37A>G|||||||rs2219471&COSV55764437||-1||EntrezGene||YES||||4:g.55961159T>C|0.2248|0.1372|0.1002|0.1955|0.4734|0.3068|0.2449|0.2172|0.1424|0.4734|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:148:2:1,1:35,111:146,2:0.0135:2,2:41.5:1:37:0:0.42857:3.14:60:4:0.014:0:1	0/1:97:39:7,32:18,40:58,39:0.4021:2,2:31.9:1:36.7:1:0.16466:2.04239:60:78:0.4105:0:1.2
    1530. 

  1530. 4	55963917	55963917	A	T	exonic	KDR	.	synonymous SNV	KDR:NM_002253:exon18:c.T2526A:p.R842R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	38	289	4	55963917	.	A	T	38	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=416;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.06846;SOR=0;LSEQ=ATCACTTGGCCAAAGGCACC;RSEQ=CGGCCAAGAGGCTTACCTAG;CSQ=T|synonymous_variant|LOW|KDR|3791|Transcript|NM_002253.3|protein_coding|18/30||NM_002253.3:c.2526T>A|NP_002244.1:p.Arg842%3D|2828|2526|842|R|cgT/cgA|||-1||EntrezGene||YES||||4:g.55963917A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:416:0:0,0:205,211:416,0:0:2,0:36.4:1:36.4:1:1:0:60:103:1:0:0.1	0/1:289:3:1,2:136,150:286,3:0.0104:2,2:39.3:1:24.3:1:1:1.80975:60:2:0.0071:0:1
    1531. 

  1531. 4	55964301	55964301	C	T	intronic	KDR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	74	265	4	55964301	.	C	T	74	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=299;VD=4;AF=0.0134;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.07824;SOR=inf;LSEQ=ATTAATAGCAATTGAAAATG;RSEQ=ACCTAGCTTCAGCCGGTCTC;CSQ=T|splice_donor_region_variant&intron_variant|LOW|KDR|3791|Transcript|NM_002253.3|protein_coding||17/29|NM_002253.3:c.2509+3G>A|||||||||-1||EntrezGene||YES||||4:g.55964301C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:299:4:2,2:213,82:295,4:0.0134:2,2:49.5:1:37:0:0.31439:2.588:60:8:0.0135:0:1	0/0:265:0:0,0:167,98:265,0:0:2,0:35.5:1:36.2:1:1:0:60:65.25:1:0:0.1
    1532. 

  1532. 4	55968044	55968044	T	-	intronic	KDR	.	.	.	0.0024	9.839e-05	0.0001	0	0	0.0013	0	0	0	rs779577525	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU128884240	GACA-JP|3|585|0.00512821	0.5	74	134	4	55968043	.	AT	A	74	PASS	STATUS=LikelySomatic;SAMPLE=LibM078FTT;TYPE=Deletion;DP=183;VD=4;AF=0.0219;SHIFT3=8;MSI=9;MSILEN=1;SSF=0.49693;SOR=1.47312;LSEQ=CCATGGTGTATATGTACCAC;RSEQ=TTTTTTTTATCCCACTGACC;CSQ=-|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||15/29|NM_002253.3:c.2266+20del|||||||rs746664609||-1||EntrezGene||YES||||4:g.55968052del|0.0002291|6.497e-05|0.0002397|0|0.0001137|0.001417|0.000159|0|3.413e-05|0.001417|gnomAD_FIN|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:183:4:2,2:101,78:179,4:0.0219:2,2:51.8:1:37:0:1:1.29301:60:8:0.0222:0:0.5	0/1:134:2:1,1:89,43:132,2:0.0149:2,2:54:0:37:0:0.55056:2.05763:60:4:0.0154:0:0
    1533. 

  1533. 4	55968053	55968053	A	C	intronic	KDR	.	.	.	0.58	0.3084	0.1496	0.5298	0.2947	0.3079	0.3853	0.3656	0.3864	rs7655964	rs7655964	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55758590;OCCURENCE=8(meninges),15(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU81784053	ESAD-UK|1|409|0.00244499,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.25	234	141	4	55968053	.	A	C	234	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=205;VD=96;AF=0.4683;SHIFT3=2;MSI=1;MSILEN=1;SSF=0;SOR=inf;LSEQ=TATGTACCACATTTTTTTTT;RSEQ=TCCCACTGACCTTCTATTAT;CSQ=C|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||15/29|NM_002253.3:c.2266+11T>G|||||||rs7655964&CR116625&COSV55758590||-1||EntrezGene||YES||||4:g.55968053A>C|0.358|0.1435|0.5601|0.3259|0.3113|0.3652|0.348|0.357|0.3145|0.5601|gnomAD_AMR||0&0&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:205:96:56,40:57,52:109,96:0.4683:2,2:35.1:1:35.6:1:0.40187:1.28:60:47:0.4845:0:1.1	0/0:141:0:0,0:89,52:141,0:0:2,0:38.2:1:34.9:1:1:0:60:19.143:1:0:0.2
    1534. 

  1534. 4	55968082	55968082	C	A	exonic	KDR	.	nonsynonymous SNV	KDR:NM_002253:exon15:c.G2248T:p.A750S	.	.	.	.	.	.	.	.	.	.	.	0.008	0.586	D	0.875	0.461	P	0.559	0.477	P	0.003	0.351	N	0.991	0.412	D	1.505	0.383	L	-0.49	0.704	T	-2.18	0.491	N	0.129	0.147	-0.500	0.687	T	0.313	0.683	T	0.084	0.744	D	2.848	0.403	21.6	0.988	0.455	0.951	0.631	D	c	-0.232	-0.340	0.063	0.153	0.707	0.730	0	0.454	0.158	1.658	0.368	-0.304	0.080	1.000	0.715	0.157	0.207	9.968	0.407	Immunoglobulin I-set|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	44	177	4	55968082	.	C	A	44	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=272;VD=3;AF=0.011;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.22135;SOR=inf;LSEQ=ACCTTCTATTATGAAAAATG;RSEQ=CTCCACTTTTGCACAGCCAA;CSQ=A|missense_variant|MODERATE|KDR|3791|Transcript|NM_002253.3|protein_coding|15/30||NM_002253.3:c.2248G>T|NP_002244.1:p.Ala750Ser|2550|2248|750|A/S|Gca/Tca|COSV55776655||-1||EntrezGene||YES||||4:g.55968082C>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:272:3:2,1:133,136:269,3:0.011:2,2:47:1:28.3:1:0.62085:2.04:60:2:0.0075:0:2	0/0:177:0:0,0:104,73:177,0:0:2,0:38.4:1:35.5:1:1:0:60:34.4:1:0:0.1
    1535. 

  1535. 4	55972974	55972974	T	A	exonic	KDR	.	nonsynonymous SNV	KDR:NM_002253:exon11:c.A1416T:p.Q472H	0.47	0.2213	0.1045	0.1265	0.1987	0.4876	0.2825	0.2518	0.2280	rs1870377	rs1870377	0.033	0.443	D	0.955	0.525	P	0.8	0.564	P	0.938	0.084	N	1	0.090	P	1.625	0.417	L	-1.02	0.763	T	-1.31	0.328	N	0.102	0.106	-1.046	0.154	T	0.000	0.000	T	.	.	.	-0.385	0.063	0.421	0.734	0.100	0.068	0.127	N	c	-0.891	-1.019	0.076	0.157	0.707	0.730	0	-1.82	0.074	-0.039	0.120	-0.227	0.095	0.012	0.185	0.010	0.111	5.530	0.162	Immunoglobulin subtype|Immunoglobulin-like domain	.	.	ID=COSV55758724;OCCURENCE=1(breast),3(penis),1(female_genital_tract_(site_indeterminate)),10(meninges),4(large_intestine),1(central_nervous_system),2(biliary_tract),2(ovary),6(bone),2(stomach),3(haematopoietic_and_lymphoid_tissue),16(soft_tissue),1(autonomic_ganglia),5(skin),47(upper_aerodigestive_tract)	138342	not_specified	MedGen:CN169374	no_assertion_provided	not_provided	Benign	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	0	0	0	0	0	1	0	0	0	MU101068	ESAD-UK|1|409|0.00244499,LAML-KR|3|205|0.0146341,COCA-CN|3|321|0.00934579,BRCA-KR|1|50|0.02	0.25	224	146	4	55972974	.	T	A	224	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=27;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGTTTGTCACTGAGACAGC;RSEQ=TGGCTATAAGAAAGAGATAA;CSQ=A|missense_variant|MODERATE|KDR|3791|Transcript|NM_002253.3|protein_coding|11/30||NM_002253.3:c.1416A>T|NP_002244.1:p.Gln472His|1718|1416|472|Q/H|caA/caT|rs1870377&CM074306&COSV55758724||-1||EntrezGene||YES||||4:g.55972974T>A|0.2227|0.1032|0.1021|0.197|0.4792|0.2975|0.2392|0.2151|0.1639|0.4792|gnomAD_EAS|not_provided|0&0&1|1&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:27:0:0,0:15,12:27,0:0:2,0:35.1:1:36:1:1:0:60:26:1:0:0.1	1/0:146:75:35,40:32,38:70,75:0.5137:2,2:41.7:1:36:1:1:1.04:60:74:0.5175:0:1.1
    1536. 

  1536. 4	55972999	55972999	G	T	intronic	KDR	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	126	4	55972999	.	G	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=20;VD=2;AF=0.1;SHIFT3=1;MSI=2;MSILEN=2;SSF=0.01795;SOR=inf;LSEQ=TATAAGAAAGAGATAACAGC;RSEQ=CATATTATGATTTAATTTTT;CSQ=T|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||10/29|NM_002253.3:c.1413-22C>A|||||||COSV99816407||-1||EntrezGene||YES||||4:g.55972999G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:20:2:1,1:8,9:17,2:0.1:2,2:25:0:37:0:1:1.12:60:4:0.1053:0:1	0/0:126:0:0,0:54,72:126,0:0:2,0:41.6:1:35.9:1:1:0:60:62:1:0:0.7
    1537. 

  1537. 4	55979602	55979602	C	A	exonic	KDR	.	nonsynonymous SNV	KDR:NM_002253:exon7:c.G845T:p.G282V	.	.	.	.	.	.	.	.	.	.	.	0.561	0.063	T	0.968	0.546	D	0.317	0.399	B	0.074	0.213	N	0.996	0.231	N	1.955	0.530	M	-0.1	0.643	T	-0.63	0.185	N	0.085	0.080	-1.004	0.289	T	0.109	0.394	T	0.026	0.491	D	1.106	0.200	11.25	0.745	0.104	0.062	0.121	N	c	-0.718	-0.753	1.000	0.415	0.722	0.854	0	1.42	0.214	0.797	0.265	0.007	0.138	0.002	0.151	0.580	0.285	2.006	0.032	Immunoglobulin|Immunoglobulin subtype|Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	.	.	0.25	37	340	4	55979602	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.13674;SOR=inf;LSEQ=AAAATTTCTTCATCTCACTC;RSEQ=CAGACTGGGTTTTTAGGTCT;CSQ=A|missense_variant|MODERATE|KDR|3791|Transcript|NM_002253.3|protein_coding|7/30||NM_002253.3:c.845G>T|NP_002244.1:p.Gly282Val|1147|845|282|G/V|gGg/gTg|||-1||EntrezGene||YES||||4:g.55979602C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:83,115:198,2:0.01:2,2:16.5:1:37:0:1:1.38:60:4:0.0102:0:1	0/0:340:0:0,0:138,202:340,0:0:2,0:34.3:1:36:1:1:0:60:67:1:0:0.1
    1538. 

  1538. 4	55979622	55979622	T	G	exonic	KDR	.	synonymous SNV	KDR:NM_002253:exon7:c.A825C:p.R275R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	286	4	55979622	.	T	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=158;VD=2;AF=0.0127;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.12612;SOR=inf;LSEQ=CCAGACTGGGTTTTTAGGTC;RSEQ=CGGTTTACAAGTTTCTTATG;CSQ=G|synonymous_variant|LOW|KDR|3791|Transcript|NM_002253.3|protein_coding|7/30||NM_002253.3:c.825A>C|NP_002244.1:p.Arg275%3D|1127|825|275|R|cgA/cgC|COSV99816335||-1||EntrezGene||YES||||4:g.55979622T>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:158:2:1,1:54,102:156,2:0.0127:2,2:17:0:37:0:1:1.88:60:4:0.013:0:1	0/0:286:0:0,0:110,176:286,0:0:2,0:36.7:1:36.4:1:1:0:60:142:1:0:0.2
    1539. 

  1539. 4	55980456	55980456	C	T	intronic	KDR	.	.	.	0.22	0.1566	0.0772	0.1229	0.3179	0.1602	0.1723	0.1963	0.1741	rs2305949	rs2305949	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV55758738;OCCURENCE=1(meninges),1(haematopoietic_and_lymphoid_tissue),7(soft_tissue)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU12035406	ESAD-UK|1|409|0.00244499,COCA-CN|1|321|0.00311526	0.25	234	169	4	55980456	.	C	T	234	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=39;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGCAAGTAAATTGAAAAAA;RSEQ=AGAACATGAGAGAGCAAATA;CSQ=T|intron_variant|MODIFIER|KDR|3791|Transcript|NM_002253.3|protein_coding||5/29|NM_002253.3:c.659-24G>A|||||||rs2305949&COSV55758738||-1||EntrezGene||YES||||4:g.55980456C>T|0.1783|0.07487|0.1011|0.2963|0.18|0.1659|0.2057|0.1954|0.1842|0.2963|gnomAD_ASJ||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:39:0:0,0:16,23:39,0:0:2,0:31.1:1:35.7:1:1:0:60:38:1:0:0	0/1:169:82:26,56:32,55:87,82:0.4852:2,2:35.3:1:36.9:1:0.5198:1.25147:60:164:0.4852:0:1.2
    1540. 

  1540. 4	55981145	55981145	A	G	exonic	KDR	.	nonsynonymous SNV	KDR:NM_002253:exon5:c.T554C:p.F185S	.	.	.	.	.	.	.	.	.	.	.	0.002	0.721	D	0.982	0.899	D	0.93	0.916	D	0.000	0.843	D	1	0.810	D	2.86	0.833	M	3.46	0.053	T	-5.95	0.891	D	0.954	0.951	-1.189	0.002	T	0.060	0.251	T	0.042	0.602	D	6.807	0.925	32	0.999	0.963	0.990	0.895	D	c	0.799	0.788	1.000	0.747	0.722	0.854	0	5.9	0.949	8.549	0.904	1.088	0.866	1.000	0.715	0.996	0.625	16.315	0.827	Immunoglobulin-like domain|Immunoglobulin-like fold	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	100	4	55981145	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=10;VD=0;AF=0;SHIFT3=2;MSI=3;MSILEN=1;SSF=0.82569;SOR=0;LSEQ=TCATGTAGCTGGGAATAGTA;RSEQ=AGCCCTTCTTGCTGTCCCAG;CSQ=G|missense_variant|MODERATE|KDR|3791|Transcript|NM_002253.3|protein_coding|5/30||NM_002253.3:c.554T>C|NP_002244.1:p.Phe185Ser|856|554|185|F/S|tTt/tCt|||-1||EntrezGene||YES||||4:g.55981145A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:10:0:0,0:5,5:10,0:0:2,0:37.3:1:37:0:1:0:60:20:1:0:0	0/1:100:2:1,1:46,52:98,2:0.02:2,2:46:1:37:0:1:1.13:60:4:0.02:0:1
    1541. 

  1541. 4	66189867	66189867	T	A	exonic	EPHA5	.	stopgain	EPHA5:NM_001281766:exon17:c.A3016T:p.K1006X,EPHA5:NM_182472:exon17:c.A3013T:p.K1005X,EPHA5:NM_001281765:exon18:c.A3082T:p.K1028X,EPHA5:NM_001318761:exon18:c.A2875T:p.K959X,EPHA5:NM_004439:exon18:c.A3079T:p.K1027X	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.000	0.559	D	1	0.810	D	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.774	0.986	40	0.995	0.700	0.966	0.698	D	c	0.914	0.778	0.093	0.162	0.554	0.246	0	5.25	0.731	5.714	0.679	1.061	0.807	1.000	0.715	1.000	0.888	15.162	0.724	Sterile alpha motif domain|Sterile alpha motif/pointed domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	218	4	66189867	.	T	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=72;VD=2;AF=0.0278;SHIFT3=2;MSI=1;MSILEN=1;SSF=0.061;SOR=inf;LSEQ=TCCGTTTACCAGCTGCACCT;RSEQ=CATTTCTTGAAGGCTGTTCA;CSQ=A|stop_gained|HIGH|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|18/18||NM_001281765.3:c.3082A>T|NP_001268694.1:p.Lys1028Ter|3829|3082|1028|K/*|Aag/Tag|||-1||EntrezGene||YES||||4:g.66189867T>A||||||||||||||,A|stop_gained|HIGH|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|17/17||NM_001281766.3:c.3016A>T|NP_001268695.1:p.Lys1006Ter|3763|3016|1006|K/*|Aag/Tag|||-1||EntrezGene||||||4:g.66189867T>A||||||||||||||,A|stop_gained|HIGH|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|18/18||NM_001318761.2:c.2875A>T|NP_001305690.1:p.Lys959Ter|2953|2875|959|K/*|Aag/Tag|||-1||EntrezGene||||||4:g.66189867T>A||||||||||||||,A|stop_gained|HIGH|EPHA5|2044|Transcript|NM_004439.8|protein_coding|18/18||NM_004439.8:c.3079A>T|NP_004430.4:p.Lys1027Ter|3826|3079|1027|K/*|Aag/Tag|||-1||EntrezGene||||||4:g.66189867T>A||||||||||||||,A|stop_gained|HIGH|EPHA5|2044|Transcript|NM_182472.5|protein_coding|17/17||NM_182472.5:c.3013A>T|NP_872272.2:p.Lys1005Ter|3760|3013|1005|K/*|Aag/Tag|||-1||EntrezGene||||||4:g.66189867T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:72:2:1,1:38,32:70,2:0.0278:2,2:54:1:31:1:1:1.18465:60:4:0.0286:0:1	0/0:218:0:0,0:125,93:218,0:0:2,0:38.1:1:36.5:1:1:0:60:108:1:0:0.1
    1542. 

  1542. 4	66197804	66197804	C	T	exonic	EPHA5	.	synonymous SNV	EPHA5:NM_001281766:exon16:c.G2832A:p.G944G,EPHA5:NM_182472:exon16:c.G2829A:p.G943G,EPHA5:NM_001281765:exon17:c.G2898A:p.G966G,EPHA5:NM_001281767:exon17:c.G2898A:p.G966G,EPHA5:NM_001318761:exon17:c.G2691A:p.G897G,EPHA5:NM_004439:exon17:c.G2895A:p.G965G	0.47	0.2977	0.1274	0.2888	0.3411	0.4289	0.3329	0.3694	0.3796	rs7349683	rs7349683	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56661916;OCCURENCE=1(breast),1(lung)	.	.	.	.	.	Benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	1	MU13984718	ESAD-UK|1|409|0.00244499,LUSC-KR|1|170|0.00588235,COCA-CN|4|321|0.0124611	0.25	224	157	4	66197804	.	C	T	224	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=75;VD=0;AF=0;SHIFT3=1;MSI=4;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACCTACTGATCTGTAGGC;RSEQ=CCAGATCCTAGTGGGCTATG;CSQ=T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|17/18||NM_001281765.3:c.2898G>A|NP_001268694.1:p.Gly966%3D|3645|2898|966|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||YES||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|16/17||NM_001281766.3:c.2832G>A|NP_001268695.1:p.Gly944%3D|3579|2832|944|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|17/17||NM_001281767.3:c.2898G>A|NP_001268696.1:p.Gly966%3D|3645|2898|966|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|17/18||NM_001318761.2:c.2691G>A|NP_001305690.1:p.Gly897%3D|2769|2691|897|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding|17/18||NM_004439.8:c.2895G>A|NP_004430.4:p.Gly965%3D|3642|2895|965|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding|16/17||NM_182472.5:c.2829G>A|NP_872272.2:p.Gly943%3D|3576|2829|943|G|ggG/ggA|rs7349683&COSV56661916||-1||EntrezGene||||||4:g.66197804C>T|0.3455|0.1244|0.2934|0.3428|0.4218|0.3457|0.3571|0.3525|0.4315|0.4714|SAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:75:0:0,0:27,48:75,0:0:2,0:32:1:36.8:1:1:0:60:150:1:0:0.1	0/1:157:74:29,45:39,43:82,74:0.4713:2,2:38.8:1:36.2:1:0.33358:1.40426:60:73:0.471:0:1.1
    1543. 

  1543. 4	66201634	66201634	G	A	intronic	EPHA5	.	.	.	0.061	0.0087	0.0009	0.0036	0	0.0638	0.0189	0.0059	0.0051	rs3752774	rs3752774	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV56633144;OCCURENCE=1(soft_tissue),1(lung)	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU82085702	LICA-CN|1|402|0.00248756,LUSC-KR|1|170|0.00588235,COCA-CN|3|321|0.00934579	0.25	251	220	4	66201634	.	G	A	251	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=82;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0;SOR=0;LSEQ=TACATTCTGGAAAATCACTC;RSEQ=GATCTGGCCTTGTACCTGCA;CSQ=A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||16/17|NM_001281765.3:c.2855+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||YES||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||15/16|NM_001281766.3:c.2789+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||16/16|NM_001281767.3:c.2855+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||16/17|NM_001318761.2:c.2648+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||16/17|NM_004439.8:c.2852+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||15/16|NM_182472.5:c.2786+16C>T|||||||rs3752774&COSV56633144||-1||EntrezGene||||||4:g.66201634G>A|0.01001|0.001061|0.001764|0.0002639|0.05588|0.01927|0.006131|0.007474|0.005666|0.0615|EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:82:0:0,0:57,25:82,0:0:2,0:21.4:1:36.1:1:1:0:60:40:1:0:0.1	1/0:220:118:79,39:61,41:102,118:0.5364:2,2:38.2:1:36.6:1:0.32542:1.36:60:117:0.5342:0:1.2
    1544. 

  1544. 4	66201705	66201705	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon15:c.G2734A:p.D912N,EPHA5:NM_182472:exon15:c.G2731A:p.D911N,EPHA5:NM_001281765:exon16:c.G2800A:p.D934N,EPHA5:NM_001281767:exon16:c.G2800A:p.D934N,EPHA5:NM_001318761:exon16:c.G2593A:p.D865N,EPHA5:NM_004439:exon16:c.G2797A:p.D933N	.	.	.	.	.	.	.	.	.	.	.	0.001	0.784	D	1.0	0.899	D	0.999	0.971	D	0.000	0.629	D	1	0.810	D	0.775	0.195	N	0.06	0.618	T	-4.29	0.769	D	0.12	0.140	-0.397	0.722	T	0.343	0.709	T	0.055	0.663	D	7.277	0.947	34	0.999	0.995	0.990	0.895	D	c	0.768	0.826	1.000	0.747	0.554	0.246	0	6.17	0.997	7.905	0.864	0.935	0.490	1.000	0.715	0.999	0.750	20.879	0.999	Protein kinase domain|Protein kinase-like domain;Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	280	4	66201705	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=200;VD=2;AF=0.01;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.1731;SOR=inf;LSEQ=TGGGTTACGTATCAGCTTGT;RSEQ=CAACATGTTGACTATTTCAT;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|16/18||NM_001281765.3:c.2800G>A|NP_001268694.1:p.Asp934Asn|3547|2800|934|D/N|Gac/Aac|||-1||EntrezGene||YES||||4:g.66201705C>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|15/17||NM_001281766.3:c.2734G>A|NP_001268695.1:p.Asp912Asn|3481|2734|912|D/N|Gac/Aac|||-1||EntrezGene||||||4:g.66201705C>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|16/17||NM_001281767.3:c.2800G>A|NP_001268696.1:p.Asp934Asn|3547|2800|934|D/N|Gac/Aac|||-1||EntrezGene||||||4:g.66201705C>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|16/18||NM_001318761.2:c.2593G>A|NP_001305690.1:p.Asp865Asn|2671|2593|865|D/N|Gac/Aac|||-1||EntrezGene||||||4:g.66201705C>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|16/18||NM_004439.8:c.2797G>A|NP_004430.4:p.Asp933Asn|3544|2797|933|D/N|Gac/Aac|||-1||EntrezGene||||||4:g.66201705C>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|15/17||NM_182472.5:c.2731G>A|NP_872272.2:p.Asp911Asn|3478|2731|911|D/N|Gac/Aac|||-1||EntrezGene||||||4:g.66201705C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:200:2:1,1:114,84:198,2:0.01:2,2:27:0:37:0:1:1.35502:60:4:0.0102:0:1	0/0:280:0:0,0:143,136:279,0:0:0:0:0:0:0:1:0:0:0:0:0:0
    1545. 

  1545. 4	66201788	66201788	G	A	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon15:c.C2651T:p.A884V,EPHA5:NM_182472:exon15:c.C2648T:p.A883V,EPHA5:NM_001281765:exon16:c.C2717T:p.A906V,EPHA5:NM_001281767:exon16:c.C2717T:p.A906V,EPHA5:NM_001318761:exon16:c.C2510T:p.A837V,EPHA5:NM_004439:exon16:c.C2714T:p.A905V	.	.	.	.	.	.	.	.	.	.	.	0.255	0.200	T	0.836	0.443	P	0.464	0.448	P	0.000	0.629	D	1.000	0.477	D	0.74	0.190	N	-1.69	0.830	D	-1.41	0.348	N	0.161	0.260	-0.240	0.766	T	0.421	0.766	T	0.016	0.372	T	2.154	0.320	17.21	0.972	0.324	0.942	0.602	D	c	0.146	0.315	0.960	0.284	0.554	0.246	0	5.93	0.959	4.724	0.614	1.048	0.713	1.000	0.715	1.000	0.888	20.354	0.988	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	243	4	66201788	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=187;VD=2;AF=0.0107;SHIFT3=0;MSI=2;MSILEN=3;SSF=0.18855;SOR=inf;LSEQ=GCATTAACTGATAGAGAGCA;RSEQ=CAGGACAATCCATGGGGCTT;CSQ=A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|16/18||NM_001281765.3:c.2717C>T|NP_001268694.1:p.Ala906Val|3464|2717|906|A/V|gCt/gTt|||-1||EntrezGene||YES||||4:g.66201788G>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|15/17||NM_001281766.3:c.2651C>T|NP_001268695.1:p.Ala884Val|3398|2651|884|A/V|gCt/gTt|||-1||EntrezGene||||||4:g.66201788G>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|16/17||NM_001281767.3:c.2717C>T|NP_001268696.1:p.Ala906Val|3464|2717|906|A/V|gCt/gTt|||-1||EntrezGene||||||4:g.66201788G>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|16/18||NM_001318761.2:c.2510C>T|NP_001305690.1:p.Ala837Val|2588|2510|837|A/V|gCt/gTt|||-1||EntrezGene||||||4:g.66201788G>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|16/18||NM_004439.8:c.2714C>T|NP_004430.4:p.Ala905Val|3461|2714|905|A/V|gCt/gTt|||-1||EntrezGene||||||4:g.66201788G>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|15/17||NM_182472.5:c.2648C>T|NP_872272.2:p.Ala883Val|3395|2648|883|A/V|gCt/gTt|||-1||EntrezGene||||||4:g.66201788G>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:187:2:1,1:74,111:185,2:0.0107:2,2:40:1:37:0:1:1.5:60:4:0.0108:0:1	0/0:243:0:0,0:101,142:243,0:0:2,0:38.2:1:36.4:1:1:0:60:242:1:0:0
    1546. 

  1546. 4	66201794	66201794	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon15:c.G2645A:p.C882Y,EPHA5:NM_182472:exon15:c.G2642A:p.C881Y,EPHA5:NM_001281765:exon16:c.G2711A:p.C904Y,EPHA5:NM_001281767:exon16:c.G2711A:p.C904Y,EPHA5:NM_001318761:exon16:c.G2504A:p.C835Y,EPHA5:NM_004439:exon16:c.G2708A:p.C903Y	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.629	D	1	0.810	D	2.775	0.813	M	-1.85	0.843	D	-10.0	0.989	D	0.986	0.991	0.780	0.942	D	0.815	0.938	D	0.325	0.916	D	6.274	0.866	29.0	0.998	0.879	0.985	0.838	D	c	0.926	0.869	1.000	0.747	0.554	0.246	0	5.8	0.921	7.905	0.864	0.935	0.490	1.000	0.715	0.987	0.523	20.054	0.976	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	236	4	66201794	.	C	T	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=182;VD=2;AF=0.011;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.18899;SOR=inf;LSEQ=ACTGATAGAGAGCAGCAGGA;RSEQ=AATCCATGGGGCTTGGCAGA;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|16/18||NM_001281765.3:c.2711G>A|NP_001268694.1:p.Cys904Tyr|3458|2711|904|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||YES||||4:g.66201794C>T|||||||||||||1|1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|15/17||NM_001281766.3:c.2645G>A|NP_001268695.1:p.Cys882Tyr|3392|2645|882|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||||||4:g.66201794C>T|||||||||||||1|1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|16/17||NM_001281767.3:c.2711G>A|NP_001268696.1:p.Cys904Tyr|3458|2711|904|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||||||4:g.66201794C>T|||||||||||||1|1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|16/18||NM_001318761.2:c.2504G>A|NP_001305690.1:p.Cys835Tyr|2582|2504|835|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||||||4:g.66201794C>T|||||||||||||1|1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|16/18||NM_004439.8:c.2708G>A|NP_004430.4:p.Cys903Tyr|3455|2708|903|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||||||4:g.66201794C>T|||||||||||||1|1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|15/17||NM_182472.5:c.2642G>A|NP_872272.2:p.Cys881Tyr|3389|2642|881|C/Y|tGt/tAt|COSV56651842||-1||EntrezGene||||||4:g.66201794C>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:182:2:1,1:69,111:180,2:0.011:2,2:34:0:37:0:1:1.6:60:4:0.011:0:1	0/0:236:0:0,0:94,142:236,0:0:2,0:38.2:1:36.4:1:1:0:60:58:1:0:0.1
    1547. 

  1547. 4	66213858	66213858	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon14:c.G2509A:p.A837T,EPHA5:NM_182472:exon14:c.G2506A:p.A836T,EPHA5:NM_001281765:exon15:c.G2575A:p.A859T,EPHA5:NM_001281767:exon15:c.G2575A:p.A859T,EPHA5:NM_001318761:exon15:c.G2368A:p.A790T,EPHA5:NM_004439:exon15:c.G2572A:p.A858T	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.000	0.452	D	1.000	0.588	D	2.22	0.631	M	-0.07	0.638	T	-3.38	0.672	D	0.817	0.836	-0.044	0.813	T	0.444	0.781	T	0.127	0.809	D	6.665	0.913	32	0.999	0.986	0.977	0.763	D	c	0.693	0.658	1.000	0.458	0.554	0.246	0	5.01	0.663	5.014	0.636	0.020	0.144	1.000	0.715	0.998	0.697	16.623	0.847	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	169	4	66213858	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=42;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.64076;SOR=0;LSEQ=ATAACTCCAGACATCACTGG;RSEQ=AGAAGTAAACTTTCGGAAAG;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|15/18||NM_001281765.3:c.2575G>A|NP_001268694.1:p.Ala859Thr|3322|2575|859|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||YES||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|14/17||NM_001281766.3:c.2509G>A|NP_001268695.1:p.Ala837Thr|3256|2509|837|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|15/17||NM_001281767.3:c.2575G>A|NP_001268696.1:p.Ala859Thr|3322|2575|859|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|15/18||NM_001318761.2:c.2368G>A|NP_001305690.1:p.Ala790Thr|2446|2368|790|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|15/18||NM_004439.8:c.2572G>A|NP_004430.4:p.Ala858Thr|3319|2572|858|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|14/17||NM_182472.5:c.2506G>A|NP_872272.2:p.Ala836Thr|3253|2506|836|A/T|Gcc/Acc|rs1401469962||-1||EntrezGene||||||4:g.66213858C>T|0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:42:0:0,0:25,17:42,0:0:2,0:42.8:1:35.5:1:1:0:60:20:1:0:0	0/1:169:2:1,1:83,84:167,2:0.0118:2,2:52:0:37:0:1:1.01:60:4:0.0122:0:1
    1548. 

  1548. 4	66213869	66213869	T	C	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon14:c.A2498G:p.K833R,EPHA5:NM_182472:exon14:c.A2495G:p.K832R,EPHA5:NM_001281765:exon15:c.A2564G:p.K855R,EPHA5:NM_001281767:exon15:c.A2564G:p.K855R,EPHA5:NM_001318761:exon15:c.A2357G:p.K786R,EPHA5:NM_004439:exon15:c.A2561G:p.K854R	.	.	.	.	.	.	.	.	.	.	.	0.003	0.682	D	0.997	0.899	D	0.997	0.916	D	0.000	0.629	D	1.000	0.588	D	0.47	0.131	N	-1.69	0.830	D	-2.44	0.539	N	0.396	0.480	0.256	0.868	D	0.568	0.843	D	0.057	0.669	D	4.740	0.636	24.7	0.999	0.979	0.988	0.869	D	c	0.656	0.710	1.000	0.747	0.554	0.246	0	5.86	0.939	8.017	0.886	1.061	0.807	1.000	0.715	1.000	0.888	16.251	0.822	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV56666347;OCCURENCE=1(large_intestine)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	168	4	66213869	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=39;VD=2;AF=0.0513;SHIFT3=1;MSI=3;MSILEN=1;SSF=0.03475;SOR=inf;LSEQ=CATCACTGGCAGAAGTAAAC;RSEQ=TTCGGAAAGCTATTGCTTCT;CSQ=C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|15/18||NM_001281765.3:c.2564A>G|NP_001268694.1:p.Lys855Arg|3311|2564|855|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||YES||||4:g.66213869T>C|||||||||||||1|1,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|14/17||NM_001281766.3:c.2498A>G|NP_001268695.1:p.Lys833Arg|3245|2498|833|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||||||4:g.66213869T>C|||||||||||||1|1,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|15/17||NM_001281767.3:c.2564A>G|NP_001268696.1:p.Lys855Arg|3311|2564|855|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||||||4:g.66213869T>C|||||||||||||1|1,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|15/18||NM_001318761.2:c.2357A>G|NP_001305690.1:p.Lys786Arg|2435|2357|786|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||||||4:g.66213869T>C|||||||||||||1|1,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|15/18||NM_004439.8:c.2561A>G|NP_004430.4:p.Lys854Arg|3308|2561|854|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||||||4:g.66213869T>C|||||||||||||1|1,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|14/17||NM_182472.5:c.2495A>G|NP_872272.2:p.Lys832Arg|3242|2495|832|K/R|aAg/aGg|COSV56666347||-1||EntrezGene||||||4:g.66213869T>C|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:39:2:1,1:21,16:37,2:0.0513:2,2:36.5:1:37:0:1:1.30327:60:4:0.0513:0:1	0/0:168:0:0,0:82,86:168,0:0:2,0:39.6:1:35.9:1:1:0:60:41:1:0:0.1
    1549. 

  1549. 4	66217127	66217127	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon13:c.G2425A:p.E809K,EPHA5:NM_182472:exon13:c.G2422A:p.E808K,EPHA5:NM_001281765:exon14:c.G2491A:p.E831K,EPHA5:NM_001281767:exon14:c.G2491A:p.E831K,EPHA5:NM_001318761:exon14:c.G2284A:p.E762K,EPHA5:NM_004439:exon14:c.G2488A:p.E830K	0.	.	.	.	.	.	.	.	.	rs767617774	.	0.001	0.784	D	1.0	0.899	D	0.999	0.916	D	0.000	0.629	D	1.000	0.588	D	0.89	0.217	L	-1.62	0.824	D	-3.08	0.650	D	0.648	0.801	0.404	0.892	D	0.690	0.893	D	0.185	0.859	D	7.395	0.950	34	0.999	0.997	0.968	0.706	D	c	0.768	0.781	1.000	0.480	0.554	0.246	0	5.98	0.971	6.081	0.707	0.892	0.403	1.000	0.715	0.995	0.604	20.437	0.991	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	ID=COSV104563633;OCCURENCE=1(breast)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	112	4	66217127	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=71;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.37327;SOR=0;LSEQ=CCTTGTGGTGTAGGCTGCCT;RSEQ=GGGATCATCTTCCAGTACCC;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|14/18||NM_001281765.3:c.2491G>A|NP_001268694.1:p.Glu831Lys|3238|2491|831|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||YES||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|13/17||NM_001281766.3:c.2425G>A|NP_001268695.1:p.Glu809Lys|3172|2425|809|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|14/17||NM_001281767.3:c.2491G>A|NP_001268696.1:p.Glu831Lys|3238|2491|831|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|14/18||NM_001318761.2:c.2284G>A|NP_001305690.1:p.Glu762Lys|2362|2284|762|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|14/18||NM_004439.8:c.2488G>A|NP_004430.4:p.Glu830Lys|3235|2488|830|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|13/17||NM_182472.5:c.2422G>A|NP_872272.2:p.Glu808Lys|3169|2422|808|E/K|Gag/Aag|rs767617774&COSV104563633&COSV56676915||-1||EntrezGene||||||4:g.66217127C>T|7.966e-06|0|0|0|0|0|8.814e-06|0.0001632|0|0.0001632|gnomAD_OTH||0&1&1|0&1&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:71:0:0,0:50,21:71,0:0:2,0:34.5:1:36.8:1:1:0:60:142:1:0:0	0/1:112:2:1,1:71,39:110,2:0.0179:2,2:18.5:1:37:0:1:1.81013:60:4:0.0179:0:1
    1550. 

  1550. 4	66217145	66217145	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon13:c.G2407A:p.V803I,EPHA5:NM_182472:exon13:c.G2404A:p.V802I,EPHA5:NM_001281765:exon14:c.G2473A:p.V825I,EPHA5:NM_001281767:exon14:c.G2473A:p.V825I,EPHA5:NM_001318761:exon14:c.G2266A:p.V756I,EPHA5:NM_004439:exon14:c.G2470A:p.V824I	0.0051	3.235e-05	0	0	0	0.0006	0	0	0	rs548263764	.	0.063	0.367	T	0.0	0.067	B	0.003	0.104	B	0.000	0.523	D	1.000	0.474	D	-0.175	0.042	N	-1.63	0.825	D	-0.43	0.183	N	0.103	0.175	-0.500	0.687	T	0.397	0.749	T	0.025	0.477	T	3.075	0.429	22.5	0.996	0.753	0.961	0.675	D	c	0.052	0.263	1.000	0.517	0.554	0.246	0	5.98	0.971	5.022	0.636	0.892	0.403	1.000	0.715	0.993	0.574	14.575	0.677	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	119	4	66217145	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=97;VD=0;AF=0;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.30237;SOR=0;LSEQ=CTCGGGATCATCTTCCAGTA;RSEQ=CCGGGAAAGTCCAAAGTCAG;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|14/18||NM_001281765.3:c.2473G>A|NP_001268694.1:p.Val825Ile|3220|2473|825|V/I|Gta/Ata|rs548263764||-1||EntrezGene||YES||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|13/17||NM_001281766.3:c.2407G>A|NP_001268695.1:p.Val803Ile|3154|2407|803|V/I|Gta/Ata|rs548263764||-1||EntrezGene||||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|14/17||NM_001281767.3:c.2473G>A|NP_001268696.1:p.Val825Ile|3220|2473|825|V/I|Gta/Ata|rs548263764||-1||EntrezGene||||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|14/18||NM_001318761.2:c.2266G>A|NP_001305690.1:p.Val756Ile|2344|2266|756|V/I|Gta/Ata|rs548263764||-1||EntrezGene||||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|14/18||NM_004439.8:c.2470G>A|NP_004430.4:p.Val824Ile|3217|2470|824|V/I|Gta/Ata|rs548263764||-1||EntrezGene||||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|13/17||NM_182472.5:c.2404G>A|NP_872272.2:p.Val802Ile|3151|2404|802|V/I|Gta/Ata|rs548263764||-1||EntrezGene||||||4:g.66217145C>T|0.000426|0|0|0|0|0|3.523e-05|0.0004897|0.003267|0.0051|SAS|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:97:0:0,0:67,30:97,0:0:2,0:34.5:1:35.9:1:1:0:60:31.333:1:0:0.1	0/1:119:2:1,1:76,41:117,2:0.0168:2,2:46:1:37:0:1:1.84354:60:4:0.0171:0:1
    1551. 

  1551. 4	66217171	66217171	T	A	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon13:c.A2381T:p.K794I,EPHA5:NM_182472:exon13:c.A2378T:p.K793I,EPHA5:NM_001281765:exon14:c.A2447T:p.K816I,EPHA5:NM_001281767:exon14:c.A2447T:p.K816I,EPHA5:NM_001318761:exon14:c.A2240T:p.K747I,EPHA5:NM_004439:exon14:c.A2444T:p.K815I	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	0.999	0.899	D	1.0	0.971	D	0.000	0.629	D	1	0.810	D	3.44	0.923	M	-0.69	0.727	T	-7.23	0.945	D	0.933	0.934	0.677	0.929	D	0.689	0.893	D	0.278	0.902	D	6.784	0.923	32	0.995	0.685	0.983	0.817	D	c	1.028	0.952	1.000	0.747	0.554	0.246	0	5.98	0.971	8.017	0.886	1.011	0.635	1.000	0.715	1.000	0.888	16.457	0.838	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	31	136	4	66217171	.	T	A	31	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=121;VD=2;AF=0.0165;SHIFT3=0;MSI=3;MSILEN=1;SSF=0.2207;SOR=inf;LSEQ=AAAGTCCAAAGTCAGACACT;RSEQ=TGCACACAAGGTTACTGTTG;CSQ=A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|14/18||NM_001281765.3:c.2447A>T|NP_001268694.1:p.Lys816Ile|3194|2447|816|K/I|aAa/aTa|||-1||EntrezGene||YES||||4:g.66217171T>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|13/17||NM_001281766.3:c.2381A>T|NP_001268695.1:p.Lys794Ile|3128|2381|794|K/I|aAa/aTa|||-1||EntrezGene||||||4:g.66217171T>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|14/17||NM_001281767.3:c.2447A>T|NP_001268696.1:p.Lys816Ile|3194|2447|816|K/I|aAa/aTa|||-1||EntrezGene||||||4:g.66217171T>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|14/18||NM_001318761.2:c.2240A>T|NP_001305690.1:p.Lys747Ile|2318|2240|747|K/I|aAa/aTa|||-1||EntrezGene||||||4:g.66217171T>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|14/18||NM_004439.8:c.2444A>T|NP_004430.4:p.Lys815Ile|3191|2444|815|K/I|aAa/aTa|||-1||EntrezGene||||||4:g.66217171T>A||||||||||||||,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|13/17||NM_182472.5:c.2378A>T|NP_872272.2:p.Lys793Ile|3125|2378|793|K/I|aAa/aTa|||-1||EntrezGene||||||4:g.66217171T>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:121:2:1,1:70,49:119,2:0.0165:2,2:44:1:31:1:1:1.42425:60:4:0.0167:0:1	0/0:136:0:0,0:80,56:136,0:0:2,0:37.1:1:35.6:1:1:0:60:33:1:0:0.1
    1552. 

  1552. 4	66217247	66217247	A	G	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon13:c.T2305C:p.Y769H,EPHA5:NM_182472:exon13:c.T2302C:p.Y768H,EPHA5:NM_001281765:exon14:c.T2371C:p.Y791H,EPHA5:NM_001281767:exon14:c.T2371C:p.Y791H,EPHA5:NM_001318761:exon14:c.T2164C:p.Y722H,EPHA5:NM_004439:exon14:c.T2368C:p.Y790H	.	.	.	.	.	.	.	.	.	.	.	0.0	0.912	D	1.0	0.899	D	1.0	0.971	D	0.002	0.387	N	1.000	0.588	D	1.555	0.395	L	-2.43	0.887	D	-4.58	0.792	D	0.732	0.738	0.670	0.928	D	0.786	0.927	D	0.189	0.861	D	3.168	0.440	22.7	0.999	0.931	0.973	0.740	D	c	0.474	0.447	0.979	0.299	0.554	0.246	0	4.8	0.610	6.314	0.726	0.197	0.251	1.000	0.715	1.000	0.888	11.926	0.519	Protein kinase domain|Protein kinase-like domain|Serine-threonine/tyrosine-protein kinase catalytic domain|Tyrosine-protein kinase, catalytic domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	201	4	66217247	.	A	G	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=126;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.3771;SOR=0;LSEQ=ATAGCCCATGTCAGAAAGGT;RSEQ=CTTCATTCCTGCAGAGATAC;CSQ=G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|14/18||NM_001281765.3:c.2371T>C|NP_001268694.1:p.Tyr791His|3118|2371|791|Y/H|Tac/Cac|||-1||EntrezGene||YES||||4:g.66217247A>G||||||||||||||,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|13/17||NM_001281766.3:c.2305T>C|NP_001268695.1:p.Tyr769His|3052|2305|769|Y/H|Tac/Cac|||-1||EntrezGene||||||4:g.66217247A>G||||||||||||||,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|14/17||NM_001281767.3:c.2371T>C|NP_001268696.1:p.Tyr791His|3118|2371|791|Y/H|Tac/Cac|||-1||EntrezGene||||||4:g.66217247A>G||||||||||||||,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|14/18||NM_001318761.2:c.2164T>C|NP_001305690.1:p.Tyr722His|2242|2164|722|Y/H|Tac/Cac|||-1||EntrezGene||||||4:g.66217247A>G||||||||||||||,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|14/18||NM_004439.8:c.2368T>C|NP_004430.4:p.Tyr790His|3115|2368|790|Y/H|Tac/Cac|||-1||EntrezGene||||||4:g.66217247A>G||||||||||||||,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|13/17||NM_182472.5:c.2302T>C|NP_872272.2:p.Tyr768His|3049|2302|768|Y/H|Tac/Cac|||-1||EntrezGene||||||4:g.66217247A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:126:0:0,0:55,71:126,0:0:2,0:40.2:1:36.1:1:1:0:60:41:1:0:0	0/1:201:2:1,1:98,101:199,2:0.01:2,2:29:0:37:0:1:1.03:60:4:0.01:0:1
    1553. 

  1553. 4	66217278	66217278	G	A	exonic	EPHA5	.	synonymous SNV	EPHA5:NM_001281766:exon13:c.C2274T:p.G758G,EPHA5:NM_182472:exon13:c.C2271T:p.G757G,EPHA5:NM_001281765:exon14:c.C2340T:p.G780G,EPHA5:NM_001281767:exon14:c.C2340T:p.G780G,EPHA5:NM_001318761:exon14:c.C2133T:p.G711G,EPHA5:NM_004439:exon14:c.C2337T:p.G779G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	ID=COSV99900174;OCCURENCE=1(lung)	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	MU130744599	LUSC-US|1|485|0.00206186	0.25	37	193	4	66217278	.	G	A	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=102;VD=0;AF=0;SHIFT3=1;MSI=2;MSILEN=1;SSF=0.42726;SOR=0;LSEQ=GCAGAGATACCTCTCAGCAT;RSEQ=CCAACAAGCTGAATCACAGT;CSQ=A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|14/18||NM_001281765.3:c.2340C>T|NP_001268694.1:p.Gly780%3D|3087|2340|780|G|ggC/ggT|COSV99900174||-1||EntrezGene||YES||||4:g.66217278G>A|||||||||||||1|1,A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|13/17||NM_001281766.3:c.2274C>T|NP_001268695.1:p.Gly758%3D|3021|2274|758|G|ggC/ggT|COSV99900174||-1||EntrezGene||||||4:g.66217278G>A|||||||||||||1|1,A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|14/17||NM_001281767.3:c.2340C>T|NP_001268696.1:p.Gly780%3D|3087|2340|780|G|ggC/ggT|COSV99900174||-1||EntrezGene||||||4:g.66217278G>A|||||||||||||1|1,A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|14/18||NM_001318761.2:c.2133C>T|NP_001305690.1:p.Gly711%3D|2211|2133|711|G|ggC/ggT|COSV99900174||-1||EntrezGene||||||4:g.66217278G>A|||||||||||||1|1,A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding|14/18||NM_004439.8:c.2337C>T|NP_004430.4:p.Gly779%3D|3084|2337|779|G|ggC/ggT|COSV99900174||-1||EntrezGene||||||4:g.66217278G>A|||||||||||||1|1,A|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding|13/17||NM_182472.5:c.2271C>T|NP_872272.2:p.Gly757%3D|3018|2271|757|G|ggC/ggT|COSV99900174||-1||EntrezGene||||||4:g.66217278G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:102:0:0,0:36,66:102,0:0:2,0:36.4:1:37:0:1:0:60:204:1:0:0	0/1:193:2:1,1:85,106:191,2:0.0104:2,2:48.5:1:37:0:1:1.25:60:4:0.0105:0:1
    1554. 

  1554. 4	66231616	66231616	A	G	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	124	4	66231616	.	A	G	37	d5;v3;f0.01;pSTD	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=1;VD=0;AF=0;SHIFT3=0;MSI=4;MSILEN=1;SSF=0.984;SOR=0;LSEQ=ACATTCTGGAATGCAAACAA;RSEQ=AGTTAAAAATGAAAGTCAAA;CSQ=G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||11/17|NM_001281765.3:c.2053+34T>C|||||||||-1||EntrezGene||YES||||4:g.66231616A>G||||||||||||||,G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||10/16|NM_001281766.3:c.1987+34T>C|||||||||-1||EntrezGene||||||4:g.66231616A>G||||||||||||||,G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||11/16|NM_001281767.3:c.2053+34T>C|||||||||-1||EntrezGene||||||4:g.66231616A>G||||||||||||||,G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||11/17|NM_001318761.2:c.1846+34T>C|||||||||-1||EntrezGene||||||4:g.66231616A>G||||||||||||||,G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||11/17|NM_004439.8:c.2050+34T>C|||||||||-1||EntrezGene||||||4:g.66231616A>G||||||||||||||,G|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||10/16|NM_182472.5:c.1984+34T>C|||||||||-1||EntrezGene||||||4:g.66231616A>G||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:37:0:1:0:60:2:1:0:0	0/1:124:2:1,1:93,29:122,2:0.0161:2,2:23:0:37:0:0.42683:3.1699:60:4:0.0165:0:1
    1555. 

  1555. 4	66233141	66233141	G	A	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281766:exon9:c.C1795T:p.R599W,EPHA5:NM_182472:exon9:c.C1792T:p.R598W,EPHA5:NM_001281765:exon10:c.C1861T:p.R621W,EPHA5:NM_001281767:exon10:c.C1861T:p.R621W,EPHA5:NM_001318761:exon10:c.C1654T:p.R552W,EPHA5:NM_004439:exon10:c.C1858T:p.R620W	0.0002	.	.	.	.	.	.	.	.	rs146757388	.	0.001	0.784	D	0.989	0.899	D	0.772	0.601	P	0.014	0.287	N	1.000	0.511	D	3.205	0.894	M	-0.83	0.745	T	-2.15	0.697	N	0.73	0.754	-0.267	0.759	T	0.326	0.694	T	0.085	0.746	D	7.454	0.951	34	0.999	0.990	0.935	0.582	D	c	0.340	0.401	0.965	0.287	0.554	0.246	0	4.35	0.513	1.584	0.360	0.998	0.613	0.964	0.336	0.996	0.625	16.239	0.821	Ephrin receptor, transmembrane domain	.	.	ID=COSV56642148;OCCURENCE=1(pancreas)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU69283154	PACA-CA|1|268|0.00373134	0.25	37	113	4	66233141	.	G	A	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=80;VD=2;AF=0.025;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.17055;SOR=inf;LSEQ=TGCTTTGCTGTAGCCACACC;RSEQ=CCTGGAACAAAGTAAGCTAG;CSQ=A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|10/18||NM_001281765.3:c.1861C>T|NP_001268694.1:p.Arg621Trp|2608|1861|621|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||YES||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1,A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|9/17||NM_001281766.3:c.1795C>T|NP_001268695.1:p.Arg599Trp|2542|1795|599|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1,A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|10/17||NM_001281767.3:c.1861C>T|NP_001268696.1:p.Arg621Trp|2608|1861|621|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1,A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|10/18||NM_001318761.2:c.1654C>T|NP_001305690.1:p.Arg552Trp|1732|1654|552|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1,A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|10/18||NM_004439.8:c.1858C>T|NP_004430.4:p.Arg620Trp|2605|1858|620|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1,A|missense_variant&splice_region_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|9/17||NM_182472.5:c.1792C>T|NP_872272.2:p.Arg598Trp|2539|1792|598|R/W|Cgg/Tgg|rs146757388&COSV56642148||-1||EntrezGene||||||4:g.66233141G>A|1.6e-05|0|0|0|0.000109|0|8.841e-06|0|3.269e-05|0.000109|gnomAD_EAS||0&1|0&1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:80:2:1,1:47,30:77,2:0.025:2,2:11:0:37:0:1:1.55745:60:4:0.025:0:1	0/0:113:0:0,0:50,63:113,0:0:2,0:43.4:1:36.5:1:1:0:60:55.5:1:0:0.2
    1556. 

  1556. 4	66242726	66242726	T	C	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon9:c.A1849G:p.S617G,EPHA5:NM_001281767:exon9:c.A1849G:p.S617G,EPHA5:NM_001318761:exon9:c.A1642G:p.S548G,EPHA5:NM_004439:exon9:c.A1846G:p.S616G	.	.	.	.	.	.	.	.	.	.	.	0.378	0.491	T	0.0	0.026	B	0.001	0.040	B	0.000	0.523	N	1	0.810	D	0.97	0.241	L	-0.74	0.737	T	-0.44	0.193	N	0.205	0.297	-0.957	0.397	T	0.167	0.505	T	0.011	0.280	T	1.213	0.211	11.82	0.931	0.222	0.802	0.396	D	c	-0.529	-0.308	0.000	0.071	0.487	0.133	0	3.99	0.454	3.208	0.506	0.113	0.207	1.000	0.715	1.000	0.888	8.961	0.348	Ephrin receptor, transmembrane domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	236	4	66242726	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=39;VD=2;AF=0.0513;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.01967;SOR=inf;LSEQ=GAACACTAACCATATTAGGC;RSEQ=TGGATGGGCAACAGCGCACA;CSQ=C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|9/18||NM_001281765.3:c.1849A>G|NP_001268694.1:p.Ser617Gly|2596|1849|617|S/G|Agc/Ggc|||-1||EntrezGene||YES||||4:g.66242726T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||8/16|NM_001281766.3:c.1794-9584A>G|||||||||-1||EntrezGene||||||4:g.66242726T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|9/17||NM_001281767.3:c.1849A>G|NP_001268696.1:p.Ser617Gly|2596|1849|617|S/G|Agc/Ggc|||-1||EntrezGene||||||4:g.66242726T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|9/18||NM_001318761.2:c.1642A>G|NP_001305690.1:p.Ser548Gly|1720|1642|548|S/G|Agc/Ggc|||-1||EntrezGene||||||4:g.66242726T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|9/18||NM_004439.8:c.1846A>G|NP_004430.4:p.Ser616Gly|2593|1846|616|S/G|Agc/Ggc|||-1||EntrezGene||||||4:g.66242726T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||8/16|NM_182472.5:c.1791-9584A>G|||||||||-1||EntrezGene||||||4:g.66242726T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:39:2:1,1:20,17:37,2:0.0513:2,2:55:0:37:0:1:1.17156:60:4:0.0513:0:1	0/0:236:0:0,0:121,115:236,0:0:2,0:40.7:1:36.5:1:1:0:60:77.667:1:0:0.1
    1557. 

  1557. 4	66242764	66242764	C	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon9:c.G1811A:p.C604Y,EPHA5:NM_001281767:exon9:c.G1811A:p.C604Y,EPHA5:NM_001318761:exon9:c.G1604A:p.C535Y,EPHA5:NM_004439:exon9:c.G1808A:p.C603Y	0.0001	.	.	.	.	.	.	.	.	rs758650433	.	0.029	0.682	D	0.943	0.511	P	0.962	0.690	D	0.000	0.629	D	0.963	0.810	D	0.69	0.170	N	2.86	0.105	T	-1.11	0.305	N	0.89	0.879	-1.073	0.086	T	0.032	0.137	T	0.011	0.288	T	3.201	0.444	22.7	0.975	0.336	0.915	0.534	D	c	0.279	0.377	0.724	0.229	0.554	0.246	0	5.37	0.769	4.488	0.598	0.892	0.403	1.000	0.715	1.000	0.888	16.608	0.846	Ephrin receptor, transmembrane domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	255	4	66242764	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=36;VD=2;AF=0.0556;SHIFT3=2;MSI=2;MSILEN=2;SSF=0.01493;SOR=inf;LSEQ=ACAGGGAAGAAGCCCTCCCA;RSEQ=AGCCACATTCGCAGCAACTG;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|9/18||NM_001281765.3:c.1811G>A|NP_001268694.1:p.Cys604Tyr|2558|1811|604|C/Y|tGt/tAt|rs758650433||-1||EntrezGene||YES||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||8/16|NM_001281766.3:c.1794-9622G>A|||||||rs758650433||-1||EntrezGene||||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|9/17||NM_001281767.3:c.1811G>A|NP_001268696.1:p.Cys604Tyr|2558|1811|604|C/Y|tGt/tAt|rs758650433||-1||EntrezGene||||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|9/18||NM_001318761.2:c.1604G>A|NP_001305690.1:p.Cys535Tyr|1682|1604|535|C/Y|tGt/tAt|rs758650433||-1||EntrezGene||||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|9/18||NM_004439.8:c.1808G>A|NP_004430.4:p.Cys603Tyr|2555|1808|603|C/Y|tGt/tAt|rs758650433||-1||EntrezGene||||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||8/16|NM_182472.5:c.1791-9622G>A|||||||rs758650433||-1||EntrezGene||||||4:g.66242764C>T|4.023e-06|0|2.934e-05|0|0|0|0|0|0|2.934e-05|gnomAD_AMR|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:36:2:1,1:16,18:34,2:0.0556:2,2:16.5:1:37:0:1:1.12:60:4:0.0556:0:1	0/0:255:0:0,0:120,135:255,0:0:2,0:38.3:1:36.2:1:1:0:60:84:1:0:0.1
    1558. 

  1558. 4	66279961	66279961	C	A	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	151	4	66279961	.	C	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=180;VD=2;AF=0.0111;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.29497;SOR=inf;LSEQ=ACTGACTCTTTTCTGGTAAC;RSEQ=ATTACTGAGACATGAGCTGA;CSQ=A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||7/17|NM_001281765.3:c.1687+41G>T|||||||||-1||EntrezGene||YES||||4:g.66279961C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||7/16|NM_001281766.3:c.1687+41G>T|||||||||-1||EntrezGene||||||4:g.66279961C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||7/16|NM_001281767.3:c.1687+41G>T|||||||||-1||EntrezGene||||||4:g.66279961C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||7/17|NM_001318761.2:c.1480+41G>T|||||||||-1||EntrezGene||||||4:g.66279961C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||7/17|NM_004439.8:c.1687+41G>T|||||||||-1||EntrezGene||||||4:g.66279961C>A||||||||||||||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||7/16|NM_182472.5:c.1687+41G>T|||||||||-1||EntrezGene||||||4:g.66279961C>A||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:180:2:1,1:110,68:178,2:0.0111:2,2:23:1:37:0:1:1.6131:60:4:0.0112:0:1	0/0:151:0:0,0:103,48:151,0:0:2,0:32.3:1:36.3:1:1:0:60:150:1:0:0.1
    1559. 

  1559. 4	66279980	66279980	G	T	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	181	4	66279980	.	G	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=215;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.20829;SOR=0;LSEQ=CCATTACTGAGACATGAGCT;RSEQ=ACAGTAATTAAAATGACTTA;CSQ=T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||7/17|NM_001281765.3:c.1687+22C>A|||||||COSV56649169||-1||EntrezGene||YES||||4:g.66279980G>T|||||||||||||1|1,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||7/16|NM_001281766.3:c.1687+22C>A|||||||COSV56649169||-1||EntrezGene||||||4:g.66279980G>T|||||||||||||1|1,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||7/16|NM_001281767.3:c.1687+22C>A|||||||COSV56649169||-1||EntrezGene||||||4:g.66279980G>T|||||||||||||1|1,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||7/17|NM_001318761.2:c.1480+22C>A|||||||COSV56649169||-1||EntrezGene||||||4:g.66279980G>T|||||||||||||1|1,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||7/17|NM_004439.8:c.1687+22C>A|||||||COSV56649169||-1||EntrezGene||||||4:g.66279980G>T|||||||||||||1|1,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||7/16|NM_182472.5:c.1687+22C>A|||||||COSV56649169||-1||EntrezGene||||||4:g.66279980G>T|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:215:0:0,0:123,92:215,0:0:2,0:37.3:1:36.4:1:1:0:60:70.667:1:0:0.1	0/1:181:2:1,1:110,69:179,2:0.011:2,2:37.5:1:37:0:1:1.5899:60:4:0.011:0:1
    1560. 

  1560. 4	66279996	66279996	A	T	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	52	205	4	66279996	.	A	T	52	PASS	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=252;VD=3;AF=0.0119;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.16677;SOR=inf;LSEQ=AGCTGACAGTAATTAAAATG;RSEQ=CTTACACACTGGGGTGGTTT;CSQ=T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||7/17|NM_001281765.3:c.1687+6T>A|||||||||-1||EntrezGene||YES||||4:g.66279996A>T||||||||||||||,T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||7/16|NM_001281766.3:c.1687+6T>A|||||||||-1||EntrezGene||||||4:g.66279996A>T||||||||||||||,T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||7/16|NM_001281767.3:c.1687+6T>A|||||||||-1||EntrezGene||||||4:g.66279996A>T||||||||||||||,T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||7/17|NM_001318761.2:c.1480+6T>A|||||||||-1||EntrezGene||||||4:g.66279996A>T||||||||||||||,T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding||7/17|NM_004439.8:c.1687+6T>A|||||||||-1||EntrezGene||||||4:g.66279996A>T||||||||||||||,T|splice_donor_region_variant&intron_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding||7/16|NM_182472.5:c.1687+6T>A|||||||||-1||EntrezGene||||||4:g.66279996A>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:252:3:1,2:135,114:249,3:0.0119:2,2:40.3:1:33:1:0.59595:2.36053:60:6:0.012:0:1.3	0/0:205:0:0,0:120,85:205,0:0:2,0:37.6:1:36.1:1:1:0:60:50.25:1:0:0.1
    1561. 

  1561. 4	66286113	66286113	-	A	intronic	EPHA5	.	.	.	0.19	0.1447	0.1643	0.1375	0.1525	0.1167	0.1279	0.1395	0.1345	rs138755728	rs138755728	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	MU112357808	BTCA-SG|1|71|0.0140845	0.25	184	73	4	66286113	.	G	GA	184	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=Insertion;DP=1;VD=0;AF=0;SHIFT3=10;MSI=11;MSILEN=1;SSF=0.60811;SOR=0;LSEQ=ATAATTGTAGTTGCTAAAAT;RSEQ=AAAAAAAAAAGAAAGTGAGG;CSQ=A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||6/17|NM_001281765.3:c.1527+45dup|||||||rs138755728||-1||EntrezGene||YES||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||6/16|NM_001281766.3:c.1527+45dup|||||||rs138755728||-1||EntrezGene||||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||6/16|NM_001281767.3:c.1527+45dup|||||||rs138755728||-1||EntrezGene||||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||6/17|NM_001318761.2:c.1320+45dup|||||||rs138755728||-1||EntrezGene||||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||6/17|NM_004439.8:c.1527+45dup|||||||rs138755728||-1||EntrezGene||||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||,A|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||6/16|NM_182472.5:c.1527+45dup|||||||rs138755728||-1||EntrezGene||||||4:g.66286123dup|0.1761|0.1969|0.1459|0.233|0.1987|0.1276|0.1859|0.1848|0.1467|0.233|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:1:0:0,0:1,0:1,0:0:0,0:66:0:37:0:1:0:60:2:1:0:2	0/1:73:29:23,6:31,11:42,29:0.3973:2,2:35.7:1:37.9:0:0.77828:1.35:61.4:58:0.4394:0:2.2
    1562. 

  1562. 4	66286139	66286139	T	C	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	31	125	4	66286139	.	T	C	31	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=5;VD=0;AF=0;SHIFT3=0;MSI=6;MSILEN=1;SSF=0.92427;SOR=0;LSEQ=AAAAAGAAAGTGAGGACATT;RSEQ=TTTATTCTGTTAGTCTTACC;CSQ=C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||6/17|NM_001281765.3:c.1527+20A>G|||||||||-1||EntrezGene||YES||||4:g.66286139T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||6/16|NM_001281766.3:c.1527+20A>G|||||||||-1||EntrezGene||||||4:g.66286139T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||6/16|NM_001281767.3:c.1527+20A>G|||||||||-1||EntrezGene||||||4:g.66286139T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||6/17|NM_001318761.2:c.1320+20A>G|||||||||-1||EntrezGene||||||4:g.66286139T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||6/17|NM_004439.8:c.1527+20A>G|||||||||-1||EntrezGene||||||4:g.66286139T>C||||||||||||||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||6/16|NM_182472.5:c.1527+20A>G|||||||||-1||EntrezGene||||||4:g.66286139T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:5:0:0,0:4,1:5,0:0:2,0:19.4:1:37:0:1:0:60:10:1:0:0.4	0/1:125:2:1,1:83,40:123,2:0.016:2,2:30:1:31:1:0.55019:2.0619:60:4:0.0161:0:2
    1563. 

  1563. 4	66356246	66356246	C	T	exonic	EPHA5	.	synonymous SNV	EPHA5:NM_001281765:exon5:c.G1251A:p.R417R,EPHA5:NM_001281766:exon5:c.G1251A:p.R417R,EPHA5:NM_001281767:exon5:c.G1251A:p.R417R,EPHA5:NM_001318761:exon5:c.G1044A:p.R348R,EPHA5:NM_004439:exon5:c.G1251A:p.R417R,EPHA5:NM_182472:exon5:c.G1251A:p.R417R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	74	396	4	66356246	.	C	T	74	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=978;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.00683;SOR=0;LSEQ=GTGTTTTTCAGGCCGCTTTG;RSEQ=CGGGGAAGGTACCTGACATG;CSQ=T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|5/18||NM_001281765.3:c.1251G>A|NP_001268694.1:p.Arg417%3D|1998|1251|417|R|cgG/cgA|||-1||EntrezGene||YES||||4:g.66356246C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|5/17||NM_001281766.3:c.1251G>A|NP_001268695.1:p.Arg417%3D|1998|1251|417|R|cgG/cgA|||-1||EntrezGene||||||4:g.66356246C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|5/17||NM_001281767.3:c.1251G>A|NP_001268696.1:p.Arg417%3D|1998|1251|417|R|cgG/cgA|||-1||EntrezGene||||||4:g.66356246C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|5/18||NM_001318761.2:c.1044G>A|NP_001305690.1:p.Arg348%3D|1122|1044|348|R|cgG/cgA|||-1||EntrezGene||||||4:g.66356246C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding|5/18||NM_004439.8:c.1251G>A|NP_004430.4:p.Arg417%3D|1998|1251|417|R|cgG/cgA|||-1||EntrezGene||||||4:g.66356246C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding|5/17||NM_182472.5:c.1251G>A|NP_872272.2:p.Arg417%3D|1998|1251|417|R|cgG/cgA|||-1||EntrezGene||||||4:g.66356246C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:978:0:0,0:472,505:977,0:0:0:0:0:0:0:1:0:0:0:0:0:0	0/1:396:4:2,2:209,183:392,4:0.0101:2,2:44.2:1:37:0:1:1.14169:60:8:0.0103:0:1
    1564. 

  1564. 4	66361064	66361064	T	C	intronic	EPHA5	.	.	.	0.0014	6.46e-05	0	0	0.0066	0	0	0	0	rs200780613	rs200780613	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	136	4	66361064	.	T	C	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=59;VD=2;AF=0.0339;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.09046;SOR=inf;LSEQ=TCATGCTGTTTCCTCAAAAC;RSEQ=GGTTAAAGTTAGCACCACCA;CSQ=C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||4/17|NM_001281765.3:c.1066+42A>G|||||||rs200780613||-1||EntrezGene||YES||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||4/16|NM_001281766.3:c.1066+42A>G|||||||rs200780613||-1||EntrezGene||||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||4/16|NM_001281767.3:c.1066+42A>G|||||||rs200780613||-1||EntrezGene||||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||4/17|NM_001318761.2:c.859+42A>G|||||||rs200780613||-1||EntrezGene||||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||4/17|NM_004439.8:c.1066+42A>G|||||||rs200780613||-1||EntrezGene||||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||,C|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||4/16|NM_182472.5:c.1066+42A>G|||||||rs200780613||-1||EntrezGene||||||4:g.66361064T>C|0.0003793|6.31e-05|0.0001955|0.00849|0|0|8.554e-05|0.0007361|0|0.00849|gnomAD_ASJ|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:59:2:1,1:46,11:57,2:0.0339:2,2:29:0:37:0:0.36821:4.04707:60:4:0.0345:0:1	0/0:136:0:0,0:103,33:136,0:0:2,0:33:1:36:1:1:0:60:44.333:1:0:0.1
    1565. 

  1565. 4	66361077	66361077	C	T	intronic	EPHA5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.25	37	151	4	66361077	.	C	T	37	v3;f0.01	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=83;VD=0;AF=0;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.41543;SOR=0;LSEQ=TCAAAACTGGTTAAAGTTAG;RSEQ=ACCACCAAATATCCGTGGGT;CSQ=T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281765.3|protein_coding||4/17|NM_001281765.3:c.1066+29G>A|||||||||-1||EntrezGene||YES||||4:g.66361077C>T||||||||||||||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281766.3|protein_coding||4/16|NM_001281766.3:c.1066+29G>A|||||||||-1||EntrezGene||||||4:g.66361077C>T||||||||||||||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001281767.3|protein_coding||4/16|NM_001281767.3:c.1066+29G>A|||||||||-1||EntrezGene||||||4:g.66361077C>T||||||||||||||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_001318761.2|protein_coding||4/17|NM_001318761.2:c.859+29G>A|||||||||-1||EntrezGene||||||4:g.66361077C>T||||||||||||||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_004439.8|protein_coding||4/17|NM_004439.8:c.1066+29G>A|||||||||-1||EntrezGene||||||4:g.66361077C>T||||||||||||||,T|intron_variant|MODIFIER|EPHA5|2044|Transcript|NM_182472.5|protein_coding||4/16|NM_182472.5:c.1066+29G>A|||||||||-1||EntrezGene||||||4:g.66361077C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:83:0:0,0:64,19:83,0:0:2,0:31.3:1:36.2:1:1:0:60:40.5:1:0:0.1	0/1:151:2:1,1:107,42:149,2:0.0132:2,2:54:0:37:0:0.4898:2.52957:60:4:0.0137:0:1
    1566. 

  1566. 4	66361172	66361172	T	C	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon4:c.A1000G:p.T334A,EPHA5:NM_001281766:exon4:c.A1000G:p.T334A,EPHA5:NM_001281767:exon4:c.A1000G:p.T334A,EPHA5:NM_001318761:exon4:c.A793G:p.T265A,EPHA5:NM_004439:exon4:c.A1000G:p.T334A,EPHA5:NM_182472:exon4:c.A1000G:p.T334A	.	.	.	.	.	.	.	.	.	.	.	0.078	0.339	T	0.06	0.241	B	0.065	0.317	B	0.000	0.559	D	1	0.810	D	1.665	0.427	L	1.58	0.973	T	-1.97	0.478	N	0.386	0.446	0.836	0.949	D	0.862	0.954	D	0.035	0.565	D	1.411	0.233	12.84	0.989	0.469	0.823	0.412	D	c	0.013	0.191	0.252	0.187	0.554	0.283	0	5.84	0.934	3.097	0.497	0.113	0.207	1.000	0.715	0.996	0.625	16.223	0.820	Growth factor receptor cysteine-rich domain	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	321	4	66361172	.	T	C	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=180;VD=2;AF=0.0111;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.12862;SOR=inf;LSEQ=CTTTTCACAGACACAAGAGG;RSEQ=TGAAGCTTCCTCATGGGTAT;CSQ=C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|4/18||NM_001281765.3:c.1000A>G|NP_001268694.1:p.Thr334Ala|1747|1000|334|T/A|Acc/Gcc|||-1||EntrezGene||YES||||4:g.66361172T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|4/17||NM_001281766.3:c.1000A>G|NP_001268695.1:p.Thr334Ala|1747|1000|334|T/A|Acc/Gcc|||-1||EntrezGene||||||4:g.66361172T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|4/17||NM_001281767.3:c.1000A>G|NP_001268696.1:p.Thr334Ala|1747|1000|334|T/A|Acc/Gcc|||-1||EntrezGene||||||4:g.66361172T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|4/18||NM_001318761.2:c.793A>G|NP_001305690.1:p.Thr265Ala|871|793|265|T/A|Acc/Gcc|||-1||EntrezGene||||||4:g.66361172T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|4/18||NM_004439.8:c.1000A>G|NP_004430.4:p.Thr334Ala|1747|1000|334|T/A|Acc/Gcc|||-1||EntrezGene||||||4:g.66361172T>C||||||||||||||,C|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|4/17||NM_182472.5:c.1000A>G|NP_872272.2:p.Thr334Ala|1747|1000|334|T/A|Acc/Gcc|||-1||EntrezGene||||||4:g.66361172T>C||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:180:2:1,1:93,85:178,2:0.0111:2,2:25:1:37:0:1:1.09357:60:4:0.0113:0:1	0/0:321:0:0,0:173,148:321,0:0:2,0:35.9:1:36.3:1:1:0:60:79.25:1:0:0.1
    1567. 

  1567. 4	66467786	66467786	C	T	exonic	EPHA5	.	synonymous SNV	EPHA5:NM_001281765:exon3:c.G483A:p.Q161Q,EPHA5:NM_001281766:exon3:c.G483A:p.Q161Q,EPHA5:NM_001281767:exon3:c.G483A:p.Q161Q,EPHA5:NM_001318761:exon3:c.G276A:p.Q92Q,EPHA5:NM_004439:exon3:c.G483A:p.Q161Q,EPHA5:NM_182472:exon3:c.G483A:p.Q161Q	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	271	4	66467786	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=171;VD=2;AF=0.0117;SHIFT3=1;MSI=1;MSILEN=1;SSF=0.14914;SOR=inf;LSEQ=TCCTTGATGTTTCTCCCATT;RSEQ=TGATCATCTGACTCAAAGTA;CSQ=T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|3/18||NM_001281765.3:c.483G>A|NP_001268694.1:p.Gln161%3D|1230|483|161|Q|caG/caA|||-1||EntrezGene||YES||||4:g.66467786C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|3/17||NM_001281766.3:c.483G>A|NP_001268695.1:p.Gln161%3D|1230|483|161|Q|caG/caA|||-1||EntrezGene||||||4:g.66467786C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|3/17||NM_001281767.3:c.483G>A|NP_001268696.1:p.Gln161%3D|1230|483|161|Q|caG/caA|||-1||EntrezGene||||||4:g.66467786C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|3/18||NM_001318761.2:c.276G>A|NP_001305690.1:p.Gln92%3D|354|276|92|Q|caG/caA|||-1||EntrezGene||||||4:g.66467786C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding|3/18||NM_004439.8:c.483G>A|NP_004430.4:p.Gln161%3D|1230|483|161|Q|caG/caA|||-1||EntrezGene||||||4:g.66467786C>T||||||||||||||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding|3/17||NM_182472.5:c.483G>A|NP_872272.2:p.Gln161%3D|1230|483|161|Q|caG/caA|||-1||EntrezGene||||||4:g.66467786C>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:171:2:1,1:79,90:169,2:0.0117:2,2:20:1:37:0:1:1.14:60:4:0.0119:0:1	0/0:271:0:0,0:135,136:271,0:0:2,0:38.7:1:36.7:1:1:0:60:542:1:0:0.1
    1568. 

  1568. 4	66467809	66467809	A	G	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon3:c.T460C:p.Y154H,EPHA5:NM_001281766:exon3:c.T460C:p.Y154H,EPHA5:NM_001281767:exon3:c.T460C:p.Y154H,EPHA5:NM_001318761:exon3:c.T253C:p.Y85H,EPHA5:NM_004439:exon3:c.T460C:p.Y154H,EPHA5:NM_182472:exon3:c.T460C:p.Y154H	.	.	.	.	.	.	.	.	.	.	.	0.033	0.586	D	0.998	0.899	D	0.985	0.916	D	0.001	0.403	N	1.000	0.477	D	2.71	0.795	M	3.13	0.080	T	-3.99	0.739	D	0.505	0.558	-1.013	0.260	T	0.093	0.354	T	0.020	0.428	T	4.699	0.630	24.6	0.998	0.911	0.947	0.618	D	c	0.810	0.760	0.937	0.272	0.638	0.428	0	5.83	0.930	6.294	0.725	1.199	0.960	1.000	0.715	1.000	0.888	16.198	0.818	Ephrin receptor ligand binding domain|Galactose-binding domain-like	.	.	ID=COSV99898980;OCCURENCE=1(endometrium)	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	MU129832946	UCEC-US|1|531|0.00188324	0.25	37	278	4	66467809	.	A	G	37	v3;pSTD	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=184;VD=2;AF=0.0109;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.1581;SOR=inf;LSEQ=ATCATCTGACTCAAAGTAAT;RSEQ=CATATTAAAGGTTTCCTTAC;CSQ=G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|3/18||NM_001281765.3:c.460T>C|NP_001268694.1:p.Tyr154His|1207|460|154|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||YES||||4:g.66467809A>G|||||||||||||1|1,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|3/17||NM_001281766.3:c.460T>C|NP_001268695.1:p.Tyr154His|1207|460|154|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||||||4:g.66467809A>G|||||||||||||1|1,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|3/17||NM_001281767.3:c.460T>C|NP_001268696.1:p.Tyr154His|1207|460|154|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||||||4:g.66467809A>G|||||||||||||1|1,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|3/18||NM_001318761.2:c.253T>C|NP_001305690.1:p.Tyr85His|331|253|85|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||||||4:g.66467809A>G|||||||||||||1|1,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|3/18||NM_004439.8:c.460T>C|NP_004430.4:p.Tyr154His|1207|460|154|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||||||4:g.66467809A>G|||||||||||||1|1,G|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|3/17||NM_182472.5:c.460T>C|NP_872272.2:p.Tyr154His|1207|460|154|Y/H|Tat/Cat|COSV99898980||-1||EntrezGene||||||4:g.66467809A>G|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:184:2:1,1:84,98:182,2:0.0109:2,2:65:0:37:0:1:1.17:60:4:0.011:0:1	0/0:278:0:0,0:135,143:278,0:0:2,0:37.5:1:36.9:1:1:0:60:556:1:0:0.1
    1569. 

  1569. 4	66467837	66467837	C	T	exonic	EPHA5	.	synonymous SNV	EPHA5:NM_001281765:exon3:c.G432A:p.L144L,EPHA5:NM_001281766:exon3:c.G432A:p.L144L,EPHA5:NM_001281767:exon3:c.G432A:p.L144L,EPHA5:NM_001318761:exon3:c.G225A:p.L75L,EPHA5:NM_004439:exon3:c.G432A:p.L144L,EPHA5:NM_182472:exon3:c.G432A:p.L144L	0.	.	.	.	.	.	.	.	.	rs780004869	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	Likely benign	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	.	.	0.25	37	305	4	66467837	.	C	T	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=191;VD=2;AF=0.0105;SHIFT3=0;MSI=1;MSILEN=1;SSF=0.14781;SOR=inf;LSEQ=AAGGTTTCCTTACAGGTCCC;RSEQ=AGTCCTCCAGGAAGGCTGTT;CSQ=T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|3/18||NM_001281765.3:c.432G>A|NP_001268694.1:p.Leu144%3D|1179|432|144|L|ctG/ctA|rs780004869||-1||EntrezGene||YES||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|3/17||NM_001281766.3:c.432G>A|NP_001268695.1:p.Leu144%3D|1179|432|144|L|ctG/ctA|rs780004869||-1||EntrezGene||||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|3/17||NM_001281767.3:c.432G>A|NP_001268696.1:p.Leu144%3D|1179|432|144|L|ctG/ctA|rs780004869||-1||EntrezGene||||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|3/18||NM_001318761.2:c.225G>A|NP_001305690.1:p.Leu75%3D|303|225|75|L|ctG/ctA|rs780004869||-1||EntrezGene||||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_004439.8|protein_coding|3/18||NM_004439.8:c.432G>A|NP_004430.4:p.Leu144%3D|1179|432|144|L|ctG/ctA|rs780004869||-1||EntrezGene||||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||,T|synonymous_variant|LOW|EPHA5|2044|Transcript|NM_182472.5|protein_coding|3/17||NM_182472.5:c.432G>A|NP_872272.2:p.Leu144%3D|1179|432|144|L|ctG/ctA|rs780004869||-1||EntrezGene||||||4:g.66467837C>T|7.96e-06|0|0|0|0|0|1.76e-05|0|0|1.76e-05|gnomAD_NFE|||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:191:2:1,1:88,101:189,2:0.0105:2,2:68.5:1:37:0:1:1.15:60:4:0.0106:0:1	0/0:305:0:0,0:156,149:305,0:0:2,0:34.3:1:36.5:1:1:0:60:75.25:1:0:0.1
    1570. 

  1570. 4	66467913	66467913	G	A	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon3:c.C356T:p.S119F,EPHA5:NM_001281766:exon3:c.C356T:p.S119F,EPHA5:NM_001281767:exon3:c.C356T:p.S119F,EPHA5:NM_001318761:exon3:c.C149T:p.S50F,EPHA5:NM_004439:exon3:c.C356T:p.S119F,EPHA5:NM_182472:exon3:c.C356T:p.S119F	.	.	.	.	.	.	.	.	.	.	.	0.177	0.259	T	0.843	0.481	P	0.61	0.493	P	0.000	0.629	D	0.977	0.394	D	1.43	0.360	L	3.8	0.038	T	-2.35	0.580	N	0.662	0.674	-1.046	0.156	T	0.025	0.106	T	0.007	0.197	T	3.744	0.507	23.3	0.984	0.405	0.895	0.497	D	c	0.381	0.475	0.603	0.217	0.638	0.428	0	5.68	0.880	4.263	0.584	1.048	0.713	1.000	0.715	0.999	0.750	19.782	0.964	Ephrin receptor ligand binding domain|Galactose-binding domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	37	271	4	66467913	.	G	A	37	v3	STATUS=StrongSomatic;SAMPLE=LibM078FTT;TYPE=SNV;DP=137;VD=2;AF=0.0146;SHIFT3=0;MSI=2;MSILEN=2;SSF=0.1122;SOR=inf;LSEQ=TTCTGGAAGCACCTTCATTG;RSEQ=AGATCCAACTGGTCAAAAGC;CSQ=A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|3/18||NM_001281765.3:c.356C>T|NP_001268694.1:p.Ser119Phe|1103|356|119|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||YES||||4:g.66467913G>A|||||||||||||1|1,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|3/17||NM_001281766.3:c.356C>T|NP_001268695.1:p.Ser119Phe|1103|356|119|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||||||4:g.66467913G>A|||||||||||||1|1,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|3/17||NM_001281767.3:c.356C>T|NP_001268696.1:p.Ser119Phe|1103|356|119|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||||||4:g.66467913G>A|||||||||||||1|1,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|3/18||NM_001318761.2:c.149C>T|NP_001305690.1:p.Ser50Phe|227|149|50|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||||||4:g.66467913G>A|||||||||||||1|1,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|3/18||NM_004439.8:c.356C>T|NP_004430.4:p.Ser119Phe|1103|356|119|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||||||4:g.66467913G>A|||||||||||||1|1,A|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|3/17||NM_182472.5:c.356C>T|NP_872272.2:p.Ser119Phe|1103|356|119|S/F|tCc/tTc|COSV56657486||-1||EntrezGene||||||4:g.66467913G>A|||||||||||||1|1	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/1:137:2:1,1:57,77:134,2:0.0146:2,2:18.5:1:37:0:1:1.35:60:4:0.0148:0:1	0/0:271:0:0,0:120,151:271,0:0:2,0:40.3:1:36.2:1:1:0:60:134.5:1:0:0.1
    1571. 

  1571. 4	66467980	66467980	G	T	exonic	EPHA5	.	nonsynonymous SNV	EPHA5:NM_001281765:exon3:c.C289A:p.H97N,EPHA5:NM_001281766:exon3:c.C289A:p.H97N,EPHA5:NM_001281767:exon3:c.C289A:p.H97N,EPHA5:NM_001318761:exon3:c.C82A:p.H28N,EPHA5:NM_004439:exon3:c.C289A:p.H97N,EPHA5:NM_182472:exon3:c.C289A:p.H97N	.	.	.	.	.	.	.	.	.	.	.	0.004	0.654	D	0.562	0.458	P	0.566	0.479	P	0.000	0.629	D	0.997	0.437	D	2.555	0.748	M	3.0	0.092	T	-2.64	0.566	D	0.438	0.516	-1.208	0.001	T	0.048	0.204	T	0.004	0.104	T	5.133	0.692	25.4	0.990	0.507	0.959	0.663	D	c	0.516	0.603	0.994	0.333	0.638	0.428	0	5.68	0.880	6.665	0.741	1.048	0.713	1.000	0.715	1.000	0.888	19.782	0.964	Ephrin receptor ligand binding domain|Galactose-binding domain-like	.	.	.	.	.	.	.	.	Uncertain significance	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	.	.	0.25	44	165	4	66467980	.	G	T	44	PASS	STATUS=StrongLOH;SAMPLE=LibM078FTT;TYPE=SNV;DP=47;VD=0;AF=0;SHIFT3=0;MSI=2;MSILEN=1;SSF=0.46955;SOR=0;LSEQ=TTTGCATACTTGGTATGTGT;RSEQ=GATAGGGGCATAATTTTCAT;CSQ=T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281765.3|protein_coding|3/18||NM_001281765.3:c.289C>A|NP_001268694.1:p.His97Asn|1036|289|97|H/N|Cac/Aac|||-1||EntrezGene||YES||||4:g.66467980G>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281766.3|protein_coding|3/17||NM_001281766.3:c.289C>A|NP_001268695.1:p.His97Asn|1036|289|97|H/N|Cac/Aac|||-1||EntrezGene||||||4:g.66467980G>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001281767.3|protein_coding|3/17||NM_001281767.3:c.289C>A|NP_001268696.1:p.His97Asn|1036|289|97|H/N|Cac/Aac|||-1||EntrezGene||||||4:g.66467980G>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_001318761.2|protein_coding|3/18||NM_001318761.2:c.82C>A|NP_001305690.1:p.His28Asn|160|82|28|H/N|Cac/Aac|||-1||EntrezGene||||||4:g.66467980G>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_004439.8|protein_coding|3/18||NM_004439.8:c.289C>A|NP_004430.4:p.His97Asn|1036|289|97|H/N|Cac/Aac|||-1||EntrezGene||||||4:g.66467980G>T||||||||||||||,T|missense_variant|MODERATE|EPHA5|2044|Transcript|NM_182472.5|protein_coding|3/17||NM_182472.5:c.289C>A|NP_872272.2:p.His97Asn|1036|289|97|H/N|Cac/Aac|||-1||EntrezGene||||||4:g.66467980G>T||||||||||||||	GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM	0/0:47:0:0,0:9,38:47,0:0:2,0:29.8:1:35.4:1:1:0:60:46:1:0:0.2	0/1:165:3:1,2:48,114:162,3:0.0182:2,2:41.7:1:28.3:1:1:1.19:60:2:0.0124:0:2.7
    1572. 

  1572. 4	66468047	66468047	A	-	intronic	EPHA5	.	.	.	0.94	0.8737	0.7754	0.9075	0.9305	0.7857	0.9342	0.9214	0.9012	rs397993765	rs5858973	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	
    1573.