TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.oxoG.snp.capture.tcga.vep.vcf 58.8 KB
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##fileformat=VCFv4.1
##fileDate=20160402
##tcgaversion=1.1
##reference=<ID=hg19,source="http://www.broadinstitute.org/ftp/pub//seq/references/Homo_sapiens_assembly19.fasta">
##assembly=.
##center="broad.mit.edu"
##phasing=none
##geneAnno=http://www.gencodegenes.org/
##vcfProcessLog=<InputVCF=<.>,InputVCFSource=<.>,InputVCFVer=<.>,InputVCFParam=<.>,InputVCFgeneAnno=<https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/>>
##INDIVIDUAL=TCGA-A1-A0SB
##SAMPLE=<ID=NORMAL,SampleTCGABarcode=TCGA-A1-A0SB-10B-01D-A142-09,SampleName=TCGA-A1-A0SB-10B-01D-A142-09,Individual=TCGA-A1-A0SB,Description="Normal sample",Platform=Illumina,Source=dbGaP,Accession=.,softwareName=<muTect,CallIndelsPipeline>,softwareVer=<119,65>,softwareParam=<.>,File=TCGA-A1-A0SB-10B-01D-A142-09,SampleUUID=a3254f8e-3bbd-42fc-abea-a5f25b7648b3,MetadataResource=https://tcga-data.nci.nih.gov/uuid/uuidws/mapping/xml/uuid/a3254f8e-3bbd-42fc-abea-a5f25b7648b3>
##SAMPLE=<ID=PRIMARY,SampleTCGABarcode=TCGA-A1-A0SB-01A-11D-A142-09,SampleName=TCGA-A1-A0SB-01A-11D-A142-09,Individual=TCGA-A1-A0SB,Description="Primary Tumor",Platform=Illumina,Source=dbGaP,Accession=.,softwareName=<muTect,CallIndelsPipeline>,softwareVer=<119,65>,softwareParam=<.>,File=TCGA-A1-A0SB-01A-11D-A142-09,SampleUUID=db9d40fb-bfce-4c3b-a6c2-41c5c88982f1,MetadataResource=https://tcga-data.nci.nih.gov/uuid/uuidws/mapping/xml/uuid/db9d40fb-bfce-4c3b-a6c2-41c5c88982f1>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Depth of reads supporting alleles 0/1/2/3...">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=FA,Number=.,Type=Float,Description="Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample">
##FORMAT=<ID=MQ0,Number=1,Type=Integer,Description="Number of Mapping Quality Zero Reads per sample">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic score between 0 and 255">
##INFO=<ID=Gene,Number=1,Type=String,Description="Hugo Gene Symbol">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=VC,Number=1,Type=String,Description="Somatic variant classification">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of sample">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth across samples">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=TID,Number=1,Type=String,Description="Transcript ID">
##INFO=<ID=VLSC,Number=1,Type=Integer,Description="Final somatic score between 0 and 255 when multiple lines of evidence are available">
##FILTER=<ID=mf1,Description="Filtered out by MuTect v.1">
##FILTER=<ID=oxoG3,Description="Filtered out by OxoG Artifact Filter v3">
##VEP="v101" time="2020-10-31 00:51:49" cache="/Users/ypradat/.vep/homo_sapiens/101_GRCh37" ensembl=101.856c8e8 ensembl-io=101.943b6c2 ensembl-funcgen=101.b918a49 ensembl-variation=101.851c7e0 1000genomes="phase3" COSMIC="90" ClinVar="201912" ESP="20141103" HGMD-PUBLIC="20194" assembly="GRCh37.p13" dbSNP="153" gencode="GENCODE 19" genebuild="2011-04" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	PRIMARY
1	44476442	.	C	T	43	PASS	DP=127;Gene=SLC6A9;MQ0=0;SOMATIC;SS=Somatic;VC=5'UTR;VT=SNP;TID=ENST00000372307.3;VLSC=255;CSQ=T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000357730|protein_coding|2/13||ENST00000357730.2:c.200G>A|ENSP00000350362.2:p.Gly67Asp|392/2168|200/1959|67/652|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056|||CCDS41316.1|ENSP00000350362|P48067|E9PJ65&B7Z589&B7Z3W8|UPI000053030A|NM_006934.3&NM_001261380.1|1|deleterious(0)|probably_damaging(0.999)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000360584|protein_coding|3/14||ENST00000360584.2:c.362G>A|ENSP00000353791.2:p.Gly121Asp|554/2330|362/2121|121/706|G/D|gGc/gAc|COSV62211565|1||-1||1|SNV|HGNC|11056|YES||CCDS41317.1|ENSP00000353791|P48067|B7Z589|UPI000053030B|NM_201649.3|1|deleterious(0)|probably_damaging(1)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000372306|protein_coding|3/12||ENST00000372306.3:c.143G>A|ENSP00000361380.3:p.Gly48Asp|283/1926|143/1740|48/579|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000361380||J3KPA5|UPI0001F7803E||1|deleterious(0)|probably_damaging(0.993)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|5_prime_UTR_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000372307|protein_coding|2/12||ENST00000372307.3:c.-53G>A||276/2162|||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000361381||B7Z3A9|UPI0001914B58||1|||||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000372310|protein_coding|3/14||ENST00000372310.3:c.143G>A|ENSP00000361384.3:p.Gly48Asp|309/3130|143/1902|48/633|G/D|gGc/gAc|COSV62211565|1||-1|||SNV|HGNC|11056|||CCDS30695.1|ENSP00000361384|P48067|B7Z589|UPI0000204F05|NM_001024845.2|1|deleterious(0)|probably_damaging(0.999)|Transmembrane_helices:TMhelix&PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000466926|protein_coding|4/4||ENST00000466926.1:c.305G>A|ENSP00000433241.1:p.Gly102Asp|547/591|305/349|102/116|G/D|gGc/gAc|COSV62211565|1||-1|cds_end_NF||SNV|HGNC|11056||||ENSP00000433241||E9PLM5|UPI0001F78040||1|deleterious(0)|probably_damaging(1)|Superfamily:0053687&Pfam:PF00209&PANTHER:PTHR11616&PANTHER:PTHR11616:SF110&PROSITE_profiles:PS50267||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000475075|protein_coding||2/11|ENST00000475075.2:c.-14-2147G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000434460||B7Z589|UPI0001914EDD||1|||||||||||||||||||||||1|1||||||,T|non_coding_transcript_exon_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000489764|retained_intron|3/3||ENST00000489764.1:n.352G>A||352/930|||||COSV62211565|1||-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000492434|processed_transcript||3/4|ENST00000492434.2:n.351+39G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|missense_variant|MODERATE|SLC6A9|ENSG00000196517|Transcript|ENST00000528803|protein_coding|3/5||ENST00000528803.1:c.200G>A|ENSP00000435652.1:p.Gly67Asp|321/524|200/403|67/134|G/D|gGc/gAc|COSV62211565|1||-1|cds_end_NF||SNV|HGNC|11056||||ENSP00000435652||E9PJ65|UPI0001F7803F||1|deleterious(0)|probably_damaging(0.999)|PROSITE_profiles:PS50267&PANTHER:PTHR11616:SF110&PANTHER:PTHR11616&Pfam:PF00209&Superfamily:0053687&Prints:PR00176||||||||||||||||||||1|1||||||,T|downstream_gene_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000533007|processed_transcript||||||||||COSV62211565|1|3860|-1|||SNV|HGNC|11056|||||||||1|||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|SLC6A9|ENSG00000196517|Transcript|ENST00000537678|protein_coding||2/10|ENST00000537678.1:c.-8-674G>A|||||||COSV62211565|1||-1|||SNV|HGNC|11056||||ENSP00000442523||B7Z9G8|UPI000191543C||1|||||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:69,0:69:0.000:0:.:2:.	0/1:42,16:58:0.276:0:31:2:.
1	244583577	.	G	T	6	PASS	DP=113;Gene=ADSS;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000366535.3;VLSC=255;CSQ=T|missense_variant|MODERATE|ADSS|ENSG00000035687|Transcript|ENST00000366535|protein_coding|8/13||ENST00000366535.3:c.685C>A|ENSP00000355493.3:p.Pro229Thr|1002/2780|685/1371|229/456|P/T|Cca/Aca||1||-1||1|SNV|HGNC|292|YES||CCDS1624.1|ENSP00000355493|P30520||UPI0000132AF5|NM_001126.3||deleterious(0.02)|probably_damaging(0.983)|HAMAP:MF_00011&HAMAP:MF_03127&PANTHER:PTHR11846:SF1&PANTHER:PTHR11846&Gene3D:2v40A01&TIGRFAM:TIGR00184&Pfam:PF00709&SMART:SM00788&Superfamily:SSF52540|||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|ADSS|ENSG00000035687|Transcript|ENST00000462358|processed_transcript|4/5||ENST00000462358.1:n.806C>A||806/932||||||1||-1|||SNV|HGNC|292|||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ADSS|ENSG00000035687|Transcript|ENST00000468215|processed_transcript|||||||||||1|1002|-1|||SNV|HGNC|292|||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:77,0:77:0.000:0:.:2:.	0/1:33,3:36:0.083:0:32:2:.
2	25678299	.	C	T	24	PASS	DP=50;Gene=DTNB;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000406818.3;VLSC=255;CSQ=T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000288642|protein_coding|11/20||ENST00000288642.8:c.1144G>A|ENSP00000288642.8:p.Val382Met|1394/2365|1144/1794|382/597|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||ENSP00000288642||Q53TC8&Q53SF9&F8W9U0&E9PE76&E7EVB6&E7ES64|UPI00015E0989|||deleterious(0.04)|possibly_damaging(0.701)|PANTHER:PTHR11915&PANTHER:PTHR11915:SF227&PIRSF:PIRSF038204||||||||||||||||||||0&1|0&1||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000356599|nonsense_mediated_decay||7/14|ENST00000356599.5:c.*433-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||ENSP00000349007||F8WD22|UPI0000E07239|||||||||||||||||||||||||0&1|0&1||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000398951|nonsense_mediated_decay|10/18||ENST00000398951.2:c.*539G>A||1155/2160|||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||ENSP00000381924||Q53TC8&E9PE76&E7ES64|UPI000022B9C3|||||||||||||||||||||||||0&1|0&1||||||,T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000404103|protein_coding|11/20||ENST00000404103.3:c.1144G>A|ENSP00000385482.3:p.Val382Met|1394/2384|1144/1794|382/597|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058|||CCDS46235.1|ENSP00000385482|O60941|Q53TC8&Q53SF9&Q53QV1&F8W9U0&E9PE76&E7ES64|UPI000002A862|NM_033147.3||deleterious(0.04)|probably_damaging(0.919)|PANTHER:PTHR11915&PANTHER:PTHR11915:SF227&PIRSF:PIRSF038204||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000405222|protein_coding||10/17|ENST00000405222.1:c.1080-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058|||CCDS46233.1|ENSP00000384787|O60941|Q53TC8&Q53SF9&F8W9U0&E9PE76&E7ES64|UPI0000072AE7|NM_183361.2||||||||||||||||||||||||0&1|0&1||||||,T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000406818|protein_coding|11/21||ENST00000406818.3:c.1144G>A|ENSP00000384084.3:p.Val382Met|1394/2474|1144/1884|382/627|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1||1|SNV|HGNC|3058|YES||CCDS46237.1|ENSP00000384084|O60941|Q53TC8&Q53T51&Q53SF9&Q53QV1&F8W9U0&E9PE76&E7ES64|UPI0000129949|NM_001256303.1&NM_021907.4||deleterious(0.03)|benign(0.379)|PANTHER:PTHR11915:SF227&PANTHER:PTHR11915&PIRSF:PIRSF038204||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000407038|protein_coding||10/18|ENST00000407038.3:c.1080-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058|||CCDS46234.1|ENSP00000384767|O60941|Q53TC8&Q53SF9&F8W9U0&E9PE76&E7ES64|UPI000002A860|NM_033148.3||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000407186|protein_coding||10/18|ENST00000407186.1:c.1080-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||ENSP00000385784||Q53TC8&Q53T51&Q53SF9&F8W9U0&E9PEY4&E9PE76&E7ES64|UPI0000D4E665|||||||||||||||||||||||||0&1|0&1||||||,T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000407661|protein_coding|11/20||ENST00000407661.3:c.1144G>A|ENSP00000385193.3:p.Val382Met|1394/2420|1144/1830|382/609|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058|||CCDS46236.1|ENSP00000385193|O60941|Q53TC8&Q53SF9&Q53QV1&Q1I0L3&F8W9U0&E9PE76&E7ES64|UPI00001D69F5|NM_183360.2&NM_001256304.1||deleterious(0.04)|possibly_damaging(0.847)|PANTHER:PTHR11915:SF268&PANTHER:PTHR11915&PIRSF:PIRSF038204||||||||||||||||||||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000479898|retained_intron|2/8||ENST00000479898.1:n.110G>A||110/865|||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000481841|processed_transcript||2/6|ENST00000481841.1:n.139-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000482145|retained_intron||1/5|ENST00000482145.1:n.246-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000485845|retained_intron|10/15||ENST00000485845.1:n.1144G>A||1144/1988|||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000486555|processed_transcript||2/3|ENST00000486555.1:n.363-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|DTNB|ENSG00000138101|Transcript|ENST00000489756|processed_transcript||2/3|ENST00000489756.1:n.401-3795G>A|||||||rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||||||||||||||||||||||||||||||0&1|0&1||||||,T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000496972|protein_coding|10/18||ENST00000496972.2:c.973G>A|ENSP00000444463.1:p.Val325Met|1280/2330|973/1638|325/545|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058|||CCDS58702.1|ENSP00000444463|O60941|Q53SF9|UPI0002065089|NM_001256308.1||tolerated(0.07)|benign(0.192)|PANTHER:PTHR11915:SF268&PANTHER:PTHR11915&PIRSF:PIRSF038204||||||||||||||||||||0&1|0&1||||||,T|missense_variant|MODERATE|DTNB|ENSG00000138101|Transcript|ENST00000545439|protein_coding|9/18||ENST00000545439.1:c.532G>A|ENSP00000444961.1:p.Val178Met|1071/1857|532/1251|178/416|V/M|Gtg/Atg|rs1230449080&COSV56481440|1||-1|||SNV|HGNC|3058||||ENSP00000444961||Q53T51&B7Z202|UPI0001914D31|||deleterious(0.03)|possibly_damaging(0.482)|PANTHER:PTHR11915:SF268&PANTHER:PTHR11915||||||||||||||||||||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:33,0:33:0.000:0:.:2:.	0/1:9,8:17:0.471:0:32:2:.
3	85932472	.	C	T	56	PASS	DP=87;Gene=CADM2;MQ0=0;SOMATIC;SS=Somatic;VC=Silent;VT=SNP;TID=ENST00000383699.3;VLSC=255;CSQ=T|synonymous_variant|LOW|CADM2|ENSG00000175161|Transcript|ENST00000383699|protein_coding|4/10||ENST00000383699.3:c.270C>T|ENSP00000373200.3:p.Arg90=|897/9488|270/1215|90/404|R|cgC/cgT|rs747906551&COSV67367857|1||1|||SNV|HGNC|29849|||CCDS54613.1|ENSP00000373200|Q8N3J6|G3XHN7&G3XHN4|UPI0000035DF5|NM_001167675.1&NM_001256504.1&NM_001256505.1||||Gene3D:2.60.40.10&Pfam:PF07686&PROSITE_profiles:PS50835&PANTHER:PTHR23277&PANTHER:PTHR23277:SF56&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726||||||||||1.595e-05|0|0|0.000298|0|0|8.821e-06|0|0||0&1|0&1||||||,T|synonymous_variant|LOW|CADM2|ENSG00000175161|Transcript|ENST00000405615|protein_coding|3/10||ENST00000405615.2:c.249C>T|ENSP00000384193.2:p.Arg83=|249/1314|249/1314|83/437|R|cgC/cgT|rs747906551&COSV67367857|1||1||1|SNV|HGNC|29849|YES||CCDS33792.1|ENSP00000384193|Q8N3J6|G3XHN8|UPI000013F077|NM_153184.3||||Gene3D:2.60.40.10&Pfam:PF07686&PROSITE_profiles:PS50835&PANTHER:PTHR23277&PANTHER:PTHR23277:SF56&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726||||||||||1.595e-05|0|0|0.000298|0|0|8.821e-06|0|0||0&1|0&1||||||,T|synonymous_variant|LOW|CADM2|ENSG00000175161|Transcript|ENST00000407528|protein_coding|3/10||ENST00000407528.2:c.243C>T|ENSP00000384575.2:p.Arg81=|305/1422|243/1308|81/435|R|cgC/cgT|rs747906551&COSV67367857|1||1|||SNV|HGNC|29849|||CCDS54614.1|ENSP00000384575|Q8N3J6|G3XHN8|UPI000006DE82|NM_001167674.1||||Gene3D:2.60.40.10&Pfam:PF07686&PROSITE_profiles:PS50835&PANTHER:PTHR23277&PANTHER:PTHR23277:SF56&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726||||||||||1.595e-05|0|0|0.000298|0|0|8.821e-06|0|0||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:50,0:50:0.000:0:.:2:.	0/1:18,19:37:0.514:0:30:2:.
6	7986778	.	G	A	27	PASS	DP=46;Gene=BLOC1S5-TXNDC5;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=SNP;TID=ENST00000539054.1;VLSC=255;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|PIP5K1P1|ENSG00000219294|Transcript|ENST00000438779|processed_pseudogene|1/1||ENST00000438779.2:n.49G>A||49/1579|||||rs1418108697|1||1|||SNV|HGNC|28372||||||||||||||||||||||4.655e-06|0|0|0|0|0|0|0|3.517e-05|||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|BLOC1S5-TXNDC5|ENSG00000259040|Transcript|ENST00000439343|nonsense_mediated_decay||4/12|ENST00000439343.2:c.372+39822C>T|||||||rs1418108697|1||-1|cds_start_NF||SNV|HGNC|42001|YES|||ENSP00000454697||H3BN57|UPI0001B793F7|||||||||||||||4.655e-06|0|0|0|0|0|0|0|3.517e-05|||||||||,A|non_coding_transcript_exon_variant|MODIFIER|PIP5K1P1|ENSG00000219294|Transcript|ENST00000460661|processed_pseudogene|1/1||ENST00000460661.1:n.9G>A||9/1656|||||rs1418108697|1||1||1|SNV|HGNC|28372|YES|||||||||||||||||||||4.655e-06|0|0|0|0|0|0|0|3.517e-05|||||||||,A|intron_variant|MODIFIER|TXNDC5|ENSG00000239264|Transcript|ENST00000539054|protein_coding||1/9|ENST00000539054.1:c.47+39822C>T|||||||rs1418108697|1||-1|||SNV|HGNC|21073||||ENSP00000442453||Q86UY0|UPI0000192760|||||||||||||||4.655e-06|0|0|0|0|0|0|0|3.517e-05|||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:23,0:23:0.000:0:.:2:.	0/1:13,10:23:0.435:0:29:2:.
7	75609837	.	C	G	13	PASS	DP=19;Gene=POR;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=SNP;TID=ENST00000394893.1;VLSC=255;CSQ=G|intron_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000394893|protein_coding||5/14|ENST00000394893.1:c.516+31C>G|||||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000378355|P16435|C9JQ78|UPI000198CD2F||1||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000412064|nonsense_mediated_decay||4/9|ENST00000412064.2:c.516+31C>G|||||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000404731|P16435|C9JQ78|UPI000198CD38||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000412521|protein_coding||||||||||rs373201804|1|108|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000409238|P16435|C9JQ78|UPI000198CD17||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000414186|protein_coding||||||||||rs373201804|1|31|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000399327|P16435|C9JQ78|UPI000198CD2D||1||||||||||||||||||||||||||||||,G|intron_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000419840|protein_coding||5/14|ENST00000419840.1:c.-43+31C>G|||||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000414244||E7EPN3|UPI0001AE7117||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000426184|protein_coding||||||||||rs373201804|1|80|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000400964||C9JU80|UPI000198CD37||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000432753|protein_coding||||||||||rs373201804|1|48|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000389409|P16435|C9JQ78|UPI000198CD36||1||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000439269|protein_coding||||||||||rs373201804|1|1392|1|||SNV|HGNC|9208||||ENSP00000412490||E7EMD0|UPI000198CD32||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000439297|protein_coding||||||||||rs373201804|1|982|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000403494||C9JDE2|UPI000155D656||1||||||||||||||||||||||||||||||,G|intron_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000439963|protein_coding||5/5|ENST00000439963.1:c.516+31C>G|||||||rs373201804|1||1|cds_end_NF||SNV|HGNC|9208||||ENSP00000390540|P16435|C9JQ78|UPI000198CD34||1||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|POR|ENSG00000127948|Transcript|ENST00000447222|protein_coding|4/15||ENST00000447222.1:c.466C>G|ENSP00000393527.1:p.Arg156Gly|464/2332|466/2178|156/725|R/G|Cgg/Ggg|rs373201804|1||1|cds_start_NF||SNV|HGNC|9208||||ENSP00000393527||E7EVY7|UPI000198CD31||1|tolerated_low_confidence(0.66)|benign(0)|PIRSF:PIRSF000208&PROSITE_profiles:PS50902&PANTHER:PTHR19384|||||||||||||||||||||||||||,G|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000448410|nonsense_mediated_decay|5/5||ENST00000448410.1:c.*544C>G||885/1104|||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000399409||E7EWU0&C9JQ78|UPI000198CD2E||1||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|POR|ENSG00000127948|Transcript|ENST00000450476|protein_coding|1/12||ENST00000450476.1:c.10C>G|ENSP00000416572.1:p.Arg4Gly|20/1888|10/1722|4/573|R/G|Cgg/Ggg|rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000416572||E7EVY7|UPI0001AE7118||1|tolerated_low_confidence(0.37)|benign(0.015)|PROSITE_profiles:PS50902|||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000453773|protein_coding||||||||||rs373201804|1|126|1|cds_end_NF||SNV|HGNC|9208||||ENSP00000395813|P16435|C9JQ78|UPI000198CD33||1||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000454934|nonsense_mediated_decay||4/13|ENST00000454934.1:c.516+31C>G|||||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000414263|P16435|C9JQ78|UPI000198CD30||1||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000460892|retained_intron||||||||||rs373201804|1|413|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|intron_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000461988|protein_coding||5/15|ENST00000461988.1:c.516+31C>G|||||||rs373201804|1||1||1|SNV|HGNC|9208|YES||CCDS5579.1|ENSP00000419970|P16435|Q59ED7&E7EMD0&C9JQ78|UPI000013D5F4|NM_000941.2|1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000471238|retained_intron||||||||||rs373201804|1|733|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000475509|processed_transcript||||||||||rs373201804|1|159|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000487247|retained_intron||||||||||rs373201804|1|2917|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000495770|retained_intron||||||||||rs373201804|1|3270|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000496888|retained_intron||||||||||rs373201804|1|2797|1|||SNV|HGNC|9208|||||||||1||||||||||||||||||||||||||||||,G|intron_variant|MODIFIER|POR|ENSG00000127948|Transcript|ENST00000545601|protein_coding||1/10|ENST00000545601.1:c.65+31C>G|||||||rs373201804|1||1|||SNV|HGNC|9208||||ENSP00000446149||F5H468&E7EMD0|UPI0000E5ADA9||1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:8,0:8:0.000:0:.:2:.	0/1:6,5:11:0.455:0:28:2:.
7	149129243	.	G	A	16	PASS	DP=45;Gene=ZNF777;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000247930.4;VLSC=255;CSQ=A|missense_variant|MODERATE|ZNF777|ENSG00000196453|Transcript|ENST00000247930|protein_coding|6/6||ENST00000247930.4:c.2120C>T|ENSP00000247930.4:p.Ser707Leu|2444/3233|2120/2496|707/831|S/L|tCg/tTg|COSV56098152|1||-1||1|SNV|HGNC|22213|YES||CCDS43675.1|ENSP00000247930|Q9ULD5|Q3KR11|UPI0000E9B152|NM_015694.2||tolerated(0.13)|probably_damaging(0.986)|PROSITE_profiles:PS50157&PANTHER:PTHR24402:SF204&PANTHER:PTHR24402&PROSITE_patterns:PS00028&Gene3D:3.30.160.60&SMART:SM00355&Superfamily:SSF57667||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:18,0:18:0.000:0:.:2:.	0/1:21,6:27:0.222:0:32:2:.
7	150840441	.	C	T	26	PASS	DP=52;Gene=AGAP3;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000463381.1;VLSC=255;CSQ=T|missense_variant|MODERATE|AGAP3|ENSG00000133612|Transcript|ENST00000397238|protein_coding|17/18||ENST00000397238.2:c.2287C>T|ENSP00000380413.2:p.Arg763Cys|2287/3225|2287/2736|763/911|R/C|Cgc/Tgc|rs372948404|1||1||1|SNV|HGNC|16923|YES||CCDS43681.1|ENSP00000380413|Q96P47|Q96T14&D3DX07|UPI0000DAC777|NM_031946.5||deleterious(0.01)|possibly_damaging(0.799)|Pfam:PF01412&PROSITE_profiles:PS50115&PANTHER:PTHR23180&PANTHER:PTHR23180:SF198&SMART:SM00105&Superfamily:SSF57863||||||||0.0002372|0.0001179|6.472e-05|0.0001292|0|0|5.565e-05|0|5.372e-05|0.0001668|0.0001977|||||||||,T|missense_variant|MODERATE|AGAP3|ENSG00000133612|Transcript|ENST00000461065|protein_coding|6/7||ENST00000461065.1:c.766C>T|ENSP00000417910.1:p.Arg256Cys|765/1707|766/1215|256/404|R/C|Cgc/Tgc|rs372948404|1||1|cds_start_NF||SNV|HGNC|16923||||ENSP00000417910||Q86XV5|UPI0001B792FC|||deleterious(0.01)|possibly_damaging(0.605)|Pfam:PF01412&PROSITE_profiles:PS50115&PANTHER:PTHR23180&PANTHER:PTHR23180:SF198&SMART:SM00105&Superfamily:SSF57863||||||||0.0002372|0.0001179|6.472e-05|0.0001292|0|0|5.565e-05|0|5.372e-05|0.0001668|0.0001977|||||||||,T|missense_variant|MODERATE|AGAP3|ENSG00000133612|Transcript|ENST00000463381|protein_coding|15/16||ENST00000463381.1:c.1294C>T|ENSP00000418016.1:p.Arg432Cys|1790/2730|1294/1743|432/580|R/C|Cgc/Tgc|rs372948404|1||1|||SNV|HGNC|16923|||CCDS64802.1|ENSP00000418016||B3KNZ8|UPI00001A8241|NM_001281300.1||deleterious(0.01)|benign(0.013)|Pfam:PF01412&PROSITE_profiles:PS50115&PANTHER:PTHR23180&PANTHER:PTHR23180:SF198&SMART:SM00105&Superfamily:SSF57863||||||||0.0002372|0.0001179|6.472e-05|0.0001292|0|0|5.565e-05|0|5.372e-05|0.0001668|0.0001977|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|AGAP3|ENSG00000133612|Transcript|ENST00000473633|retained_intron|4/5||ENST00000473633.1:n.2813C>T||2813/3751|||||rs372948404|1||1|||SNV|HGNC|16923||||||||||||||||||||0.0002372|0.0001179|6.472e-05|0.0001292|0|0|5.565e-05|0|5.372e-05|0.0001668|0.0001977|||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001415095|||||||||||rs372948404|1|||||SNV||||||||||||||||||||||0.0002372|0.0001179|6.472e-05|0.0001292|0|0|5.565e-05|0|5.372e-05|0.0001668|0.0001977|||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:28,0:28:0.000:0:.:2:.	0/1:15,9:24:0.375:0:32:2:.
10	116247760	.	T	C	26	PASS	DP=117;Gene=ABLIM1;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000392952.3;VLSC=255;CSQ=C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000277895|protein_coding|8/23||ENST00000277895.5:c.998A>G|ENSP00000277895.5:p.His333Arg|1096/2657|998/2337|333/778|H/R|cAt/cGt|COSV53311631|1||-1||1|SNV|HGNC|78|YES||CCDS7590.1|ENSP00000277895|O14639||UPI0000418D06|NM_002313.5||deleterious(0)|possibly_damaging(0.887)|Gene3D:2.10.110.10&PROSITE_profiles:PS50023&PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&SMART:SM00132&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000369252|protein_coding|8/23||ENST00000369252.4:c.818A>G|ENSP00000358256.4:p.His273Arg|1120/7606|818/2157|273/718|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78|||CCDS31288.1|ENSP00000358256|O14639||UPI0000418D07|NM_001003408.1&NM_001003407.1||deleterious(0)|benign(0.279)|Gene3D:2.10.110.10&PROSITE_profiles:PS50023&PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&SMART:SM00132&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000369253|protein_coding|3/16||ENST00000369253.2:c.50A>G|ENSP00000358257.2:p.His17Arg|280/2255|50/1206|17/401|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78||||ENSP00000358257|O14639||UPI0000072AEB|||deleterious(0)|possibly_damaging(0.595)|PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant&NMD_transcript_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000369256|nonsense_mediated_decay|8/24||ENST00000369256.2:c.818A>G|ENSP00000358260.2:p.His273Arg|1468/3203|818/2066|273/688|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78||||ENSP00000358260||Q5T6N2&B3KVH2|UPI0002B83214|||deleterious(0)|probably_damaging(0.992)|Gene3D:2.10.110.10&PROSITE_profiles:PS50023&PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&SMART:SM00132&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000369266|protein_coding|3/18||ENST00000369266.3:c.50A>G|ENSP00000358270.3:p.His17Arg|371/6836|50/1368|17/455|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78||||ENSP00000358270||J3QSX6|UPI0002064DFC|||deleterious(0)|benign(0.408)|PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000392952|protein_coding|3/18||ENST00000392952.3:c.50A>G|ENSP00000376679.3:p.His17Arg|376/6841|50/1368|17/455|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78|||CCDS31289.1|ENSP00000376679|O14639||UPI0000373525|NM_006720.3||deleterious(0)|probably_damaging(0.999)|PANTHER:PTHR24213:SF18&PANTHER:PTHR24213&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant&NMD_transcript_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000392955|nonsense_mediated_decay|8/22||ENST00000392955.3:c.818A>G|ENSP00000376682.3:p.His273Arg|922/7400|818/1968|273/655|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78||||ENSP00000376682||H0Y3K7|UPI0002B83210|||deleterious(0)|benign(0.258)|Gene3D:2.10.110.10&PROSITE_profiles:PS50023&PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&SMART:SM00132&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000428430|protein_coding|3/8||ENST00000428430.1:c.50A>G|ENSP00000400934.1:p.His17Arg|384/854|50/520|17/173|H/R|cAt/cGt|COSV53311631|1||-1|cds_end_NF||SNV|HGNC|78||||ENSP00000400934||F6XFR5|UPI00004A2D61|||deleterious(0)|possibly_damaging(0.603)|PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|ABLIM1|ENSG00000099204|Transcript|ENST00000440467|protein_coding||||||||||COSV53311631|1|8|-1|cds_start_NF||SNV|HGNC|78||||ENSP00000414154||H0Y7N6|UPI00004A2D5F|||||||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ABLIM1|ENSG00000099204|Transcript|ENST00000533213|protein_coding|8/23||ENST00000533213.2:c.818A>G|ENSP00000433629.2:p.His273Arg|1120/7606|818/2157|273/718|H/R|cAt/cGt|COSV53311631|1||-1|||SNV|HGNC|78||||ENSP00000433629||F8W8M4|UPI0002064DFB|||deleterious(0)|benign(0.279)|Gene3D:2.10.110.10&PROSITE_profiles:PS50023&PANTHER:PTHR24213&PANTHER:PTHR24213:SF18&SMART:SM00132&Superfamily:SSF57716||||||||||||||||||||1|1||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000990007|||||||||||COSV53311631|1|||||SNV||||||||||||||||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:72,0:72:0.000:0:.:2:.	0/1:34,11:45:0.244:0:28:2:.
12	43944926	.	T	C	44	PASS	DP=82;Gene=ADAMTS20;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000389420.3;VLSC=255;CSQ=C|missense_variant|MODERATE|ADAMTS20|ENSG00000173157|Transcript|ENST00000389420|protein_coding|2/39||ENST00000389420.3:c.239A>G|ENSP00000374071.3:p.Tyr80Cys|239/6076|239/5733|80/1910|Y/C|tAt/tGt|COSV67136109|1||-1||1|SNV|HGNC|17178|YES||CCDS31778.2|ENSP00000374071|P59510||UPI00004565F4|NM_025003.3||deleterious(0)|probably_damaging(0.986)|Pfam:PF01562&PANTHER:PTHR13723&PANTHER:PTHR13723:SF165||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|ADAMTS20|ENSG00000173157|Transcript|ENST00000553158|protein_coding|2/29||ENST00000553158.1:c.239A>G|ENSP00000448341.1:p.Tyr80Cys|239/4633|239/4515|80/1504|Y/C|tAt/tGt|COSV67136109|1||-1|||SNV|HGNC|17178||||ENSP00000448341||G3V1X8|UPI0000EE65C8|||deleterious(0)|probably_damaging(1)|Pfam:PF01562&PANTHER:PTHR13723&PANTHER:PTHR13723:SF165||||||||||||||||||||1|1||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001029344|||||||||||COSV67136109|1|||||SNV||||||||||||||||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:50,0:50:0.000:0:.:2:.	0/1:17,15:32:0.469:0:31:2:.
13	50464902	.	T	C	8	PASS	DP=140;Gene=.;MQ0=0;SOMATIC;SS=Somatic;VC=IGR;VT=SNP;TID=.;VLSC=255;CSQ=C|non_coding_transcript_exon_variant|MODIFIER|CTAGE10P|ENSG00000181358|Transcript|ENST00000318353|processed_pseudogene|1/1||ENST00000318353.2:n.176T>C||176/2408||||||1||1||1|SNV|HGNC|37288|YES||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|RNY4P30|ENSG00000222148|Transcript|ENST00000410216|misc_RNA|||||||||||1|1038|-1|||SNV|HGNC|42498|YES||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:75,0:75:0.000:0:.:2:.	0/1:60,5:65:0.077:0:26:2:.
14	65266493	.	T	C	20	PASS	DP=41;Gene=SPTB;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000556626.1;VLSC=255;CSQ=C|missense_variant|MODERATE|SPTB|ENSG00000070182|Transcript|ENST00000389720|protein_coding|8/30||ENST00000389720.3:c.1036A>G|ENSP00000374370.3:p.Thr346Ala|1036/6321|1036/6321|346/2106|T/A|Acc/Gcc|COSV67633870|1||-1|||SNV|HGNC|11274||||ENSP00000374370|P11277|Q71VG2&Q71VG1&Q71VG0&Q71VF9&O14726&O14725|UPI00015DFD73||1|tolerated(0.34)|benign(0.133)|PANTHER:PTHR11915&PANTHER:PTHR11915:SF248&Pfam:PF00435&Gene3D:1.20.58.60&PIRSF:PIRSF002297&SMART:SM00150&Superfamily:SSF46966||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|SPTB|ENSG00000070182|Transcript|ENST00000389721|protein_coding|8/31||ENST00000389721.5:c.1036A>G|ENSP00000374371.5:p.Thr346Ala|1069/6705|1036/6414|346/2137|T/A|Acc/Gcc|COSV67633870|1||-1|||SNV|HGNC|11274|||CCDS32100.1|ENSP00000374371|P11277|Q71VG2&Q71VG1&Q71VG0&Q71VF9&Q71VF8&O14726&O14725|UPI000053030C|NM_000347.5|1|tolerated(0.28)|benign(0.119)|PANTHER:PTHR11915:SF248&PANTHER:PTHR11915&Gene3D:1.20.58.60&Pfam:PF00435&SMART:SM00150&PIRSF:PIRSF002297&Superfamily:SSF46966||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|SPTB|ENSG00000070182|Transcript|ENST00000389722|protein_coding|8/35||ENST00000389722.3:c.1036A>G|ENSP00000374372.3:p.Thr346Ala|1090/10063|1036/6987|346/2328|T/A|Acc/Gcc|COSV67633870|1||-1||1|SNV|HGNC|11274|YES||CCDS32099.1|ENSP00000374372|P11277|Q71VG2&Q71VG1&Q71VG0&Q71VF9&Q71VF8&Q59FP5&O14726&O14725|UPI000053030D|NM_001024858.2|1|tolerated(0.28)|benign(0.074)|Gene3D:1.20.58.60&Pfam:PF00435&PIRSF:PIRSF002297&PANTHER:PTHR11915&PANTHER:PTHR11915:SF248&SMART:SM00150&Superfamily:SSF46966||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|SPTB|ENSG00000070182|Transcript|ENST00000542895|protein_coding|9/32||ENST00000542895.1:c.1036A>G|ENSP00000443882.1:p.Thr346Ala|1133/6768|1036/6414|346/2137|T/A|Acc/Gcc|COSV67633870|1||-1|||SNV|HGNC|11274|||CCDS32100.1|ENSP00000443882|P11277|Q71VG2&Q71VG1&Q71VG0&Q71VF9&Q71VF8&O14726&O14725|UPI000053030C||1|tolerated(0.28)|benign(0.119)|Superfamily:SSF46966&SMART:SM00150&PIRSF:PIRSF002297&Gene3D:1.20.58.60&Pfam:PF00435&PANTHER:PTHR11915:SF248&PANTHER:PTHR11915||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|SPTB|ENSG00000070182|Transcript|ENST00000556626|protein_coding|9/36||ENST00000556626.1:c.1036A>G|ENSP00000451752.1:p.Thr346Ala|1179/7481|1036/6987|346/2328|T/A|Acc/Gcc|COSV67633870|1||-1|||SNV|HGNC|11274|||CCDS32099.1|ENSP00000451752|P11277|Q71VG2&Q71VG1&Q71VG0&Q71VF9&Q71VF8&Q59FP5&O14726&O14725|UPI000053030D||1|tolerated(0.28)|benign(0.074)|PANTHER:PTHR11915:SF248&PANTHER:PTHR11915&Pfam:PF00435&Gene3D:1.20.58.60&PIRSF:PIRSF002297&SMART:SM00150&Superfamily:SSF46966||||||||||||||||||||1|1||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001568868|||||||||||COSV67633870|1|||||SNV||||||||||||||||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:21,0:21:0.000:0:.:2:.	0/1:12,8:20:0.400:0:27:2:.
15	91043489	.	C	T	9	PASS	DP=24;Gene=IQGAP1;MQ0=0;SOMATIC;SS=Somatic;VC=3'UTR;VT=SNP;TID=ENST00000268182.5;VLSC=255;CSQ=T|3_prime_UTR_variant|MODIFIER|IQGAP1|ENSG00000140575|Transcript|ENST00000268182|protein_coding|38/38||ENST00000268182.5:c.*149C>T||5247/7233|||||rs922590103|1||1||1|SNV|HGNC|6110|YES||CCDS10362.1|ENSP00000268182|P46940|H0YKA5|UPI000012D863|NM_003870.3|||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|IQGAP1|ENSG00000140575|Transcript|ENST00000558957|retained_intron|3/3||ENST00000558957.1:n.1181C>T||1181/2313|||||rs922590103|1||1|||SNV|HGNC|6110|||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant|MODIFIER|IQGAP1|ENSG00000140575|Transcript|ENST00000560738|protein_coding|25/25||ENST00000560738.1:c.*149C>T||3488/3602|||||rs922590103|1||1|||SNV|HGNC|6110||||ENSP00000453181||H0YLE8|UPI00022F876B||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|IQGAP1|ENSG00000140575|Transcript|ENST00000561086|retained_intron|2/2||ENST00000561086.1:n.890C>T||890/2871|||||rs922590103|1||1|||SNV|HGNC|6110|||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:18,0:18:0.000:0:.:2:.	0/1:3,3:6:0.500:0:32:2:.
16	88790292	.	T	C	20	PASS	DP=59;Gene=PIEZO1;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000301015.9;VLSC=255;CSQ=C|missense_variant|MODERATE|PIEZO1|ENSG00000103335|Transcript|ENST00000301015|protein_coding|31/51||ENST00000301015.9:c.4322A>G|ENSP00000301015.9:p.Gln1441Arg|4569/8072|4322/7566|1441/2521|Q/R|cAg/cGg|COSV56341017|1||-1||1|SNV|HGNC|28993|YES||CCDS54058.1|ENSP00000301015|Q92508||UPI0001B300F3|NM_001142864.2|1|tolerated(0.25)|possibly_damaging(0.78)|PANTHER:PTHR13167&PANTHER:PTHR13167:SF40||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000327397|protein_coding||||||||||COSV56341017|1|3994|-1|||SNV|HGNC|28993||||ENSP00000333704||E7EUT2|UPI0000366B79||1|||||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000419505|nonsense_mediated_decay||||||||||COSV56341017|1|3994|-1|cds_start_NF||SNV|HGNC|28993||||ENSP00000406358||H7C2J5|UPI000198C788||1|||||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000466823|protein_coding||||||||||COSV56341017|1|3626|-1|cds_start_NF||SNV|HGNC|28993||||ENSP00000456373|||UPI00024671F4||1|||||||||||||||||||||||1|1||||||,C|missense_variant|MODERATE|PIEZO1|ENSG00000103335|Transcript|ENST00000474606|protein_coding|4/7||ENST00000474606.1:c.344A>G|ENSP00000428673.1:p.Gln115Arg|343/544|344/545|115/181|Q/R|cAg/cGg|COSV56341017|1||-1|cds_start_NF&cds_end_NF||SNV|HGNC|28993||||ENSP00000428673|||UPI0001E8EFD9||1|tolerated(0.11)|probably_damaging(0.959)|PANTHER:PTHR13167&PANTHER:PTHR13167:SF40||||||||||||||||||||1|1||||||,C|downstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000475586|retained_intron||||||||||COSV56341017|1|63|-1|||SNV|HGNC|28993|||||||||1|||||||||||||||||||||||1|1||||||,C|downstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000491917|retained_intron||||||||||COSV56341017|1|3190|-1|||SNV|HGNC|28993|||||||||1|||||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000495568|retained_intron||||||||||COSV56341017|1|3411|-1|||SNV|HGNC|28993|||||||||1|||||||||||||||||||||||1|1||||||,C|upstream_gene_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000497793|retained_intron||||||||||COSV56341017|1|3497|-1|||SNV|HGNC|28993|||||||||1|||||||||||||||||||||||1|1||||||,C|downstream_gene_variant|MODIFIER|RP5-1142A6.9|ENSG00000260121|Transcript|ENST00000564984|antisense||||||||||COSV56341017|1|3425|1|||SNV|Clone_based_vega_gene||YES|||||||||||||||||||||||||||||||1|1||||||,C|non_coding_transcript_exon_variant|MODIFIER|PIEZO1|ENSG00000103335|Transcript|ENST00000566414|retained_intron|1/5||ENST00000566414.1:n.51A>G||51/564|||||COSV56341017|1||-1|||SNV|HGNC|28993|||||||||1|||||||||||||||||||||||1|1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:34,0:34:0.000:0:.:2:.	0/1:18,7:25:0.280:0:33:2:.
17	40272381	.	G	A	99	PASS	DP=96;Gene=KAT2A;MQ0=0;SOMATIC;SS=Somatic;VC=Silent;VT=SNP;TID=ENST00000225916.5;VLSC=255;CSQ=A|synonymous_variant|LOW|KAT2A|ENSG00000108773|Transcript|ENST00000225916|protein_coding|3/18||ENST00000225916.5:c.471C>T|ENSP00000225916.5:p.His157=|525/3109|471/2514|157/837|H|caC/caT|rs536716483&COSV56792144|1||-1||1|SNV|HGNC|4201|YES||CCDS11417.1|ENSP00000225916|Q92830|K7ERS6|UPI000000D978|NM_021078.2||||PANTHER:PTHR22880:SF124&PANTHER:PTHR22880&Pfam:PF06466&PIRSF:PIRSF003048||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|RAB5C|ENSG00000108774|Transcript|ENST00000346213|protein_coding||||||||||rs536716483&COSV56792144|1|4613|-1|||SNV|HGNC|9785|||CCDS11419.1|ENSP00000345689|P51148|K7EIP6&F8VWU4&F8VVK3&F8VSF8|UPI000000125E|NM_004583.3||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|HSPB9|ENSG00000197723|Transcript|ENST00000355067|protein_coding||||||||||rs536716483&COSV56792144|1|2375|1|||SNV|HGNC|30589|YES||CCDS11418.1|ENSP00000347178|Q9BQS6||UPI00000375B4|NM_033194.2||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|RAB5C|ENSG00000108774|Transcript|ENST00000393860|protein_coding||||||||||rs536716483&COSV56792144|1|4617|-1|||SNV|HGNC|9785|||CCDS11419.1|ENSP00000377440|P51148|K7EIP6&F8VWU4&F8VVK3&F8VSF8|UPI000000125E|NM_201434.2||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|synonymous_variant&NMD_transcript_variant|LOW|KAT2A|ENSG00000108773|Transcript|ENST00000465682|nonsense_mediated_decay|3/18||ENST00000465682.1:c.225C>T|ENSP00000468390.1:p.His75=|225/2990|225/831|75/276|H|caC/caT|rs536716483&COSV56792144|1||-1|cds_start_NF||SNV|HGNC|4201||||ENSP00000468390||K7ERS6|UPI000268B4B2|||||Pfam:PF06466&PANTHER:PTHR22880:SF124&PANTHER:PTHR22880||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CTD-2132N18.3|ENSG00000267261|Transcript|ENST00000585562|nonsense_mediated_decay|3/5||ENST00000585562.1:c.*289C>T||373/646|||||rs536716483&COSV56792144|1||-1|cds_start_NF||SNV|Clone_based_vega_gene|||||ENSP00000464838||K7EIP6|UPI000284107B|||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|KAT2A|ENSG00000108773|Transcript|ENST00000588759|nonsense_mediated_decay||||||||||rs536716483&COSV56792144|1|4530|-1|cds_start_NF||SNV|HGNC|4201||||ENSP00000467324||K7EPC4|UPI000284107A|||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|missense_variant&NMD_transcript_variant|MODERATE|CTD-2132N18.3|ENSG00000267261|Transcript|ENST00000592248|nonsense_mediated_decay|4/5||ENST00000592248.1:c.449C>T|ENSP00000468275.1:p.Thr150Met|511/694|449/486|150/161|T/M|aCg/aTg|rs536716483&COSV56792144|1||-1|||SNV|Clone_based_vega_gene|||||ENSP00000468275||K7ERI8&F8VWU4&F8VVK3&F8VSF8|UPI000284107C|||deleterious_low_confidence(0.05)|benign(0.001)|PROSITE_profiles:PS51419&SMART:SM00175&SMART:SM00174&SMART:SM00173||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|KAT2A|ENSG00000108773|Transcript|ENST00000592310|retained_intron||||||||||rs536716483&COSV56792144|1|2874|-1|||SNV|HGNC|4201||||||||||||||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||,A|synonymous_variant|LOW|CTD-2132N18.3|ENSG00000267261|Transcript|ENST00000592574|protein_coding|6/8||ENST00000592574.1:c.573C>T|ENSP00000468367.1:p.His191=|685/958|573/846|191/282|H|caC/caT|rs536716483&COSV56792144|1||-1|cds_end_NF||SNV|Clone_based_vega_gene||YES|||ENSP00000468367||K7ERQ8&F8VWU4&F8VVK3&F8VSF8|UPI000284107D|||||SMART:SM00175&SMART:SM00176&Pfam:PF06466&PROSITE_profiles:PS51419||0.0002|0|0|0.001|0|0|||2.386e-05|0|2.892e-05|0|0.0001087|0|2.638e-05|0|0||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:35,0:35:0.000:0:.:2:.	0/1:29,32:61:0.525:0:32:2:.
19	42585066	.	G	A	17	PASS	DP=44;Gene=ZNF574;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000600245.1;VLSC=255;CSQ=A|missense_variant|MODERATE|ZNF574|ENSG00000105732|Transcript|ENST00000222339|protein_coding|2/2||ENST00000222339.7:c.2578G>A|ENSP00000222339.6:p.Asp860Asn|2813/3309|2578/2961|860/986|D/N|Gac/Aac|COSV55905712&COSV55906893&COSV55907568|1||1|||SNV|HGNC|26166||||ENSP00000222339|Q6ZN55|Q9NT61&M0R133|UPI000035E797|||tolerated(0.13)|probably_damaging(0.963)|Gene3D:3.30.160.60&Pfam:PF13465&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&PANTHER:PTHR24375&PANTHER:PTHR24375:SF38&SMART:SM00355&Superfamily:SSF57667||||||||||||||||||||1&1&1|1&1&1||||||,A|missense_variant|MODERATE|ZNF574|ENSG00000105732|Transcript|ENST00000359044|protein_coding|2/2||ENST00000359044.4:c.2308G>A|ENSP00000351939.3:p.Asp770Asn|2449/2940|2308/2691|770/896|D/N|Gac/Aac|COSV55905712&COSV55906893&COSV55907568|1||1|||SNV|HGNC|26166|||CCDS12596.1|ENSP00000351939|Q6ZN55|Q9NT61&M0R133|UPI00001AE536|NM_022752.5||deleterious(0.01)|probably_damaging(0.917)|Gene3D:3.30.160.60&Pfam:PF13465&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&PANTHER:PTHR24375&PANTHER:PTHR24375:SF38&SMART:SM00355&Superfamily:SSF57667||||||||||||||||||||1&1&1|1&1&1||||||,A|upstream_gene_variant|MODIFIER|CTB-59C6.3|ENSG00000268525|Transcript|ENST00000594531|antisense||||||||||COSV55905712&COSV55906893&COSV55907568|1|807|-1|||SNV|Clone_based_vega_gene||YES|||||||||||||||||||||||||||||||1&1&1|1&1&1||||||,A|downstream_gene_variant|MODIFIER|ZNF574|ENSG00000105732|Transcript|ENST00000597391|protein_coding||||||||||COSV55905712&COSV55906893&COSV55907568|1|1932|1|cds_end_NF||SNV|HGNC|26166||||ENSP00000471611||M0R133|UPI0002A47219|||||||||||||||||||||||||1&1&1|1&1&1||||||,A|missense_variant|MODERATE|ZNF574|ENSG00000105732|Transcript|ENST00000600245|protein_coding|2/2||ENST00000600245.1:c.2308G>A|ENSP00000469029.1:p.Asp770Asn|2963/3598|2308/2691|770/896|D/N|Gac/Aac|COSV55905712&COSV55906893&COSV55907568|1||1||1|SNV|HGNC|26166|YES||CCDS12596.1|ENSP00000469029|Q6ZN55|Q9NT61&M0R133|UPI00001AE536|||deleterious(0.01)|probably_damaging(0.917)|Gene3D:3.30.160.60&Pfam:PF13465&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&PANTHER:PTHR24375&PANTHER:PTHR24375:SF38&SMART:SM00355&Superfamily:SSF57667||||||||||||||||||||1&1&1|1&1&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:19,0:19:0.000:0:.:2:.	0/1:18,7:25:0.280:0:29:2:.
20	16730581	.	G	A	21	PASS	DP=95;Gene=OTOR;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000246081.2;VLSC=255;CSQ=A|missense_variant|MODERATE|OTOR|ENSG00000125879|Transcript|ENST00000246081|protein_coding|3/4||ENST00000246081.2:c.289G>A|ENSP00000246081.2:p.Val97Met|333/1477|289/387|97/128|V/M|Gtg/Atg|rs776130394&COSV55722123|1||1||1|SNV|HGNC|8517|YES||CCDS13124.1|ENSP00000246081|Q9NRC9||UPI0000047809|NM_020157.3||deleterious(0)|probably_damaging(0.961)|PANTHER:PTHR23158&Gene3D:2.30.30.40&Pfam:PF07653&SMART:SM00326&Superfamily:SSF50044||||||||||1.593e-05|0|0|0|0.000109|0|1.761e-05|0|0||0&1|0&1||||||,A|non_coding_transcript_exon_variant|MODIFIER|OTOR|ENSG00000125879|Transcript|ENST00000486129|processed_transcript|2/3||ENST00000486129.1:n.285G>A||285/1047|||||rs776130394&COSV55722123|1||1|||SNV|HGNC|8517||||||||||||||||||||||1.593e-05|0|0|0|0.000109|0|1.761e-05|0|0||0&1|0&1||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|OTOR|ENSG00000125879|Transcript|ENST00000490148|processed_transcript||1/2|ENST00000490148.1:n.101+462G>A|||||||rs776130394&COSV55722123|1||1|||SNV|HGNC|8517||||||||||||||||||||||1.593e-05|0|0|0|0.000109|0|1.761e-05|0|0||0&1|0&1||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001640104|||||||||||rs776130394&COSV55722123|1|||||SNV||||||||||||||||||||||||1.593e-05|0|0|0|0.000109|0|1.761e-05|0|0||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:52,0:52:0.000:0:.:2:.	0/1:35,8:43:0.186:0:33:2:.
22	23040479	.	C	G	41	PASS	DP=48;Gene=IGLV2-23;MQ0=0;SOMATIC;SS=Somatic;VC=RNA;VT=SNP;TID=ENST00000390306.2;VLSC=255;CSQ=G|non_coding_transcript_exon_variant|MODIFIER|D86994.1|ENSG00000207830|Transcript|ENST00000385095|miRNA|1/1||ENST00000385095.1:n.89C>G||89/95||||||1||1|||SNV|Clone_based_ensembl_gene||YES||||||||||||||||||||||||||||||||||||||,G|missense_variant&splice_region_variant|MODERATE|IGLV2-23|ENSG00000211660|Transcript|ENST00000390306|IG_V_gene|1/2||ENST00000390306.2:c.44C>G|ENSP00000374841.2:p.Thr15Arg|206/502|44/340|15/113|T/R|aCa/aGa||1||1|cds_end_NF|1|SNV|HGNC|5890|YES|||ENSP00000374841|||UPI000173A2CA|||deleterious_low_confidence(0)|possibly_damaging(0.852)|Cleavage_site_(Signalp):SignalP-noTM&PANTHER:PTHR23267:SF138&PANTHER:PTHR23267|||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|LL22NC03-102D1.18|ENSG00000223999|Transcript|ENST00000438185|lincRNA|||||||||||1|4682|-1|||SNV|Clone_based_vega_gene||YES||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|IGLV3-24|ENSG00000253822|Transcript|ENST00000517477|IG_V_pseudogene|||||||||||1|3042|1|||SNV|HGNC|5907|YES||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|IGLVVI-22-1|ENSG00000253546|Transcript|ENST00000521183|IG_V_pseudogene|||||||||||1|2766|1|||SNV|HGNC|15689|YES||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:23,0:23:0.000:0:.:2:.	0/1:12,13:25:0.520:0:33:2:.
X	51076024	rs143435240	G	A	6	PASS	DB;DP=122;Gene=NUDT10;MQ0=0;SOMATIC;SS=Somatic;VC=Silent;VT=SNP;TID=ENST00000376006.3;VLSC=255;CSQ=A|synonymous_variant|LOW|NUDT10|ENSG00000122824|Transcript|ENST00000356450|protein_coding|1/2||ENST00000356450.2:c.207G>A|ENSP00000348831.2:p.Glu69=|343/1917|207/495|69/164|E|gaG/gaA|rs2801626&COSV62853869|1||1|||SNV|HGNC|17621|||CCDS35278.1|ENSP00000348831|Q8NFP7||UPI000006D69E|||||PROSITE_profiles:PS51462&PANTHER:PTHR12629:SF2&PANTHER:PTHR12629&PROSITE_patterns:PS00893&Gene3D:3.90.79.10&Pfam:PF00293&Superfamily:SSF55811||||||||||0.000682|0.0004641|3.658e-05|0|0.0007976|0.0002512|0.001234|0.0004457|0||0&1|0&1||||||,A|synonymous_variant|LOW|NUDT10|ENSG00000122824|Transcript|ENST00000376006|protein_coding|2/3||ENST00000376006.3:c.207G>A|ENSP00000365174.3:p.Glu69=|427/2001|207/495|69/164|E|gaG/gaA|rs2801626&COSV62853869|1||1||1|SNV|HGNC|17621|YES||CCDS35278.1|ENSP00000365174|Q8NFP7||UPI000006D69E|NM_153183.2||||Gene3D:3.90.79.10&Pfam:PF00293&PROSITE_patterns:PS00893&PROSITE_profiles:PS51462&PANTHER:PTHR12629&PANTHER:PTHR12629:SF2&Superfamily:SSF55811||||||||||0.000682|0.0004641|3.658e-05|0|0.0007976|0.0002512|0.001234|0.0004457|0||0&1|0&1||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000423420|||||||||||rs2801626&COSV62853869|1|||||SNV||||||||||||||||||||||||0.000682|0.0004641|3.658e-05|0|0.0007976|0.0002512|0.001234|0.0004457|0||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:77,1:78:0.013:0:35:2:.	0/1:41,3:44:0.068:0:32:2:.
X	77160816	.	A	G	7	PASS	DP=74;Gene=COX7B;MQ0=0;SOMATIC;SS=Somatic;VC=3'UTR;VT=SNP;TID=ENST00000481445.1;VLSC=255;CSQ=G|downstream_gene_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000373335|processed_transcript||||||||||rs782235659&COSV64864574|1|44|1|||SNV|HGNC|2291|||||||||1|||||||||||||||||||||||0&1|0&1||||||,G|downstream_gene_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000475465|processed_transcript||||||||||rs782235659&COSV64864574|1|2123|1|||SNV|HGNC|2291|||||||||1|||||||||||||||||||||||0&1|0&1||||||,G|3_prime_UTR_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000481445|protein_coding|3/3||ENST00000481445.1:c.*58A>G||417/2471|||||rs782235659&COSV64864574|1||1||1|SNV|HGNC|2291|YES||CCDS14437.1|ENSP00000417656|P24311||UPI0000049C75|NM_001866.2|1|||||||||||||||||||||||0&1|0&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:51,0:51:0.000:0:.:2:.	0/1:20,3:23:0.130:0:32:2:.
X	77160852	.	T	A	7	PASS	DP=52;Gene=COX7B;MQ0=0;SOMATIC;SS=Somatic;VC=3'UTR;VT=SNP;TID=ENST00000481445.1;VLSC=255;CSQ=A|downstream_gene_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000373335|processed_transcript||||||||||rs1557221045|1|80|1|||SNV|HGNC|2291|||||||||1||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000475465|processed_transcript||||||||||rs1557221045|1|2159|1|||SNV|HGNC|2291|||||||||1||||||||||||||||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|COX7B|ENSG00000131174|Transcript|ENST00000481445|protein_coding|3/3||ENST00000481445.1:c.*94T>A||453/2471|||||rs1557221045|1||1||1|SNV|HGNC|2291|YES||CCDS14437.1|ENSP00000417656|P24311||UPI0000049C75|NM_001866.2|1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:35,0:35:0.000:0:.:2:.	0/1:14,3:17:0.176:0:30:2:.
X	78216689	.	C	T	26	PASS	DP=117;Gene=P2RY10;MQ0=0;SOMATIC;SS=Somatic;VC=Silent;VT=SNP;TID=ENST00000171757.2;VLSC=255;CSQ=T|synonymous_variant|LOW|P2RY10|ENSG00000078589|Transcript|ENST00000171757|protein_coding|4/4||ENST00000171757.2:c.672C>T|ENSP00000171757.2:p.Ser224=|952/1714|672/1020|224/339|S|tcC/tcT|rs866278031&COSV50681285&COSV50683757|1||1||1|SNV|HGNC|19906|YES||CCDS14442.1|ENSP00000171757|O00398||UPI0000050471|NM_014499.2||||Gene3D:1.20.1070.10&Pfam:PF00001&PROSITE_profiles:PS50262&PANTHER:PTHR24232&PANTHER:PTHR24232:SF6&Superfamily:SSF81321||||||||||||||||||||0&1&1|0&1&1||||||,T|downstream_gene_variant|MODIFIER|P2RY10|ENSG00000078589|Transcript|ENST00000461541|processed_transcript||||||||||rs866278031&COSV50681285&COSV50683757|1|321|1|||SNV|HGNC|19906||||||||||||||||||||||||||||||||0&1&1|0&1&1||||||,T|downstream_gene_variant|MODIFIER|P2RY10|ENSG00000078589|Transcript|ENST00000475374|processed_transcript||||||||||rs866278031&COSV50681285&COSV50683757|1|112|1|||SNV|HGNC|19906||||||||||||||||||||||||||||||||0&1&1|0&1&1||||||,T|synonymous_variant|LOW|P2RY10|ENSG00000078589|Transcript|ENST00000544091|protein_coding|2/2||ENST00000544091.1:c.672C>T|ENSP00000443138.1:p.Ser224=|849/1597|672/1020|224/339|S|tcC/tcT|rs866278031&COSV50681285&COSV50683757|1||1|||SNV|HGNC|19906|||CCDS14442.1|ENSP00000443138|O00398||UPI0000050471|NM_198333.1||||PROSITE_profiles:PS50262&PANTHER:PTHR24232:SF6&PANTHER:PTHR24232&Gene3D:1.20.1070.10&Pfam:PF00001&Superfamily:SSF81321||||||||||||||||||||0&1&1|0&1&1||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:63,0:63:0.000:0:.:2:.	0/1:44,10:54:0.185:0:33:2:.
X	122757148	.	A	T	6	PASS	DP=61;Gene=THOC2;MQ0=0;SOMATIC;SS=Somatic;VC=Intron;VT=SNP;TID=ENST00000245838.8;VLSC=255;CSQ=T|intron_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000245838|protein_coding||28/38|ENST00000245838.8:c.3504-14T>A||||||||1||-1||1|SNV|HGNC|19073|YES||CCDS43988.1|ENSP00000245838|Q8NI27||UPI00001D7C42|NM_001081550.1|1||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000355725|protein_coding||28/38|ENST00000355725.4:c.3504-14T>A||||||||1||-1|||SNV|HGNC|19073|||CCDS43988.1|ENSP00000347959|Q8NI27||UPI00001D7C42||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000416618|protein_coding|||||||||||1|2349|-1|cds_start_NF||SNV|HGNC|19073||||ENSP00000415244||B7ZBA0&B7ZB98|UPI000173A1A4||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000432353|nonsense_mediated_decay|||||||||||1|1718|-1|cds_start_NF||SNV|HGNC|19073||||ENSP00000415947|||UPI0001610C6D||1||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000438358|protein_coding||6/8|ENST00000438358.1:c.787-14T>A||||||||1||-1|cds_start_NF&cds_end_NF||SNV|HGNC|19073||||ENSP00000416639|||UPI000155D6BF||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000441692|protein_coding|||||||||||1|452|-1|cds_start_NF||SNV|HGNC|19073||||ENSP00000415211|||UPI000059DB80||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000448128|protein_coding|||||||||||1|2138|-1|cds_start_NF||SNV|HGNC|19073||||ENSP00000397317|||UPI000173A1A1||1||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000459945|retained_intron|1/3||ENST00000459945.1:n.329T>A||329/689||||||1||-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000464161|retained_intron|||||||||||1|216|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000464604|retained_intron|||||||||||1|2116|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000464982|retained_intron|||||||||||1|255|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000464992|retained_intron|||||||||||1|2627|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000491737|protein_coding||24/33|ENST00000491737.1:c.3159-14T>A||||||||1||-1|||SNV|HGNC|19073||||ENSP00000419795|Q8NI27||UPI000006CF58||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000496830|retained_intron|||||||||||1|3119|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|THOC2|ENSG00000125676|Transcript|ENST00000497887|processed_transcript|||||||||||1|3092|-1|||SNV|HGNC|19073|||||||||1||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:48,0:48:0.000:0:.:2:.	0/1:10,3:13:0.231:0:28:2:.
X	152684244	.	T	G	6	PASS	DP=113;Gene=ZFP92;MQ0=0;SOMATIC;SS=Somatic;VC=Missense_Mutation;VT=SNP;TID=ENST00000338647.5;VLSC=255;CSQ=G|missense_variant|MODERATE|ZFP92|ENSG00000189420|Transcript|ENST00000338647|protein_coding|2/4||ENST00000338647.5:c.147T>G|ENSP00000462054.1:p.His49Gln|148/1253|147/1251|49/416|H/Q|caT/caG||1||1||1|SNV|HGNC|12865|YES||CCDS59177.1|ENSP00000462054|A6NM28||UPI000052B478|NM_001136273.1||deleterious(0.03)|probably_damaging(0.913)|Superfamily:0044637&Pfam:PF01352&PROSITE_profiles:PS50805&PANTHER:PTHR24375&PANTHER:PTHR24375:SF97&SMART:SM00349|||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|U82695.10|ENSG00000259886|Transcript|ENST00000569962|lincRNA|||||||||||1|4966|1|||SNV|Clone_based_vega_gene||YES||||||||||||||||||||||||||||||||||||||	GT:AD:DP:FA:MQ0:BQ:SS:SSC	0/0:62,0:62:0.000:0:.:2:.	0/1:48,3:51:0.059:0:34:2:.