Mercurial > repos > artbio > varscan_vaf
diff test-data/computed_VAFs_1.vcf @ 0:0b6ec297a6bc draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf commit ff9426700b78da43ad64bf4905d358ee4986127b
| author | artbio |
|---|---|
| date | Mon, 28 Nov 2022 21:59:34 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computed_VAFs_1.vcf Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,189 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/galaxy/galaxy/tool-data/hg38-bgi-light/sam_indexes/hg38-bgi-light/hg38-bgi-light.fa +##source=varscan.py +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> +##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> +##FILTER=<ID=VarAvgRL,Description="Average clipped length of variant-supporting reads < 90"> +##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100"> +##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> +##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 15"> +##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> +##FILTER=<ID=RefAvgRL,Description="Average clipped length of ref-supporting reads < 90"> +##FILTER=<ID=RefReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=RefDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> +##FILTER=<ID=RefBaseQual,Description="Average base quality of ref-supporting reads < 15"> +##FILTER=<ID=RefMMQS,Description="Average mismatch quality sum for ref-supporting reads > 100"> +##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (var - ref) > 50"> +##FILTER=<ID=MinMMQSdiff,Description="Mismatch quality sum difference (var - ref) < 50"> +##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> +##FILTER=<ID=MaxBAQdiff,Description="Average base quality difference (ref - var) > 50"> +##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand"> +##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand"> +##bcftools_filterVersion=1.10.2+htslib-1.10.2 +##bcftools_filterCommand=filter --include 'INFO/SPV < 0.12 | INFO/GPV < 0.12' --output-type v --threads 1 input.vcf.gz; Date=Thu Apr 21 00:18:01 2022 +##bcftools_filterCommand=filter --include 'FILTER ~ "PASS" | FILTER ~ "MinMMQSdiff" | FILTER ~ "RefReadPos"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:48:58 2022 +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view --output-type v; Date=Wed Sep 7 20:49:09 2022 +##bcftools_filterCommand=filter --include 'INFO/SS ~ "2"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:49:20 2022 +##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpSiftCmd="SnpSift Annotate -info GENEINFO,PSEUDOGENEINFO,SAO,SSR,VC,NSF,NSM,NSN,SYN,U3,U5,ASS,DSS,INT,R3,R5,FREQ,COMMON,CLNVI,CLNORIGIN,CLNSIG,CLNDISDB,CLNDN,CLNREVSTAT,CLNACC dbSnp.vcf /home/galaxy/galaxy/database/datasets/001/336/dataset_1336143.dat" +##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44"> +##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13"> +##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15"> +##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 8 - confers sensitivity, 9 - risk-factor, 10 - association, 11 - protective, 12 - conflict, 13 - affects, 255 - other"> +##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41"> +##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42"> +##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be summed: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"> +##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar Review Status: no_assertion - No asserition provided by submitter, no_criteria - No assertion criteria provided by submitter, single - Classified by single submitter, mult - Classified by multiple submitters, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline"> +##INFO=<ID=COMMON,Number=0,Type=Flag,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency."> +##INFO=<ID=FREQ,Number=.,Type=String,Description="An ordered list of allele frequencies as reported by various genomic studies starting with the reference allele followed by alternate alleles as ordered in the ALT column. When not already in the dbSNP allele set alleles from the studies are added to the ALT column. The minor allele which was previuosly reported in VCF as the GMAF is the second largest value in the list. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter"> +##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73"> +##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53"> +##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55"> +##INFO=<ID=CLNACC,Number=.,Type=String,Description="For each allele (comma delimited), this is a pipe-delimited list of the Clinvar RCV phenotype accession.version strings associated with that allele."> +##INFO=<ID=CLNDN,Number=.,Type=String,Description="Preferred ClinVar disease name"> +##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75"> +##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3"> +##INFO=<ID=CLNVI,Number=.,Type=String,Description="Variant Identifiers provided and maintained by organizations outside of NCBI, such as OMIM. Source and id separated by colon (:). Each identifier is separated by a vertical bar (|)"> +##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> +##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both"> +##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id. The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"> +##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Variant disease database name and ID, separated by colon (:)"> +##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|). Does not include pseudogenes."> +##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6"> +##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"> +##bcftools_concatVersion=1.10.2+htslib-1.10.2 +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Wed Sep 7 20:53:30 2022 +##bcftools_filterCommand=filter --include 'INFO/COMMON = 0' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:53:35 2022 +##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336196.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336194.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> +##INFO=<ID=cosmic70,Number=.,Type=String,Description="cosmic70 annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> +##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> +##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> +##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> +##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> +##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> +##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> +##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> +##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> +##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> +##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> +##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> +##INFO=<ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"> +##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> +##bcftools_filterCommand=filter --include 'INFO/LOF != "." | INFO/CLNSIG != "." | INFO/cosmic70 != "." | INFO/Polyphen2_HDIV_pred != "." | INFO/LRT_pred != "." | INFO/MutationTaster_pred != "." | INFO/MutationAssessor_pred != "." | INFO/FATHMM_pred != "."' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:55:15 2022 +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336200.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336198.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##FORMAT=<ID=VAF,Number=R,Type=float,Description="VariantAllele Frequency"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01002_normal 01002_tumor +chr1 42536528 . AAG A . MinMMQSdiff DP=160;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10106;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM391243\x3bOCCURENCE\x3d1(lung),1(pancreas),4(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=A|frameshift_variant|HIGH|CCDC30|CCDC30|transcript|NM_001080850.2|protein_coding|2/16|c.60_61delGA|p.Lys21fs|170/3098|60/2352|20/783||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:50:50,0:26,0:24,0:0.000 0/1:.:110:104,6:56,2:48,4:0.055 +chr1 100206310 . TA T . MinMMQSdiff DP=144;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1157;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=433480;CLNDN=Maple_syrup_urine_disease|not_specified;CLNDISDB=MONDO:MONDO:0009563,MeSH:D008375,MedGen:C0024776,OMIM:248600,OMIM:PS248600,Orphanet:ORPHA511,SNOMED_CT:27718001|MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=T|intron_variant|MODIFIER|DBT|DBT|transcript|NM_001918.3|protein_coding|9/10|c.1210-10delT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:40,0:23,0:17,0:0.000 0/1:.:102:89,6:54,3:35,3:0.063 +chr1 100539628 . T C . PASS DP=18;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.068627;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.77;SIFT_pred=T;Polyphen2_HDIV_score=0.386;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.157;Polyphen2_HVAR_pred=B;LRT_score=0.119;LRT_pred=U;MutationTaster_score=0.982;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=1.27;FATHMM_pred=T;RadialSVM_score=-0.979;RadialSVM_pred=T;LR_score=0.014;LR_pred=T;VEST3_score=0.371;CADD_raw=-1.497;CADD_phred=0.017;GERP++_RS=2.92;phyloP46way_placental=1.237;phyloP100way_vertebrate=1.470;SiPhy_29way_logOdds=8.418;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GPR88|GPR88|transcript|NM_022049.2|protein_coding|2/2|c.662T>C|p.Val221Ala|1066/3465|662/1155|221/384|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:10:10,0:8,0:2,0:0.000 0/1:.:8:5,3:0,0:5,3:0.375 +chr1 112912805 . TA T . PASS DP=142;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039564;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=276120;CLNDN=Hyperinsulinism,_Dominant;CLNDISDB=MedGen:CN239341;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_001166496.1|protein_coding|5/5|c.*1085delT|||||1085|,T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_003051.3|protein_coding|5/5|c.*1085delT|||||1085| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:43:43,0:22,0:21,0:0.000 0/1:.:99:82,8:45,7:37,1:0.089 +chr1 151088217 . T G . PASS DP=134;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11875;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.01;SIFT_pred=D;Polyphen2_HDIV_score=0.999;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.977;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=0.996;MutationTaster_pred=D;MutationAssessor_score=2.48;MutationAssessor_pred=M;FATHMM_score=-0.17;FATHMM_pred=T;RadialSVM_score=-0.479;RadialSVM_pred=T;LR_score=0.294;LR_pred=T;VEST3_score=0.897;CADD_raw=4.062;CADD_phred=20.9;GERP++_RS=0.551;phyloP46way_placental=0.181;phyloP100way_vertebrate=0.031;SiPhy_29way_logOdds=9.216;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323910.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2027|28/1395|10/464||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323907.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1745|28/1113|10/370||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323908.1|protein_coding|2/9|c.28T>G|p.Leu10Val|417/2011|28/1347|10/448||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323909.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1865|28/1233|10/410||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323912.1|protein_coding|3/8|c.28T>G|p.Leu10Val|504/1816|28/1065|10/354||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323913.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1811|28/1179|10/392||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323906.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2946|28/1359|10/452||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323911.1|protein_coding|2/9|c.28T>G|p.Leu10Val|385/2832|28/1245|10/414||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_144618.2|protein_coding|2/9|c.28T>G|p.Leu10Val|359/1953|28/1347|10/448|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:18,0:21,0:0.000 0/1:.:95:88,6:48,5:40,1:0.064 +chr1 193251844 . G GT . MinMMQSdiff DP=181;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039165;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=279150;CLNDN=Parathyroid_carcinoma|Hyperparathyroidism_2|Isolated_Hyperparathyroidism;CLNDISDB=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|MedGen:CN239442;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|CDC73|CDC73|transcript|NM_024529.4|protein_coding|17/17|c.*1144dupT|||||1145|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:49:48,0:23,0:25,0:0.000 0/1:.:132:120,10:60,4:60,6:0.077 +chr1 197090091 . G GA . MinMMQSdiff DP=139;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.073566;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=193063;CLNDN=not_provided;CLNDISDB=MedGen:CN517202;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_018136.4|protein_coding|24/27|c.9830-8dupT||||||,GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_001206846.1|protein_coding|23/26|c.5075-8dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:22,0:20,0:0.000 0/1:.:97:89,7:56,5:33,2:0.073 +chr1 215741541 . G GA . MinMMQSdiff DP=159;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.09137;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=195468;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|USH2A|USH2A|transcript|NM_206933.2|protein_coding|59/71|c.11549-5dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:44,0:20,0:24,0:0.000 0/1:.:113:104,7:59,3:45,4:0.063 +chr1 247949492 rs200574966 G C . MinMMQSdiff DP=58;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.076494;FREQ=ExAC:0.9999,.,9.101e-05|GnomAD_exomes:1,.,1.196e-05|KOREAN:0.9798,.,0.02019|TOMMO:0.9837,.,0.01629|dbGaP_PopFreq:0.9983,0,0.001659;GENEINFO=OR2L13:284521|OR2L8:391190;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.11;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.021;Polyphen2_HVAR_pred=B;LRT_score=0.447;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.13;MutationAssessor_pred=N;FATHMM_score=1.28;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.035;LR_pred=T;VEST3_score=0.097;CADD_raw=-1.748;CADD_phred=0.010;GERP++_RS=-3.61;phyloP46way_placental=-1.273;phyloP100way_vertebrate=-1.473;SiPhy_29way_logOdds=5.646;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|OR2L8|OR2L8|transcript|NM_001001963.1|protein_coding|1/1|c.635G>C|p.Gly212Ala|635/939|635/939|212/312||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_001304535.1|protein_coding|1/1|c.-19+12108G>C||||||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_175911.3|protein_coding|1/2|c.-144+12108G>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:11:11,0:6,0:5,0:0.000 0/1:.:47:36,11:23,3:13,8:0.234 +chr2 43819994 rs200839584 C T . PASS DP=162;SOMATIC;SS=2;SSC=94;GPV=1;SPV=3.2187e-10;CLNACC=.,RCV000310689.2|RCV001143371.1;CLNDISDB=.,MedGen:CN517202|GeneReviews:NBK131810/MONDO:MONDO:0020747/MedGen:C5231390/OMIM:210250;CLNDN=.,not_provided|Sitosterolemia_1;CLNORIGIN=.,1;CLNREVSTAT=.,single|single;CLNSIG=.,0|0;CLNVI=.,Illumina_Clinical_Services_Laboratory\x2cIllumina:764360;FREQ=1000Genomes:0.9996,0.0003994|ExAC:0.9999,9.887e-05|GnomAD:1,4.28e-05|GnomAD_exomes:0.9999,0.0001074|PAGE_STUDY:0.9998,0.0001652|TOPMED:0.9999,6.8e-05|dbGaP_PopFreq:0.9999,7.061e-05;GENEINFO=DYNC2LI1:51626|ABCG5:64240;INT;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.33;SIFT_pred=T;Polyphen2_HDIV_score=0.279;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.04;Polyphen2_HVAR_pred=B;LRT_score=0.078;LRT_pred=N;MutationTaster_score=0.997;MutationTaster_pred=N;MutationAssessor_score=1.375;MutationAssessor_pred=L;FATHMM_score=-0.63;FATHMM_pred=T;RadialSVM_score=-0.980;RadialSVM_pred=T;LR_score=0.189;LR_pred=T;VEST3_score=0.114;CADD_raw=-0.627;CADD_phred=1.219;GERP++_RS=-2.75;phyloP46way_placental=-0.921;phyloP100way_vertebrate=0.120;SiPhy_29way_logOdds=12.741;CLNALLELEID=268994;CLNDN=Sitosterolemia_1|not_provided;CLNDISDB=MONDO:MONDO:0020747,MedGen:C5231390,OMIM:210250|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCG5|ABCG5|transcript|NM_022436.2|protein_coding|11/13|c.1570G>A|p.Val524Ile|1710/2740|1570/1956|524/651|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:48:48,0:27,0:21,0:0.000 0/1:.:114:64,50:32,33:32,17:0.439 +chr2 47805601 . AT A . MinMMQSdiff DP=126;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.025068;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=94891;CLNDN=Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_000179.2|protein_coding|6/9|c.3557-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281492.1|protein_coding|4/7|c.3167-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281493.1|protein_coding|5/8|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281494.1|protein_coding|6/9|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_001190274.1|protein_coding||c.*2516delA|||||1318|,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_025133.4|protein_coding||c.*2516delA|||||1318| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:35:33,0:19,0:14,0:0.000 0/1:.:91:77,11:44,6:33,5:0.125 +chr2 165953651 . G GCCCGCTCACCCGCTCA . MinMMQSdiff DP=49;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018691;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=405364;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=GCCCGCTCACCCGCTCA|upstream_gene_variant|MODIFIER|LOC102724058|LOC102724058|transcript|NR_110598.1|pseudogene||n.-3767_-3766insCCCGCTCACCCGCTCA|||||3766|,GCCCGCTCACCCGCTCA|intron_variant|MODIFIER|TTC21B|TTC21B|transcript|NM_024753.4|protein_coding|1/28|c.21+18_21+33dupTGAGCGGGTGAGCGGG|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:11:6,1:5,0:1,1:0.143 0/1:.:38:7,15:5,6:2,9:0.682 +chr4 2898230 . T C . PASS DP=150;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048075;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=1.0;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.75;MutationAssessor_pred=L;FATHMM_score=0.82;FATHMM_pred=T;RadialSVM_score=-0.555;RadialSVM_pred=T;LR_score=0.270;LR_pred=T;VEST3_score=0.978;CADD_raw=4.849;CADD_phred=27.6;GERP++_RS=5.86;phyloP46way_placental=2.235;phyloP100way_vertebrate=7.975;SiPhy_29way_logOdds=16.256;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014189.3|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/4047|788/2307|263/768||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001119.4|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/3954|788/2214|263/737||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014190.3|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/3988|788/1896|263/631||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_176801.2|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/4081|788/1989|263/662||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001286645.1|protein_coding|8/18|c.788T>C|p.Leu263Pro|1651/4756|788/1989|263/662|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:52:51,0:20,0:31,0:0.000 0/1:.:98:90,7:25,6:65,1:0.072 +chr5 38476522 . C CT . PASS DP=153;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11056;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=297531;CLNDN=Stüve-Wiedemann_syndrome;CLNDISDB=MONDO:MONDO:0011108,MedGen:C0796176,OMIM:601559,Orphanet:ORPHA3206;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_001127671.1|protein_coding|20/20|c.*5072dupA|||||5072|,CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_002310.5|protein_coding|20/20|c.*5072dupA|||||5072| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:48:45,0:22,0:23,0:0.000 0/1:.:105:98,6:60,3:38,3:0.058 +chr5 112775612 . TA T . PASS DP=161;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.042342;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=180169;CLNDN=Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_000038.5|protein_coding|4/15|c.423-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127511.2|protein_coding|3/13|c.453-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127510.2|protein_coding|5/16|c.423-4delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:46,1:24,1:22,0:0.021 0/1:.:114:98,13:52,7:46,6:0.117 +chr5 141527699 . TA T . MinMMQSdiff DP=123;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.039946;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=501019;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_005219.4|protein_coding|23/27|c.3149-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001079812.2|protein_coding|22/26|c.3122-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001314007.1|protein_coding|23/28|c.3149-3delT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:34:22,1:12,1:10,0:0.043 0/1:.:89:59,17:31,7:28,10:0.224 +chr6 13364935 rs1407685850 A C . PASS DP=73;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.078592;FREQ=GnomAD:1,.,7.13e-06|TOMMO:0.9993,0.0006563,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:0.9999,.,7.117e-05;GENEINFO=GFOD1:54438;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.902;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.468;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.32;MutationAssessor_pred=L;FATHMM_score=1.6;FATHMM_pred=T;RadialSVM_score=-1.023;RadialSVM_pred=T;LR_score=0.037;LR_pred=T;VEST3_score=0.42;CADD_raw=2.989;CADD_phred=15.97;GERP++_RS=1.29;phyloP46way_placental=0.058;phyloP100way_vertebrate=-0.523;SiPhy_29way_logOdds=11.050;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_018988.3|protein_coding|2/2|c.981T>G|p.Asp327Glu|1728/3308|981/1173|327/390||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242630.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|956/2536|672/864|224/287||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242628.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|901/2481|672/864|224/287|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:6,0:15,0:0.000 0/1:.:52:44,7:17,6:27,1:0.137 +chr6 47878370 rs746678221 C T . PASS DP=178;SOMATIC;SS=2;SSC=88;GPV=1;SPV=1.5004e-09;FREQ=ExAC:1,1.68e-05|GnomAD:1,1.428e-05|GnomAD_exomes:1,2.007e-05|TOPMED:1,1.889e-05|dbGaP_PopFreq:1,4.341e-05;GENEINFO=PTCHD4:442213;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.57;SIFT_pred=T;Polyphen2_HDIV_score=0.105;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.001;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.95;FATHMM_pred=D;RadialSVM_score=-0.486;RadialSVM_pred=T;LR_score=0.343;LR_pred=T;VEST3_score=0.375;CADD_raw=2.859;CADD_phred=15.52;GERP++_RS=5.29;phyloP46way_placental=1.612;phyloP100way_vertebrate=4.614;SiPhy_29way_logOdds=15.443;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|PTCHD4|PTCHD4|transcript|NM_001013732.3|protein_coding|3/3|c.2474G>A|p.Arg825Gln|2508/2850|2474/2541|825/846|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:18,0:28,0:0.000 0/1:.:132:77,55:38,30:39,25:0.417 +chr7 103149391 rs1813278496 T C . PASS DP=37;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.057896;FREQ=TOMMO:0.9981,0.00191;GENEINFO=NAPEPLD:222236|LOC105375434:105375434;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.82;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_pred=B;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=1.34;FATHMM_pred=T;RadialSVM_score=-0.990;RadialSVM_pred=T;LR_score=0.034;LR_pred=T;VEST3_score=0.019;CADD_raw=-0.828;CADD_phred=0.604;GERP++_RS=0.629;phyloP46way_placental=0.144;phyloP100way_vertebrate=-0.534;SiPhy_29way_logOdds=4.841;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_001122838.1|protein_coding||c.-20615A>G|||||269|,C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_198990.4|protein_coding||c.-20615A>G|||||269|,C|intergenic_region|MODIFIER|NAPEPLD-DPY19L2P2|NAPEPLD-DPY19L2P2|intergenic_region|NAPEPLD-DPY19L2P2|||n.103149391T>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:5,0:8,0:0.000 0/1:.:24:18,6:4,4:14,2:0.250 +chr7 107202971 . AT A . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.043842;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=301392;CLNDN=Congenital_disorder_of_glycosylation;CLNDISDB=MONDO:MONDO:0015286,MedGen:C0282577,OMIM:PS212065,Orphanet:ORPHA137,SNOMED_CT:238049009;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_006348.3|protein_coding|22/22|c.*544delA|||||544|,A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_181733.2|protein_coding|21/21|c.*544delA|||||544|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_001244262.1|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_012257.3|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|COG5|COG5|transcript|NM_001161520.1|protein_coding||c.*7550delA|||||4881| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:38:37,1:27,0:10,1:0.026 0/1:.:134:107,17:60,13:47,4:0.137 +chr8 31076300 . CT C . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087593;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=790795;CLNDN=Werner_syndrome;CLNDISDB=MONDO:MONDO:0010196,MedGen:C0043119,OMIM:277700,Orphanet:ORPHA902,SNOMED_CT:51626007;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|WRN|WRN|transcript|NM_000553.4|protein_coding|8/34|c.839+25delT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:50:47,0:24,0:23,0:0.000 0/1:.:122:109,7:61,5:48,2:0.060 +chr8 80687384 rs1585953247 T C . PASS DP=63;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.094475;FREQ=Korea1K:1,0,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:1,.,0;GENEINFO=ZNF704:619279;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.39;SIFT_pred=T;Polyphen2_HDIV_score=0.143;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.143;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.08;MutationAssessor_pred=M;FATHMM_score=1.55;FATHMM_pred=T;RadialSVM_score=-1.053;RadialSVM_pred=T;LR_score=0.097;LR_pred=T;VEST3_score=0.34;CADD_raw=3.183;CADD_phred=16.65;GERP++_RS=5.7;phyloP46way_placental=2.173;phyloP100way_vertebrate=4.803;SiPhy_29way_logOdds=15.974;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ZNF704|ZNF704|transcript|NM_001033723.2|protein_coding|4/9|c.400A>G|p.Ser134Gly|632/14386|400/1239|134/412|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:19:19,0:8,0:11,0:0.000 0/1:.:44:36,6:19,3:17,3:0.143 +chr9 85956346 . C CT . PASS DP=182;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10506;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321881.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_024635.3|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321882.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME;LOF=(NAA35|NAA35|3|1.00) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:56:54,0:38,0:16,0:0.000 0/1:.:126:115,6:67,5:48,1:0.050 +chr9 112574594 . C T . PASS DP=124;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.01311;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.996;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=0.96;FATHMM_pred=T;RadialSVM_score=-0.785;RadialSVM_pred=T;LR_score=0.190;LR_pred=T;VEST3_score=0.829;CADD_raw=3.837;CADD_phred=19.49;GERP++_RS=6.07;phyloP46way_placental=2.884;phyloP100way_vertebrate=4.349;SiPhy_29way_logOdds=20.644;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287036.1|protein_coding|2/5|c.514C>T|p.Arg172Cys|689/7652|514/2235|172/744||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287038.1|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7558|514/1347|172/448||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_133465.3|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7568|514/2151|172/716|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:13,0:29,0:0.000 0/1:.:82:72,10:39,4:33,6:0.122 +chr9 127651572 . CCT C . MinMMQSdiff DP=149;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10418;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=202275;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_003165.3|protein_coding|1/19|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_001032221.3|protein_coding|1/18|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:30,0:16,0:0.000 0/1:.:103:97,6:53,3:44,3:0.058 +chr9 130664691 . T C . PASS DP=51;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11761;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.04;SIFT_pred=D;Polyphen2_HDIV_score=0.009;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=2.56;FATHMM_pred=T;RadialSVM_score=-1.060;RadialSVM_pred=T;LR_score=0.022;LR_pred=T;VEST3_score=0.912;CADD_raw=2.439;CADD_phred=14.11;GERP++_RS=3.23;phyloP46way_placental=1.594;phyloP100way_vertebrate=7.058;SiPhy_29way_logOdds=8.170;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PRDM12|PRDM12|transcript|NM_021619.2|protein_coding|1/5|c.38T>C|p.Leu13Pro|98/2492|38/1104|13/367|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:12,0:4,0:0.000 0/1:.:35:27,5:18,1:9,4:0.156 +chr10 87965536 . CT C . PASS DP=175;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.01923;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=240890;CLNDN=PTEN_hamartoma_tumor_syndrome;CLNDISDB=MONDO:MONDO:0017623,MedGen:C1959582,OMIM:601728,Orphanet:ORPHA306498;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304717.2|protein_coding|10/10|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_000314.6|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304718.1|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:55:54,0:30,0:24,0:0.000 0/1:.:120:106,10:66,9:40,1:0.086 +chr11 62786683 rs2084280733 T C . PASS DP=52;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.040211;FREQ=TOMMO:0.9989,0.001074;GENEINFO=TAF6L:10629|TMEM179B:374395;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.09;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.071;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_pred=N;MutationAssessor_score=0.345;MutationAssessor_pred=N;FATHMM_score=0.88;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.051;LR_pred=T;VEST3_score=0.314;CADD_raw=0.607;CADD_phred=7.271;GERP++_RS=1.57;phyloP46way_placental=0.485;phyloP100way_vertebrate=1.378;SiPhy_29way_logOdds=4.335;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|TAF6L|TAF6L|transcript|NM_006473.3|protein_coding|11/11|c.1256T>C|p.Leu419Pro|1457/2115|1256/1869|419/622||,C|upstream_gene_variant|MODIFIER|TMEM179B|TMEM179B|transcript|NM_199337.2|protein_coding||c.-749T>C|||||719|,C|upstream_gene_variant|MODIFIER|MIR6748|MIR6748|transcript|NR_106806.1|pseudogene||n.-3132T>C|||||3132|,C|downstream_gene_variant|MODIFIER|TMEM223|TMEM223|transcript|NM_001080501.2|protein_coding||c.*3940A>G|||||3632| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:9,0:7,0:0.000 0/1:.:36:28,8:16,1:12,7:0.222 +chr12 52601418 . T C . PASS DP=87;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10996;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.212;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.055;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=-0.46;MutationAssessor_pred=N;FATHMM_score=-1.52;FATHMM_pred=D;RadialSVM_score=-0.798;RadialSVM_pred=T;LR_score=0.191;LR_pred=T;VEST3_score=0.351;CADD_raw=0.738;CADD_phred=7.920;GERP++_RS=3.26;phyloP46way_placental=1.025;phyloP100way_vertebrate=-0.187;SiPhy_29way_logOdds=8.397;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146225.1|protein_coding|1/10|c.35A>G|p.Glu12Gly|121/1888|35/1536|12/511||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146226.1|protein_coding|1/8|c.35A>G|p.Glu12Gly|121/1889|35/1410|12/469||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_080747.2|protein_coding|1/9|c.35A>G|p.Glu12Gly|121/2015|35/1536|12/511|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:17,0:9,0:0.000 0/1:.:61:55,6:40,5:15,1:0.098 +chr12 53467852 . TA T . PASS DP=136;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10327;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1606323\x3bOCCURENCE\x3d1(liver);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|downstream_gene_variant|MODIFIER|PCBP2-OT1|PCBP2-OT1|transcript|NR_109828.1|pseudogene||n.*2796delA|||||2796|,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_005016.5|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001098620.2|protein_coding|11/13|c.733+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128911.1|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128912.1|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128913.1|protein_coding|11/13|c.745+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128914.1|protein_coding|10/12|c.694+572delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_031989.4|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:38:36,0:18,0:18,0:0.000 0/1:.:98:90,7:39,3:51,4:0.072 +chr12 75207331 . A G . PASS DP=78;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10007;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.993;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=3.105;MutationAssessor_pred=M;FATHMM_score=-4.78;FATHMM_pred=D;RadialSVM_score=1.096;RadialSVM_pred=D;LR_score=0.966;LR_pred=D;VEST3_score=0.989;CADD_raw=4.158;CADD_phred=21.5;GERP++_RS=4.44;phyloP46way_placental=1.973;phyloP100way_vertebrate=8.932;SiPhy_29way_logOdds=14.145;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139137.3|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/5505|653/1917|218/638||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260497.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/6077|653/1857|218/618||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260498.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3470|653/1890|218/629||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260499.1|protein_coding|2/4|c.653T>C|p.Leu218Pro|1214/5340|653/1752|218/583||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139136.3|protein_coding|2/6|c.653T>C|p.Leu218Pro|1214/3565|653/1842|218/613||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_153748.2|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3400|653/1677|218/558|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:9,0:12,0:0.000 0/1:.:57:50,7:20,4:30,3:0.123 +chr12 109999777 rs1889849841 A G . PASS DP=67;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099397;FREQ=TOMMO:0.9961,0.003878;GENEINFO=ANKRD13A:88455;INT;NSM;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.090;LRT_pred=N;MutationTaster_score=0.835;MutationTaster_pred=D;MutationAssessor_score=0.315;MutationAssessor_pred=N;FATHMM_score=-0.11;FATHMM_pred=T;RadialSVM_score=-0.977;RadialSVM_pred=T;LR_score=0.089;LR_pred=T;VEST3_score=0.07;CADD_raw=0.273;CADD_phred=5.475;GERP++_RS=1.08;phyloP46way_placental=0.419;phyloP100way_vertebrate=0.106;SiPhy_29way_logOdds=7.367;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|ANKRD13A|ANKRD13A|transcript|NM_033121.1|protein_coding|1/15|c.89A>G|p.Gln30Arg|348/3908|89/1773|30/590||,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057169.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135213.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135214.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330153.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_014776.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057170.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330154.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_139201.2|protein_coding||c.-3553T>C|||||3388| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:14:14,0:12,0:2,0:0.000 0/1:.:53:43,9:37,1:6,8:0.173 +chr13 36845100 . ATGTG A . MinMMQSdiff DP=122;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.036896;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=336095;CLNDN=Primary_pulmonary_hypertension_1;CLNDISDB=MONDO:MONDO:0024533,MedGen:C4552070,OMIM:178600;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_001127217.2|protein_coding|7/7|c.*3572_*3575delCACA|||||3572|,A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_005905.5|protein_coding|6/6|c.*3572_*3575delCACA|||||3572| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:33:33,0:16,0:17,0:0.000 0/1:.:89:79,10:42,9:37,1:0.112 +chr14 53055920 . T TA . MinMMQSdiff DP=180;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.070254;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=685399;CLNDN=Spastic_paraplegia_28,_autosomal_recessive;CLNDISDB=MONDO:MONDO:0012256,MedGen:C1836295,OMIM:609340,Orphanet:ORPHA101008;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160148.1|protein_coding|9/12|c.1993-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160147.1|protein_coding|10/12|c.2014-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_030637.2|protein_coding|9/11|c.1993-9dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:49:49,0:29,0:20,0:0.000 0/1:.:131:120,8:60,2:60,6:0.062 +chr14 60282825 . C T . PASS DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10575;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=0.984;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.564;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.18;MutationAssessor_pred=M;FATHMM_score=2.25;FATHMM_pred=T;RadialSVM_score=-1.090;RadialSVM_pred=T;LR_score=0.081;LR_pred=T;VEST3_score=0.891;CADD_raw=4.216;CADD_phred=21.9;GERP++_RS=5.75;phyloP46way_placental=2.704;phyloP100way_vertebrate=7.818;SiPhy_29way_logOdds=19.923;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|1A6Q:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXJ:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXK:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXL:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXM:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXO:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|4RA2:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177952.2|protein_coding|2/6|c.341C>T|p.Thr114Met|437/8069|341/1368|114/455||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177951.2|protein_coding|3/4|c.122C>T|p.Thr41Met|674/4317|122/975|41/324||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_021003.4|protein_coding|2/6|c.122C>T|p.Thr41Met|572/8204|122/1149|41/382|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:18,0:24,0:0.000 0/1:.:95:89,6:39,4:50,2:0.063 +chr14 73064954 . C CT . MinMMQSdiff DP=141;SOMATIC;SS=2;SSC=20;GPV=1;SPV=0.0082366;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=794309;CLNDN=CIC-DUX_Sarcoma;CLNDISDB=MedGen:C3899764;CLNREVSTAT=no_assertion_provided;CLNSIG=not_provided;ALLELE_END;ANN=CT|intron_variant|MODIFIER|RBM25|RBM25|transcript|NM_021239.2|protein_coding|1/18|c.-16+6264dupT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:41,0:23,0:18,0:0.000 0/1:.:94:77,12:40,4:37,8:0.135 +chr14 95535217 . A G . PASS DP=25;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.093333;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.09;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.009;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.94;MutationAssessor_pred=M;FATHMM_score=1.25;FATHMM_pred=T;RadialSVM_score=-0.923;RadialSVM_pred=T;LR_score=0.126;LR_pred=T;VEST3_score=0.231;CADD_raw=3.581;CADD_phred=18.24;GERP++_RS=3.55;phyloP46way_placental=0.813;phyloP100way_vertebrate=3.504;SiPhy_29way_logOdds=10.604;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GLRX5|GLRX5|transcript|NM_016417.2|protein_coding|1/2|c.128A>G|p.Glu43Gly|232/1171|128/474|43/157||,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_003138.3|pseudogene||n.-345T>C|||||345|,G|upstream_gene_variant|MODIFIER|SCARNA13|SCARNA13|transcript|NR_003002.1|pseudogene||n.-1588T>C|||||1588|,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_001459.2|pseudogene||n.-345T>C|||||345| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:17:17,0:2,0:15,0:0.000 0/1:.:8:6,2:6,2:0,0:0.250 +chr14 104939447 . T C . PASS DP=137;SOMATIC;SS=2;SSC=42;GPV=1;SPV=5.4204e-05;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.38;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.002;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.345;MutationAssessor_pred=N;FATHMM_score=6.06;FATHMM_pred=T;RadialSVM_score=-0.921;RadialSVM_pred=T;LR_score=0.005;LR_pred=T;VEST3_score=0.032;CADD_raw=-0.972;CADD_phred=0.304;GERP++_RS=-4.01;phyloP46way_placental=-0.747;phyloP100way_vertebrate=-1.890;SiPhy_29way_logOdds=7.542;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|AHNAK2|AHNAK2|transcript|NM_138420.2|protein_coding|7/7|c.16004A>G|p.His5335Arg|16124/18317|16004/17388|5335/5795|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:30:30,0:18,0:12,0:0.000 0/1:.:107:73,34:35,17:38,17:0.318 +chr16 72788664 . T TTGC . MinMMQSdiff DP=85;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.020937;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1379701\x3bOCCURENCE\x3d1(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_006885.3|protein_coding|10/10|c.9609_9611dupGCA|p.Gln3204dup|10284/16062|9611/11112|3204/3703||,TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_001164766.1|protein_coding|9/9|c.6867_6869dupGCA|p.Gln2290dup|6998/12776|6869/8370|2290/2789|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:19,2:7,2:12,0:0.095 0/1:.:64:39,21:19,12:20,9:0.350 +chr17 44248849 . G GT . MinMMQSdiff DP=41;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10791;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=344704;CLNDN=Hemolytic_anemia|Distal_Renal_Tubular_Acidosis,_Dominant|Spherocytosis,_Dominant;CLNDISDB=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|MedGen:CN239155|MedGen:CN239455;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|SLC4A1|SLC4A1|transcript|NM_000342.3|protein_coding|20/20|c.*1608dupA|||||1608| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:10,0:7,0:3,0:0.000 0/1:.:26:11,4:3,2:8,2:0.267 +chr17 76736877 rs751713049 G T . PASS DP=41;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.021382;CLNACC=.,.,RCV001293765.1,.;CLNDISDB=.,.,MONDO:MONDO:0020526/MedGen:CN207426,.;CLNDN=.,.,Acute_megakaryoblastic_leukemia_in_down_syndrome,.;CLNORIGIN=.,.,2,.;CLNREVSTAT=.,.,single,.;CLNSIG=.,.,4,.;FREQ=Korea1K:0.9994,0.0005593,.,.|TOMMO:0.9998,.,.,0.0002388|dbGaP_PopFreq:1,0,0,0;GENEINFO=SRSF2:6427|MFSD11:79157|MIR636:693221;NSM;R5;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM211029,COSM211505,COSM211504\x3bOCCURENCE\x3d80(haematopoietic_and_lymphoid_tissue);SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.984;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.56;MutationAssessor_pred=M;FATHMM_score=-0.94;FATHMM_pred=T;RadialSVM_score=-0.044;RadialSVM_pred=T;LR_score=0.532;LR_pred=D;VEST3_score=0.311;CADD_raw=2.169;CADD_phred=13.21;GERP++_RS=2.76;phyloP46way_placental=0.413;phyloP100way_vertebrate=8.573;SiPhy_29way_logOdds=8.660;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_001195427.1|protein_coding|1/3|c.284C>A|p.Pro95His|535/1968|284/666|95/221||,T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_003016.4|protein_coding|1/2|c.284C>A|p.Pro95His|535/2963|284/666|95/221||,T|5_prime_UTR_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242534.1|protein_coding|1/14|c.-286G>T|||||1476|,T|upstream_gene_variant|MODIFIER|MIR636|MIR636|transcript|NR_030366.1|pseudogene||n.-329C>A|||||329|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242532.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242533.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242535.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242536.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242537.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_024311.3|protein_coding||c.-1476G>T|||||624|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001080510.4|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206983.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206984.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206985.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206986.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206987.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302703.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302704.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302705.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NR_038193.2|pseudogene||n.*2996G>T|||||2996|,T|non_coding_transcript_exon_variant|MODIFIER|SRSF2|SRSF2|transcript|NR_036608.1|pseudogene|1/4|n.535C>A|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:10,0:6,0:0.000 0/1:.:25:18,7:14,2:4,5:0.280 +chr19 1065393 . G T . PASS DP=119;SOMATIC;SS=2;SSC=64;GPV=1;SPV=3.6034e-07;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.979;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.511;Polyphen2_HVAR_pred=P;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.22;FATHMM_pred=D;RadialSVM_score=-0.593;RadialSVM_pred=T;LR_score=0.375;LR_pred=T;VEST3_score=0.486;CADD_raw=2.144;CADD_phred=13.13;GERP++_RS=1.46;phyloP46way_placental=0.760;phyloP100way_vertebrate=0.687;SiPhy_29way_logOdds=5.290;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCA7|ABCA7|transcript|NM_019112.3|protein_coding|47/47|c.6409G>T|p.Asp2137Tyr|6640/6818|6409/6441|2137/2146||,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001258328.2|protein_coding||c.-633G>T|||||530|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_012292.4|protein_coding||c.-2013G>T|||||1773|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001321232.1|protein_coding||c.-2180G>T|||||2105| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:32:32,0:21,0:11,0:0.000 0/1:.:87:49,38:31,30:18,8:0.437 +chr19 10467500 . A G . PASS DP=74;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11838;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.48;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=N;MutationTaster_score=0.958;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=0.21;FATHMM_pred=T;RadialSVM_score=-1.029;RadialSVM_pred=T;LR_score=0.109;LR_pred=T;VEST3_score=0.042;CADD_raw=0.477;CADD_phred=6.589;GERP++_RS=-0.855;phyloP46way_placental=0.043;phyloP100way_vertebrate=0.494;SiPhy_29way_logOdds=6.149;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111307.1|protein_coding|15/15|c.2540A>G|p.Glu847Gly|2648/4779|2540/2661|847/886||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001243121.1|protein_coding|17/17|c.2474A>G|p.Glu825Gly|2558/4689|2474/2595|825/864||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111308.1|protein_coding|15/15|c.2462A>G|p.Glu821Gly|2462/4593|2462/2583|821/860||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111309.1|protein_coding|15/15|c.2357A>G|p.Glu786Gly|2357/4488|2357/2478|786/825||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_006202.2|protein_coding|10/10|c.1823A>G|p.Glu608Gly|2130/4261|1823/1944|608/647|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:25,0:6,0:19,0:0.000 0/1:.:49:44,5:18,4:26,1:0.102 +chr19 12721349 rs1966929781 A G . PASS DP=48;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018465;FREQ=TOMMO:0.9993,0.0006567;GENEINFO=TNPO2:30000;INT;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=0.992;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=-1.032;RadialSVM_pred=T;LR_score=0.082;LR_pred=T;VEST3_score=.;CADD_raw=1.556;CADD_phred=11.16;GERP++_RS=2.16;phyloP46way_placental=1.245;phyloP100way_vertebrate=-0.288;SiPhy_29way_logOdds=6.333;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136196.1|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_013433.4|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136195.1|protein_coding|2/25|c.-13-359T>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:8,0:5,0:0.000 0/1:.:35:24,11:15,8:9,3:0.314 +chr19 45795880 . T TCTCCTCGCCCTCCTCCTC . MinMMQSdiff DP=102;SOMATIC;SS=2;SSC=19;GPV=1;SPV=0.010588;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM253920\x3bOCCURENCE\x3d1(urinary_tract);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TCTCCTCGCCCTCCTCCTC|conservative_inframe_insertion|MODERATE|RSPH6A|RSPH6A|transcript|NM_030785.3|protein_coding|6/6|c.2125_2142dupGAGGAGGAGGGCGAGGAG|p.Glu714_Thr715insGluGluGluGlyGluGlu|2313/2484|2142/2154|714/717||,TCTCCTCGCCCTCCTCCTC|upstream_gene_variant|MODIFIER|DMWD|DMWD|transcript|NM_004943.1|protein_coding||c.-3142_-3125dupGAGGAGGAGGGCGAGGAG|||||3079| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:24,0:12,0:12,0:0.000 0/1:.:77:60,15:36,8:24,7:0.200 +chr20 6075049 . G GT . PASS DP=149;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.037662;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=351325;CLNDN=Kindler_syndrome;CLNDISDB=MONDO:MONDO:0008260,MedGen:C0406557,OMIM:173650,Orphanet:ORPHA2908,SNOMED_CT:238835001,SNOMED_CT:238836000;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|FERMT1|FERMT1|transcript|NM_017671.4|protein_coding|15/15|c.*2123dupA|||||2123| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:45,1:22,0:23,1:0.022 0/1:.:102:84,12:37,5:47,7:0.125 +chr20 32808191 . CT C . MinMMQSdiff DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10114;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=345075;CLNDN=Immunodeficiency-centromeric_instability-facial_anomalies_syndrome_1;CLNDISDB=MONDO:MONDO:0009454,MedGen:C4551557,OMIM:242860;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_006892.3|protein_coding|23/23|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207055.1|protein_coding|19/19|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207056.1|protein_coding|18/18|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175848.1|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175849.1|protein_coding|20/20|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175850.2|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:37:36,0:21,0:15,0:0.000 0/1:.:100:89,7:46,5:43,2:0.073 +chr20 38836101 . G C . PASS DP=82;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.089735;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.018;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.02;Polyphen2_HVAR_pred=B;LRT_score=0.175;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0.105;MutationAssessor_pred=N;FATHMM_score=-0.21;FATHMM_pred=T;RadialSVM_score=-0.989;RadialSVM_pred=T;LR_score=0.100;LR_pred=T;VEST3_score=0.167;CADD_raw=-1.674;CADD_phred=0.012;GERP++_RS=3.46;phyloP46way_placental=1.288;phyloP100way_vertebrate=1.830;SiPhy_29way_logOdds=4.802;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_015568.3|protein_coding|2/11|c.176G>C|p.Gly59Ala|377/6263|176/1704|59/567||,C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_001172735.2|protein_coding|2/10|c.176G>C|p.Gly59Ala|377/6137|176/1578|59/525|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:23:23,0:14,0:9,0:0.000 0/1:.:59:52,7:41,1:11,6:0.119 +chr20 63307547 rs759710143 A G . PASS DP=90;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.074052;FREQ=ExAC:1,8.47e-06|GnomAD_exomes:1,4.036e-06|TOPMED:1,3.778e-06|dbGaP_PopFreq:1,0;GENEINFO=COL20A1:57642;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=U;MutationTaster_score=0.999;MutationTaster_pred=D;MutationAssessor_score=4.565;MutationAssessor_pred=H;FATHMM_score=-4.64;FATHMM_pred=D;RadialSVM_score=1.047;RadialSVM_pred=D;LR_score=0.974;LR_pred=D;VEST3_score=0.769;CADD_raw=4.119;CADD_phred=21.2;GERP++_RS=3.92;phyloP46way_placental=1.418;phyloP100way_vertebrate=6.103;SiPhy_29way_logOdds=11.020;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|COL20A1|COL20A1|transcript|NM_020882.2|protein_coding|6/36|c.554A>G|p.Asp185Gly|654/4172|554/3855|185/1284|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:27:27,0:11,0:16,0:0.000 0/1:.:63:56,7:26,6:30,1:0.111 +chr21 32361892 rs371227097 C T . PASS DP=118;SOMATIC;SS=2;SSC=45;GPV=1;SPV=3.1599e-05;FREQ=1000Genomes:0.9998,0.0001997|ALSPAC:1,0|ExAC:1,4.72e-05|GnomAD:0.9998,0.0001711|GnomAD_exomes:0.9998,0.0002368|GoESP:0.9998,0.000219|MGP:0.9981,0.001873|TOPMED:0.9998,0.0002116|TWINSUK:0.9992,0.0008091|dbGaP_PopFreq:0.9998,0.0002345;GENEINFO=URB1:9875;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.926;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.045;MutationAssessor_pred=M;FATHMM_score=1.49;FATHMM_pred=T;RadialSVM_score=-0.911;RadialSVM_pred=T;LR_score=0.169;LR_pred=T;VEST3_score=0.087;CADD_raw=3.753;CADD_phred=19.05;GERP++_RS=5.26;phyloP46way_placental=2.608;phyloP100way_vertebrate=1.875;SiPhy_29way_logOdds=15.945;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant&splice_region_variant|MODERATE|URB1|URB1|transcript|NM_014825.2|protein_coding|12/39|c.1639G>A|p.Asp547Asn|1732/10808|1639/6816|547/2271|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:31,0:14,0:17,0:0.000 0/1:.:87:58,29:31,16:27,13:0.333