{"took":33,"total":1313709002,"max_score":1.14209415e-8,"hits":[{"_id":"chr1:g.11147530C>G","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"G","anc":"C","annotype":"CodingTranscript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.921,"txflnk":0.0,"txwk":0.031,"znfrpts":0.039},"chrom":1,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.07,"dna":{"helt":3.32,"mgw":-0.18,"prot":0.17,"roll":-1.01},"encode":{"exp":247.28,"h3k27ac":5.76,"h3k4me1":2.0,"h3k4me3":5.0,"nucleo":2.8},"exon":"9/25","fitcons":0.701516,"gc":0.44,"gene":{"ccds_id":"CCDS30584.1","cds":{"cdna_pos":1114,"cds_pos":1064,"rel_cdna_pos":0.4,"rel_cds_pos":0.4},"feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10","prot":{"domain":"ndomain","protpos":355,"rel_prot_pos":0.4}},"gerp":{"n":6.07,"rs":553.4,"rs_pval":8.93158e-80,"s":6.07},"grantham":58,"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":20852,"min_dist_tss":12365,"mutindex":1,"naa":"T","oaa":"S","phast_cons":{"mammalian":1.0,"primate":0.994,"vertebrate":1.0},"phred":17.4,"phylop":{"mammalian":2.882,"primate":0.651,"vertebrate":3.176},"polyphen":{"cat":"benign","val":0.05},"pos":11147530,"rawscore":2.183102,"ref":"C","segway":"GM1","sift":{"cat":"tolerated","val":0.7},"type":"SNV"},"chrom":"1","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"T","codon_degeneracy":[0,0],"codonpos":[2,2],"pos":[355,355],"ref":"S","refcodon":["AGC","AGC"]},"alfa":{"african":{"ac":0,"af":0.0,"an":2294},"african_american":{"ac":0,"af":0.0,"an":2210},"african_others":{"ac":0,"af":0.0,"an":84},"asian":{"ac":0,"af":0.0,"an":108},"east_asian":{"ac":0,"af":0.0,"an":84},"european":{"ac":0,"af":0.0,"an":6962},"latin_american_1":{"ac":0,"af":0.0,"an":146},"latin_american_2":{"ac":0,"af":0.0,"an":610},"other":{"ac":0,"af":0.0,"an":466},"other_asian":{"ac":0,"af":0.0,"an":24},"south_asian":{"ac":0,"af":0.0,"an":94},"total":{"ac":0,"af":0.0,"an":10680}},"alphamissense":{"pred":["B","B"],"rankscore":0.12084,"score":[0.0889,0.0786]},"alt":"G","altai_neandertal":["C","C"],"ancestral_allele":"C","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.33378,"score":-0.118443},"no_af":{"pred":"T","rankscore":0.32467,"score":-0.407912}},"bstatistic":{"converted_rankscore":0.82135,"score":410.0},"chagyrskaya_neandertal":["C","C"],"chrom":"1","clinpred":{"pred":"T","rankscore":0.31032,"score":0.456367313861847},"dann":{"rankscore":0.27574,"score":0.9569411036560186},"denisova":["C","C"],"deogen2":{"pred":"T","rankscore":0.52088,"score":0.172399},"eigen":{"phred_coding":2.609251,"raw_coding":0.0272210134220703,"raw_coding_rankscore":0.43095},"eigen-pc":{"phred_coding":3.481824,"raw_coding":0.258111504849844,"raw_coding_rankscore":0.53111},"ensembl":{"geneid":["ENSG00000171824","ENSG00000171824"],"proteinid":["ENSP00000307307","ENSP00000366135"],"transcriptid":["ENST00000304457","ENST00000376936"]},"esm1b":{"pred":["D","D"],"rankscore":0.70747,"score":[-9.482,-9.372]},"fathmm":{"converted_rankscore":0.62762,"pred":["T","T"],"score":[-0.01,-0.01]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.53735,"coding_score":0.91536},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.3789,"coding_score":0.260828},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.89359,"score":0.724815},"h1-hesc":{"confidence_value":0,"rankscore":0.87919,"score":0.724815},"huvec":{"confidence_value":0,"rankscore":0.83352,"score":0.714379},"integrated":{"confidence_value":0,"rankscore":0.73137,"score":0.706548}},"gencode_basic":["Y","Y"],"genename":["EXOSC10","EXOSC10"],"genocanyon":{"rankscore":0.40607,"score":0.999584053617402},"gerp++":{"nr":6.07,"rs":6.07,"rs_rankscore":0.98675},"gmvp":{"rankscore":0.46531,"score":0.4661285570685301},"hg18":{"end":11070117,"start":11070117},"hg19":{"end":11147530,"start":11147530},"hg38":{"end":11087473,"start":11087473},"hgvsc":"c.1064G>C","hgvsp":["p.S355T","p.Ser355Thr"],"interpro":{"domain":"3'-5' exonuclease domain|3'-5' exonuclease domain"},"list-s2":{"pred":["D","D"],"rankscore":0.5464,"score":[0.857114,0.854215]},"lrt":{"converted_rankscore":0.8433,"omega":0.122222,"pred":"D","score":0.0},"m-cap":{"pred":"T","rankscore":0.06044,"score":0.002876},"metalr":{"pred":"T","rankscore":0.50242,"score":0.1648},"metarnn":{"pred":["T","T"],"rankscore":0.3583,"score":[0.19855851,0.19855851]},"metasvm":{"pred":"T","rankscore":0.41431,"score":-0.9473},"mpc":{"rankscore":0.24293,"score":0.217698442251},"mutationassessor":{"pred":["N","N"],"rankscore":0.04423,"score":[-0.145,-0.145]},"mutationtaster":{"aae":["S355T","S355T","S355T"],"converted_rankscore":0.44783,"model":["simple_aae","simple_aae","simple_aae"],"pred":["D","D","D"],"score":[0.99833,0.99833,0.99833]},"mutformer":{"rankscore":0.41762,"score":0.01025419},"mutpred":{"aa_change":["S355T","S355T"],"accession":["Q01780","Q01780"],"pred":[{"mechanism":"Loss of stability","p_val":0.0624},{"mechanism":"Loss of stability","p_val":0.0624}],"rankscore":0.57732,"score":[0.491,0.491]},"mvp":{"rankscore":0.70273,"score":[0.705290213559,0.705290213559]},"phactboost":{"rankscore":0.10816,"score":0.0013137924921171},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.79791,"score":0.997},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.5625,"score":3.932},"17way_primate":{"rankscore":0.4025,"score":0.599},"470way_mammalian":{"rankscore":0.67011,"score":7.715}},"polyphen2":{"hdiv":{"pred":["B","B"],"rankscore":0.17332,"score":[0.008,0.016]},"hvar":{"pred":["B","B"],"rankscore":0.22546,"score":[0.012,0.034]}},"primateai":{"pred":"T","rankscore":0.47514,"score":0.561746656895},"provean":{"converted_rankscore":0.03407,"pred":["N","N"],"score":[0.41,0.41]},"ref":"C","reliability_index":10,"revel":{"rankscore":0.31546,"score":[0.112,0.112]},"rsid":"rs1640557503","sift":{"converted_rankscore":0.07545,"pred":["T","T"],"score":[0.508,0.686]},"sift4g":{"converted_rankscore":0.13215,"pred":["T","T"],"score":[0.449,0.443]},"siphy_29way":{"logodds_rankscore":0.78748,"logodds_score":15.8546,"pi":{"a":0.0,"c":0.8554,"g":0.1446,"t":0.0}},"tsl":[1,1],"uniprot":[{"acc":"Q01780-2","entry":"EXOSX_HUMAN"},{"acc":"Q01780","entry":"EXOSX_HUMAN"}],"varity":{"er":{"rankscore":0.42992,"score":0.1939495},"er_loo":{"rankscore":0.42991,"score":0.1939495},"r":{"rankscore":0.57075,"score":0.35009864},"r_loo":{"rankscore":0.57075,"score":0.35009864}},"vep_canonical":"YES","vest4":{"rankscore":0.34228,"score":[0.281,0.303]},"vindijia_neandertal":["C","C"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"C","freq":{"dbgap_popfreq":1.0,"gnomad":1.0}},{"allele":"G","freq":{"dbgap_popfreq":0.0,"gnomad":0.0}}],"alt":"G","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"AGC","inserted_sequence":"AGC","position":1100,"seq_id":"NM_001001998.3"},"hgvs":"NM_001001998.3:c.1064=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":354,"seq_id":"NP_001001998.1"}}},"protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"AGC","inserted_sequence":"AGC","position":1100,"seq_id":"NM_002685.4"},"hgvs":"NM_002685.4:c.1064=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":354,"seq_id":"NP_002676.1"}}},"protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"AGC","inserted_sequence":"AGC","position":1100,"seq_id":"XM_005263475.3"},"hgvs":"XM_005263475.3:c.1064=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":354,"seq_id":"XP_005263532.2"}}},"protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GCC","inserted_sequence":"GCC","position":111,"seq_id":"XM_047422661.1"},"hgvs":"XM_047422661.1:c.7=","protein":{"variant":{"spdi":{"deleted_sequence":"A","inserted_sequence":"A","position":2,"seq_id":"XP_047278617.1"}}},"protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147530,"start":11147530},"ref":"C","rsid":"rs1640557503","vartype":"snv"},"hg19":{"end":11147530,"start":11147530},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"effect":"structural_interaction_variant","feature_id":"3SAF:A_301-A_355:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:B_301-B_355:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_301-A_355:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:B_301-B_355:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_301-B_355:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:A_301-A_355:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:B_301-B_355:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_301-A_355:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:B_301-B_355:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_301-B_355:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","putative_impact":"HIGH","rank":"9","total":"24","transcript_biotype":"protein_coding"},{"cdna":{"length":"2842","position":"1143"},"cds":{"length":"2658","position":"1064"},"effect":"missense_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","hgvs_p":"p.Ser355Thr","protein":{"length":"885","position":"355"},"putative_impact":"MODERATE","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"2767","position":"1143"},"cds":{"length":"2583","position":"1064"},"effect":"missense_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1064G>C","hgvs_p":"p.Ser355Thr","protein":{"length":"860","position":"355"},"putative_impact":"MODERATE","rank":"9","total":"24","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"11147530","ref":"C"}},{"_id":"chr1:g.11147559A>G","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"G","anc":"A","annotype":"CodingTranscript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.921,"txflnk":0.0,"txwk":0.031,"znfrpts":0.039},"chrom":1,"consdetail":"synonymous","consequence":"SYNONYMOUS","consscore":5,"cpg":0.07,"dna":{"helt":-0.26,"mgw":0.4,"prot":3.05,"roll":2.74},"encode":{"exp":466.12,"h3k27ac":5.44,"h3k4me1":2.0,"h3k4me3":4.28,"nucleo":4.0},"exon":"9/25","fitcons":0.701516,"gc":0.5,"gene":{"ccds_id":"CCDS30584.1","cds":{"cdna_pos":1085,"cds_pos":1035,"rel_cdna_pos":0.39,"rel_cds_pos":0.39},"feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10","prot":{"domain":"ndomain","protpos":345,"rel_prot_pos":0.39}},"gerp":{"n":6.07,"rs":553.4,"rs_pval":8.93158e-80,"s":-2.69},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":20881,"min_dist_tss":12336,"mutindex":-28,"naa":"L","oaa":"L","phast_cons":{"mammalian":0.968,"primate":0.849,"vertebrate":0.987},"phred":7.105,"phylop":{"mammalian":-0.358,"primate":0.53,"vertebrate":-0.07},"pos":11147559,"rawscore":0.458466,"ref":"A","segway":"GM1","type":"SNV"},"chrom":"1","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"A","freq":{"dbgap_popfreq":1.0,"exac":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"G","freq":{"dbgap_popfreq":0.0,"exac":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"G","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"CTT","inserted_sequence":"CTT","position":1070,"seq_id":"NM_001001998.3"},"hgvs":"NM_001001998.3:c.1035=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":344,"seq_id":"NP_001001998.1"}}},"protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"CTT","inserted_sequence":"CTT","position":1070,"seq_id":"NM_002685.4"},"hgvs":"NM_002685.4:c.1035=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":344,"seq_id":"NP_002676.1"}}},"protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"CTT","inserted_sequence":"CTT","position":1070,"seq_id":"XM_005263475.3"},"hgvs":"XM_005263475.3:c.1035=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":344,"seq_id":"XP_005263532.2"}}},"protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"hgvs":"XM_047422661.1:c.-23=","protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001623","name":"5_prime_UTR_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147559,"start":11147559},"ref":"A","rsid":"rs779835357","vartype":"snv"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":1,"ac_adj":1,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":1,"ac_fin":0,"ac_het":1,"ac_hom":0,"ac_male":0,"ac_nfe":1,"ac_oth":0,"ac_sas":0},"af":8.236e-6,"alleles":"G","alt":"G","an":{"an":121412,"an_adj":121410,"an_afr":10406,"an_amr":11578,"an_eas":8654,"an_female":54124,"an_fin":6614,"an_male":67286,"an_nfe":66738,"an_oth":908,"an_sas":16512},"baseqranksum":3.11,"chrom":1,"clippingranksum":0.041,"culprit":"FS","fs":2.244,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":1,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.79,"mq0":0,"mqranksum":0.294},"ncc":0,"pos":11147559,"qd":14.23,"readposranksum":0.425,"ref":"A","type":"snp","vqslod":2.31},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":1,"ac_adj":1,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":1,"ac_fin":0,"ac_het":1,"ac_hom":0,"ac_male":0,"ac_nfe":1,"ac_oth":0,"ac_sas":0},"af":9.415e-6,"alleles":"G","alt":"G","an":{"an":106210,"an_adj":106208,"an_afr":9066,"an_amr":11216,"an_eas":7866,"an_female":45874,"an_fin":6614,"an_male":60334,"an_nfe":54344,"an_oth":694,"an_sas":16408},"baseqranksum":3.11,"chrom":1,"clippingranksum":0.041,"culprit":"FS","fs":2.244,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":1,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.79,"mq0":0,"mqranksum":0.294},"ncc":0,"pos":11147559,"qd":14.23,"readposranksum":0.425,"ref":"A","type":"snp","vqslod":2.31},"hg19":{"end":11147559,"start":11147559},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"2842","position":"1114"},"cds":{"length":"2658","position":"1035"},"effect":"synonymous_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1035T>C","hgvs_p":"p.Leu345Leu","protein":{"length":"885","position":"345"},"putative_impact":"LOW","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"2767","position":"1114"},"cds":{"length":"2583","position":"1035"},"effect":"synonymous_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1035T>C","hgvs_p":"p.Leu345Leu","protein":{"length":"860","position":"345"},"putative_impact":"LOW","rank":"9","total":"24","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"11147559","ref":"A"}},{"_id":"chr1:g.11147574A>G","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"G","anc":"A","annotype":"CodingTranscript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.921,"txflnk":0.0,"txwk":0.031,"znfrpts":0.039},"chrom":1,"consdetail":"synonymous","consequence":"SYNONYMOUS","consscore":5,"cpg":0.07,"dna":{"helt":-0.75,"mgw":0.47,"prot":3.04,"roll":1.41},"encode":{"exp":491.37,"h3k27ac":5.44,"h3k4me1":2.0,"h3k4me3":4.28,"nucleo":2.8},"exon":"9/25","fitcons":0.722197,"gc":0.51,"gene":{"ccds_id":"CCDS30584.1","cds":{"cdna_pos":1070,"cds_pos":1020,"rel_cdna_pos":0.38,"rel_cds_pos":0.38},"feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10","prot":{"domain":"ndomain","protpos":340,"rel_prot_pos":0.38}},"gerp":{"n":6.07,"rs":553.4,"rs_pval":8.93158e-80,"s":-12.1},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":20896,"min_dist_tss":12321,"mutindex":-12,"naa":"I","oaa":"I","phast_cons":{"mammalian":0.001,"primate":0.943,"vertebrate":0.021},"phred":10.26,"phylop":{"mammalian":-3.339,"primate":0.53,"vertebrate":-1.912},"pos":11147574,"rawscore":0.931479,"ref":"A","segway":"GE1","type":"SNV"},"chrom":"1","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"A","freq":{"dbgap_popfreq":1.0,"topmed":1.0}},{"allele":"G","freq":{"dbgap_popfreq":0.0,"topmed":0.0}}],"alt":"G","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"ATT","inserted_sequence":"ATT","position":1055,"seq_id":"NM_001001998.3"},"hgvs":"NM_001001998.3:c.1020=","protein":{"variant":{"spdi":{"deleted_sequence":"I","inserted_sequence":"I","position":339,"seq_id":"NP_001001998.1"}}},"protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ATT","inserted_sequence":"ATT","position":1055,"seq_id":"NM_002685.4"},"hgvs":"NM_002685.4:c.1020=","protein":{"variant":{"spdi":{"deleted_sequence":"I","inserted_sequence":"I","position":339,"seq_id":"NP_002676.1"}}},"protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ATT","inserted_sequence":"ATT","position":1055,"seq_id":"XM_005263475.3"},"hgvs":"XM_005263475.3:c.1020=","protein":{"variant":{"spdi":{"deleted_sequence":"I","inserted_sequence":"I","position":339,"seq_id":"XP_005263532.2"}}},"protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"hgvs":"XM_047422661.1:c.-38=","protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001623","name":"5_prime_UTR_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147574,"start":11147574},"ref":"A","rsid":"rs1640561159","vartype":"snv"},"hg19":{"end":11147574,"start":11147574},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"2842","position":"1099"},"cds":{"length":"2658","position":"1020"},"effect":"synonymous_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1020T>C","hgvs_p":"p.Ile340Ile","protein":{"length":"885","position":"340"},"putative_impact":"LOW","rank":"9","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"2767","position":"1099"},"cds":{"length":"2583","position":"1020"},"effect":"synonymous_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.1020T>C","hgvs_p":"p.Ile340Ile","protein":{"length":"860","position":"340"},"putative_impact":"LOW","rank":"9","total":"24","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"11147574","ref":"A"}},{"_id":"chr11:g.3051247T>A","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"T","annotype":"NonCodingTranscript","bstatistic":883,"chmm":{"bivflnk":0.0,"enh":0.173,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.685,"txflnk":0.0,"txwk":0.126,"znfrpts":0.0},"chrom":11,"consdetail":"non_coding_exon,nc","consequence":"NONCODING_CHANGE","consscore":5,"cpg":0.01,"dna":{"helt":-2.75,"mgw":-0.21,"prot":2.35,"roll":-1.29},"encode":{"h3k27ac":6.56,"h3k4me1":4.68,"h3k4me3":3.92,"nucleo":1.9},"exon":"1/2","fitcons":0.062364,"gc":0.5,"gene":{"cds":{"cdna_pos":624,"rel_cdna_pos":0.23},"feature_id":"ENST00000499962","gene_id":"ENSG00000247473","genename":"CARS-AS1"},"gerp":{"n":1.35,"s":-2.7},"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":933,"min_dist_tss":623,"mutindex":-59,"phast_cons":{"mammalian":0.0,"primate":0.001,"vertebrate":0.0},"phred":2.545,"phylop":{"mammalian":-0.999,"primate":-0.432,"vertebrate":-0.961},"pos":3051247,"rawscore":-0.004305,"ref":"T","segway":"GE2","type":"SNV"},"chrom":"11","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"T","freq":{"dbgap_popfreq":1.0,"topmed":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"topmed":0.0}}],"alt":"A","chrom":"11","dbsnp_build":156,"gene":[{"geneid":833,"is_pseudo":false,"name":"cysteinyl-tRNA synthetase 1","rnas":[{"hgvs":"NM_001014437.3:c.802-574=","protein_product":{"refseq":"NP_001014437.1"},"refseq":"NM_001014437.3","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001194997.2:c.802-574=","protein_product":{"refseq":"NP_001181926.1"},"refseq":"NM_001194997.2","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378136.1:c.592-574=","protein_product":{"refseq":"NP_001365065.1"},"refseq":"NM_001378136.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378137.1:c.523-574=","protein_product":{"refseq":"NP_001365066.1"},"refseq":"NM_001378137.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378138.1:c.523-574=","protein_product":{"refseq":"NP_001365067.1"},"refseq":"NM_001378138.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378139.1:c.523-574=","protein_product":{"refseq":"NP_001365068.1"},"refseq":"NM_001378139.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378140.1:c.277-574=","protein_product":{"refseq":"NP_001365069.1"},"refseq":"NM_001378140.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001751.6:c.553-574=","protein_product":{"refseq":"NP_001742.1"},"refseq":"NM_001751.6","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_139273.4:c.553-574=","protein_product":{"refseq":"NP_644802.1"},"refseq":"NM_139273.4","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_036542.2","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165428.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165429.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165430.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427672.1:c.802-574=","protein_product":{"refseq":"XP_047283628.1"},"refseq":"XM_047427672.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427673.1:c.523-574=","protein_product":{"refseq":"XP_047283629.1"},"refseq":"XM_047427673.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427674.1:c.802-574=","protein_product":{"refseq":"XP_047283630.1"},"refseq":"XM_047427674.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]}],"strand":"-","symbol":"CARS1"},{"geneid":100852407,"is_pseudo":false,"name":"CARS1 antisense RNA 1","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"T","inserted_sequence":"T","position":623,"seq_id":"NR_046580.1"},"hgvs":"NR_046580.1:n.624=","refseq":"NR_046580.1","so":[{"accession":"SO:0001619","name":"non_coding_transcript_variant"}]}],"strand":"+","symbol":"CARS1-AS1"}],"hg19":{"end":3051247,"start":3051247},"ref":"T","rsid":"rs972715104","vartype":"snv"},"hg19":{"end":3051247,"start":3051247},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"effect":"intron_variant","feature_id":"NM_001014437.2","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.802-574A>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_001194997.1","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.802-574A>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_001751.5","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.553-574A>T","putative_impact":"MODIFIER","rank":"6","total":"21","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_139273.3","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.553-574A>T","putative_impact":"MODIFIER","rank":"6","total":"21","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NR_036542.1","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"n.933-574A>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"pseudogene"}]},"vcf":{"alt":"A","position":"3051247","ref":"T"}},{"_id":"chr11:g.3051322C>A","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"C","annotype":"NonCodingTranscript","bstatistic":883,"chmm":{"bivflnk":0.0,"enh":0.173,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.685,"txflnk":0.0,"txwk":0.126,"znfrpts":0.0},"chrom":11,"consdetail":"non_coding_exon,nc","consequence":"NONCODING_CHANGE","consscore":5,"cpg":0.05,"dna":{"helt":0.47,"mgw":0.05,"prot":-4.07,"roll":-1.37},"encode":{"h3k27ac":7.56,"h3k4me1":7.0,"h3k4me3":4.0,"nucleo":1.6},"exon":"1/2","fitcons":0.062364,"gc":0.55,"gene":{"cds":{"cdna_pos":699,"rel_cdna_pos":0.26},"feature_id":"ENST00000499962","gene_id":"ENSG00000247473","genename":"CARS-AS1"},"gerp":{"n":1.16,"s":-1.17},"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":1008,"min_dist_tss":698,"mutindex":83,"phast_cons":{"mammalian":0.0,"primate":0.003,"vertebrate":0.0},"phred":3.616,"phylop":{"mammalian":-0.393,"primate":-1.102,"vertebrate":-0.376},"pos":3051322,"rawscore":0.100761,"ref":"C","segway":"GE2","type":"SNV"},"chrom":"11","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"C","freq":{"dbgap_popfreq":1.0,"gnomad":1.0,"gonl":0.999,"sgdp_prj":0.5,"topmed":1.0}},{"allele":"A","freq":{"gonl":0.001}},{"allele":"T","freq":{"dbgap_popfreq":0.0,"gnomad":0.0,"sgdp_prj":0.5,"topmed":0.0}}],"alt":"A","chrom":"11","dbsnp_build":156,"gene":[{"geneid":833,"is_pseudo":false,"name":"cysteinyl-tRNA synthetase 1","rnas":[{"hgvs":"NM_001014437.3:c.802-649=","protein_product":{"refseq":"NP_001014437.1"},"refseq":"NM_001014437.3","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001194997.2:c.802-649=","protein_product":{"refseq":"NP_001181926.1"},"refseq":"NM_001194997.2","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378136.1:c.592-649=","protein_product":{"refseq":"NP_001365065.1"},"refseq":"NM_001378136.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378137.1:c.523-649=","protein_product":{"refseq":"NP_001365066.1"},"refseq":"NM_001378137.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378138.1:c.523-649=","protein_product":{"refseq":"NP_001365067.1"},"refseq":"NM_001378138.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378139.1:c.523-649=","protein_product":{"refseq":"NP_001365068.1"},"refseq":"NM_001378139.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001378140.1:c.277-649=","protein_product":{"refseq":"NP_001365069.1"},"refseq":"NM_001378140.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_001751.6:c.553-649=","protein_product":{"refseq":"NP_001742.1"},"refseq":"NM_001751.6","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_139273.4:c.553-649=","protein_product":{"refseq":"NP_644802.1"},"refseq":"NM_139273.4","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_036542.2","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165428.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165429.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"refseq":"NR_165430.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427672.1:c.802-649=","protein_product":{"refseq":"XP_047283628.1"},"refseq":"XM_047427672.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427673.1:c.523-649=","protein_product":{"refseq":"XP_047283629.1"},"refseq":"XM_047427673.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_047427674.1:c.802-649=","protein_product":{"refseq":"XP_047283630.1"},"refseq":"XM_047427674.1","so":[{"accession":"SO:0001627","name":"intron_variant"}]}],"strand":"-","symbol":"CARS1"},{"geneid":100852407,"is_pseudo":false,"name":"CARS1 antisense RNA 1","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"C","inserted_sequence":"C","position":698,"seq_id":"NR_046580.1"},"hgvs":"NR_046580.1:n.699=","refseq":"NR_046580.1","so":[{"accession":"SO:0001619","name":"non_coding_transcript_variant"}]}],"strand":"+","symbol":"CARS1-AS1"}],"hg19":{"end":3051322,"start":3051322},"ref":"C","rsid":"rs556204760","vartype":"snv"},"hg19":{"end":3051322,"start":3051322},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"effect":"intron_variant","feature_id":"NM_001014437.2","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.802-649G>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_001194997.1","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.802-649G>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_001751.5","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.553-649G>T","putative_impact":"MODIFIER","rank":"6","total":"21","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_139273.3","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"c.553-649G>T","putative_impact":"MODIFIER","rank":"6","total":"21","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NR_036542.1","feature_type":"transcript","gene_id":"CARS","genename":"CARS","hgvs_c":"n.933-649G>T","putative_impact":"MODIFIER","rank":"7","total":"22","transcript_biotype":"pseudogene"}]},"vcf":{"alt":"A","position":"3051322","ref":"C"}},{"_id":"chr20:g.5515955T>C","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"C","anc":"T","annotype":"NonCodingTranscript","bstatistic":829,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.441,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.008,"tssaflnk":0.016,"tssbiv":0.0,"tx":0.0,"txflnk":0.0,"txwk":0.362,"znfrpts":0.0},"chrom":20,"consdetail":"non_coding_exon,nc","consequence":"NONCODING_CHANGE","consscore":5,"cpg":0.03,"dna":{"helt":-4.25,"mgw":0.16,"prot":4.67,"roll":0.39},"encode":{"exp":1.33,"h3k27ac":6.6,"h3k4me1":8.0,"h3k4me3":5.0,"nucleo":1.4,"occ":1,"p_val":{"comb":2.37,"ctcf":0.0,"dnas":1.88,"faire":1.42,"mycp":0.0,"polii":1.33},"sig":{"ctcf":0.01,"dnase":0.04,"faire":0.01,"myc":0.03,"polii":0.02}},"exon":"2/3","fitcons":0.078537,"gc":0.44,"gene":{"cds":{"cdna_pos":113,"rel_cdna_pos":0.24},"feature_id":"ENST00000413249","gene_id":"ENSG00000235820","genename":"RP5-1022P6.5"},"gerp":{"n":2.11,"s":0.994},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":581,"min_dist_tss":1681,"mutindex":-72,"phast_cons":{"mammalian":0.006,"primate":0.023,"vertebrate":0.007},"phred":1.643,"phylop":{"mammalian":0.27,"primate":0.478,"vertebrate":0.302},"pos":5515955,"rawscore":-0.111982,"ref":"T","segway":"GM0","tf":{"bs":9,"bs_peaks":14,"bs_peaks_max":297.3301},"type":"SNV"},"chrom":"20","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"T","freq":{"dbgap_popfreq":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"C","freq":{"dbgap_popfreq":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"C","chrom":"20","dbsnp_build":156,"hg19":{"end":5515955,"start":5515955},"ref":"T","rsid":"rs1005409949","vartype":"snv"},"hg19":{"end":5515955,"start":5515955},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"effect":"intergenic_region","feature_id":"LOC101929207-GPCPD1","feature_type":"intergenic_region","gene_id":"LOC101929207-GPCPD1","genename":"LOC101929207-GPCPD1","hgvs_c":"n.5515955T>C","putative_impact":"MODIFIER"}},"vcf":{"alt":"C","position":"5515955","ref":"T"}},{"_id":"chr1:g.11147670G>A","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"G","annotype":"Transcript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.929,"txflnk":0.0,"txwk":0.063,"znfrpts":0.0},"chrom":1,"consdetail":"intron","consequence":"INTRONIC","consscore":2,"cpg":0.0,"dna":{"helt":-2.13,"mgw":0.08,"prot":2.06,"roll":-0.97},"encode":{"exp":0.84,"h3k27ac":3.44,"h3k4me1":2.52,"h3k4me3":4.0,"nucleo":1.2},"fitcons":0.099652,"gc":0.4,"gene":{"ccds_id":"CCDS30584.1","feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10"},"gerp":{"n":4.55,"s":1.48},"intron":"8/24","isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":20992,"min_dist_tss":12225,"motif":{"dist":-0.32,"toverlap":1},"mutindex":-5,"phast_cons":{"mammalian":0.0,"primate":0.004,"vertebrate":0.0},"phred":4.717,"phylop":{"mammalian":0.371,"primate":0.651,"vertebrate":0.19},"pos":11147670,"rawscore":0.20362,"ref":"G","segway":"GE1","type":"SNV"},"chrom":"1","dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"dbgap_popfreq":1.0,"exac":1.0,"gnomad":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"exac":0.0,"gnomad":0.0}},{"allele":"C","freq":{"dbgap_popfreq":0.0}}],"alt":"A","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"hgvs":"NM_001001998.3:c.946-22=","protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"NM_002685.4:c.946-22=","protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"hgvs":"XM_005263475.3:c.946-22=","protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001627","name":"intron_variant"}]},{"protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001986","name":"upstream_transcript_variant"},{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147670,"start":11147670},"ref":"G","rsid":"rs781656210","vartype":"snv"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":2,"ac_adj":2,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":1,"ac_fin":0,"ac_het":2,"ac_hom":0,"ac_male":1,"ac_nfe":2,"ac_oth":0,"ac_sas":0},"af":0.00001647,"alleles":"A","alt":"A","an":{"an":121412,"an_adj":121210,"an_afr":10360,"an_amr":11574,"an_eas":8640,"an_female":53986,"an_fin":6612,"an_male":67224,"an_nfe":66646,"an_oth":906,"an_sas":16472},"baseqranksum":-6.091,"chrom":1,"clippingranksum":0.289,"culprit":"FS","fs":0.0,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":2,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.69,"mq0":0,"mqranksum":0.637},"ncc":8,"pos":11147670,"qd":14.17,"readposranksum":0.26,"ref":"G","type":"snp","vqslod":2.1},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":2,"ac_adj":2,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":1,"ac_fin":0,"ac_het":2,"ac_hom":0,"ac_male":1,"ac_nfe":2,"ac_oth":0,"ac_sas":0},"af":0.00001883,"alleles":"A","alt":"A","an":{"an":106210,"an_adj":106034,"an_afr":9024,"an_amr":11212,"an_eas":7856,"an_female":45754,"an_fin":6612,"an_male":60280,"an_nfe":54268,"an_oth":694,"an_sas":16368},"baseqranksum":-6.091,"chrom":1,"clippingranksum":0.289,"culprit":"FS","fs":0.0,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":2,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.69,"mq0":0,"mqranksum":0.637},"ncc":8,"pos":11147670,"qd":14.17,"readposranksum":0.26,"ref":"G","type":"snp","vqslod":2.1},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":2,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":0,"ac_amr_female":0,"ac_amr_male":0,"ac_asj":0,"ac_asj_female":0,"ac_asj_male":0,"ac_eas":0,"ac_eas_female":0,"ac_eas_jpn":0,"ac_eas_kor":0,"ac_eas_male":0,"ac_eas_oea":0,"ac_female":1,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":1,"ac_nfe":2,"ac_nfe_bgr":1,"ac_nfe_est":0,"ac_nfe_female":1,"ac_nfe_male":1,"ac_nfe_nwe":0,"ac_nfe_onf":0,"ac_nfe_seu":1,"ac_nfe_swe":0,"ac_oth":0,"ac_oth_female":0,"ac_oth_male":0,"ac_sas":0,"ac_sas_female":0,"ac_sas_male":0},"af":{"af":8.0271e-6,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0,"af_amr_female":0.0,"af_amr_male":0.0,"af_asj":0.0,"af_asj_female":0.0,"af_asj_male":0.0,"af_eas":0.0,"af_eas_female":0.0,"af_eas_jpn":0.0,"af_eas_kor":0.0,"af_eas_male":0.0,"af_eas_oea":0.0,"af_female":8.73027e-6,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":7.42876e-6,"af_nfe":0.0000177107,"af_nfe_bgr":0.000376223,"af_nfe_est":0.0,"af_nfe_female":0.0000200948,"af_nfe_male":0.0000158323,"af_nfe_nwe":0.0,"af_nfe_onf":0.0,"af_nfe_seu":0.0000874432,"af_nfe_swe":0.0,"af_oth":0.0,"af_oth_female":0.0,"af_oth_male":0.0,"af_sas":0.0,"af_sas_female":0.0,"af_sas_male":0.0},"alleles":"A","alt":"A","an":{"an":249156,"an_afr":16222,"an_afr_female":10054,"an_afr_male":6168,"an_amr":34024,"an_amr_female":19900,"an_amr_male":14124,"an_asj":9952,"an_asj_female":4846,"an_asj_male":5106,"an_eas":18350,"an_eas_female":9310,"an_eas_jpn":150,"an_eas_kor":3818,"an_eas_male":9040,"an_eas_oea":14382,"an_female":114544,"an_fin":21598,"an_fin_female":10346,"an_fin_male":11252,"an_male":134612,"an_nfe":112926,"an_nfe_bgr":2658,"an_nfe_est":240,"an_nfe_female":49764,"an_nfe_male":63162,"an_nfe_nwe":41810,"an_nfe_onf":30722,"an_nfe_seu":11436,"an_nfe_swe":26060,"an_oth":6068,"an_oth_female":2888,"an_oth_male":3180,"an_sas":30016,"an_sas_female":7436,"an_sas_male":22580},"baseqranksum":-1.917,"chrom":"1","clippingranksum":-0.059,"dp":9277977,"fs":3.533,"hom":{"hom":0,"hom_afr":0,"hom_afr_female":0,"hom_afr_male":0,"hom_amr":0,"hom_amr_female":0,"hom_amr_male":0,"hom_asj":0,"hom_asj_female":0,"hom_asj_male":0,"hom_eas":0,"hom_eas_female":0,"hom_eas_jpn":0,"hom_eas_kor":0,"hom_eas_male":0,"hom_eas_oea":0,"hom_female":0,"hom_fin":0,"hom_fin_female":0,"hom_fin_male":0,"hom_male":0,"hom_nfe":0,"hom_nfe_bgr":0,"hom_nfe_est":0,"hom_nfe_female":0,"hom_nfe_male":0,"hom_nfe_nwe":0,"hom_nfe_onf":0,"hom_nfe_seu":0,"hom_nfe_swe":0,"hom_oth":0,"hom_oth_female":0,"hom_oth_male":0,"hom_sas":0,"hom_sas_female":0,"hom_sas_male":0},"inbreedingcoeff":0.0035,"mq":{"mq":59.63,"mqranksum":0.274},"pab_max":1.0,"pos":11147670,"qd":13.41,"readposranksum":-0.045,"ref":"G","rf":0.853621,"rsid":"rs781656210","sor":1.134,"type":"snp","vqslod":0.344,"vqsr_culprit":"FS"},"hg19":{"end":11147670,"start":11147670},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"effect":"intron_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.946-22C>T","putative_impact":"MODIFIER","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"intron_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.946-22C>T","putative_impact":"MODIFIER","rank":"8","total":"23","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"A","position":"11147670","ref":"G"}},{"_id":"chr20:g.5528374G>A","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","annotype":["CodingTranscript","Intergenic"],"bstatistic":668,"chmm":{"bivflnk":0.0,"enh":0.016,"enhbiv":0.0,"het":0.0,"quies":0.047,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.535,"txflnk":0.0,"txwk":0.402,"znfrpts":0.0},"chrom":20,"consdetail":["missense","upstream"],"consequence":["NON_SYNONYMOUS","UPSTREAM"],"consscore":[7,1],"cpg":0.05,"dna":{"helt":-1.78,"mgw":0.05,"prot":1.59,"roll":-0.67},"encode":{"exp":308.65,"h3k27ac":4.0,"h3k4me1":6.04,"h3k4me3":4.0,"nucleo":2.3,"occ":3,"p_val":{"comb":0.52,"ctcf":0.0,"dnas":0.0,"faire":1.05,"mycp":0.0,"polii":0.0},"sig":{"ctcf":0.02,"dnase":0.01,"faire":0.01,"myc":0.0,"polii":0.0}},"exon":"20/20","fitcons":0.650528,"gc":0.46,"gene":[{"ccds_id":"CCDS13090.1","cds":{"cdna_pos":2165,"cds_pos":1952,"rel_cdna_pos":0.4,"rel_cds_pos":0.97},"feature_id":"ENST00000379019","gene_id":"ENSG00000125772","genename":"GPCPD1","prot":{"protpos":651,"rel_prot_pos":0.97}},{"feature_id":"ENST00000422311","gene_id":"ENSG00000233578","genename":"RP5-1022P6.3"}],"gerp":{"n":5.43,"rs":4203.7,"rs_pval":0,"s":4.45},"grantham":145,"isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":387,"min_dist_tss":654,"mutindex":7,"naa":"L","oaa":"S","phast_cons":{"mammalian":0.787,"primate":0.495,"vertebrate":0.017},"phred":9.246,"phylop":{"mammalian":2.54,"primate":0.645,"vertebrate":1.026},"polyphen":{"cat":"benign","val":0},"pos":5528374,"rawscore":0.765,"ref":"G","scoresegdup":0.95,"segway":"GE1","sift":{"cat":"tolerated","val":0.53},"type":"SNV"},"chrom":"20","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"L","codon_degeneracy":0,"codonpos":2,"pos":651,"ref":"S","refcodon":"TCA"},"alphamissense":{"pred":"B","rankscore":0.05756,"score":0.0756},"alt":"A","ancestral_allele":"G","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.16042,"score":-0.234613},"no_af":{"pred":"T","rankscore":0.32727,"score":-0.405654}},"bstatistic":{"converted_rankscore":0.6485,"score":632.0},"chrom":"20","clinpred":{"pred":"T","rankscore":0.15711,"score":0.133610770106316},"dann":{"rankscore":0.26797,"score":0.9537756066655413},"deogen2":{"pred":"T","rankscore":0.15857,"score":0.020053},"eigen":{"phred_coding":1.828805,"raw_coding":-0.217160964006767,"raw_coding_rankscore":0.3243},"eigen-pc":{"phred_coding":2.116901,"raw_coding":-0.075961628895607,"raw_coding_rankscore":0.36388},"ensembl":{"geneid":"ENSG00000125772","proteinid":"ENSP00000368305","transcriptid":"ENST00000379019"},"esm1b":{"pred":"T","rankscore":0.22318,"score":-3.901},"exac":{"ac":1,"adj_ac":1,"adj_af":8.26e-6,"af":8.236e-6,"afr":{"ac":0,"af":0.0},"amr":{"ac":0,"af":0.0},"eas":{"ac":1,"af":0.0001157},"fin":{"ac":0,"af":0.0},"nfe":{"ac":0,"af":0.0},"sas":{"ac":0,"af":0.0}},"exac_nontcga":{"ac":1,"adj_ac":1,"adj_af":9.431e-6,"af":9.415e-6,"afr":{"ac":0,"af":0.0},"amr":{"ac":0,"af":0.0},"eas":{"ac":1,"af":0.0001272},"fin":{"ac":0,"af":0.0},"nfe":{"ac":0,"af":0.0},"sas":{"ac":0,"af":0.0}},"fathmm":{"converted_rankscore":0.43279,"pred":"T","score":0.95},"fathmm-mkl":{"coding_group":"AEFDGBHCI","coding_pred":"D","coding_rankscore":0.29147,"coding_score":0.52503},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.15401,"coding_score":0.076551},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.68747,"score":0.697927},"h1-hesc":{"confidence_value":0,"rankscore":0.55881,"score":0.658983},"huvec":{"confidence_value":0,"rankscore":0.5635,"score":0.636168},"integrated":{"confidence_value":0,"rankscore":0.41029,"score":0.631515}},"gencode_basic":"Y","genename":"GPCPD1","genocanyon":{"rankscore":0.17886,"score":0.182091636265321},"gerp":{"91_mammals":{"rankscore":0.55828,"score":3.06}},"gerp++":{"nr":5.43,"rs":4.45,"rs_rankscore":0.53365},"gmvp":{"rankscore":0.33698,"score":0.3378536845766039},"hg18":{"end":5476374,"start":5476374},"hg19":{"end":5528374,"start":5528374},"hg38":{"end":5547728,"start":5547728},"hgvsc":"c.1952C>T","hgvsp":["p.S651L","p.Ser651Leu"],"list-s2":{"pred":"T","rankscore":0.37642,"score":0.754025},"lrt":{"converted_rankscore":0.17011,"omega":0.578852,"pred":"N","score":0.184596},"m-cap":{"pred":"T","rankscore":0.16406,"score":0.006255},"metalr":{"pred":"T","rankscore":0.28969,"score":0.0712},"metarnn":{"pred":"T","rankscore":0.19443,"score":0.10523993},"metasvm":{"pred":"T","rankscore":0.09216,"score":-1.0709},"mpc":{"rankscore":0.40145,"score":0.388881298341},"mutationassessor":{"pred":"L","rankscore":0.38595,"score":1.525},"mutationtaster":{"aae":"S651L","converted_rankscore":0.08975,"model":"simple_aae","pred":"N","score":1.0},"mutformer":{"rankscore":0.41566,"score":0.01008919},"mutpred":{"aa_change":"S651L","accession":"Q9NPB8","pred":{"mechanism":"Loss of disorder","p_val":0.0331},"rankscore":0.3997,"score":0.382},"mvp":{"rankscore":0.37526,"score":0.379193981924},"phactboost":{"rankscore":0.12966,"score":0.00197618754350116},"phastcons":{"100way_vertebrate":{"rankscore":0.28295,"score":0.664},"17way_primate":{"rankscore":0.29267,"score":0.511},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.45819,"score":2.59},"17way_primate":{"rankscore":0.7674,"score":0.676},"470way_mammalian":{"rankscore":0.58739,"score":7.424}},"polyphen2":{"hdiv":{"pred":"B","rankscore":0.18235,"score":0.02},"hvar":{"pred":"B","rankscore":0.12133,"score":0.006}},"primateai":{"pred":"T","rankscore":0.1363,"score":0.321371287107},"provean":{"converted_rankscore":0.47683,"pred":"N","score":-2.09},"ref":"G","reliability_index":10,"revel":{"rankscore":0.21907,"score":0.075},"rsid":"rs777014844","sift":{"converted_rankscore":0.34444,"pred":"T","score":0.075},"sift4g":{"converted_rankscore":0.10714,"pred":"T","score":0.513},"siphy_29way":{"logodds_rankscore":0.31405,"logodds_score":8.341,"pi":{"a":0.0749,"c":0.0,"g":0.6548,"t":0.2703}},"tsl":1,"uniprot":{"acc":"Q9NPB8","entry":"GPCP1_HUMAN"},"varity":{"er":{"rankscore":0.2267,"score":0.095565006},"er_loo":{"rankscore":0.22669,"score":0.095565006},"r":{"rankscore":0.18559,"score":0.080894046},"r_loo":{"rankscore":0.18559,"score":0.080894046}},"vep_canonical":"YES","vest4":{"rankscore":0.15888,"score":0.154}},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"exac":1.0,"gnomad_exomes":1.0}},{"allele":"A","freq":{"exac":0.0,"gnomad_exomes":0.0}}],"alt":"A","chrom":"20","dbsnp_build":156,"gene":{"geneid":56261,"is_pseudo":false,"name":"glycerophosphocholine phosphodiesterase 1","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2143,"seq_id":"NM_019593.5"},"hgvs":"NM_019593.5:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"NP_062539.1"}}},"protein_product":{"refseq":"NP_062539.1"},"refseq":"NM_019593.5","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2315,"seq_id":"XM_005260758.6"},"hgvs":"XM_005260758.6:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"XP_005260815.1"}}},"protein_product":{"refseq":"XP_005260815.1"},"refseq":"XM_005260758.6","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2066,"seq_id":"XM_024451949.2"},"hgvs":"XM_024451949.2:c.1805=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":601,"seq_id":"XP_024307717.1"}}},"protein_product":{"refseq":"XP_024307717.1"},"refseq":"XM_024451949.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2751,"seq_id":"XM_047440308.1"},"hgvs":"XM_047440308.1:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"XP_047296264.1"}}},"protein_product":{"refseq":"XP_047296264.1"},"refseq":"XM_047440308.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2459,"seq_id":"XM_047440309.1"},"hgvs":"XM_047440309.1:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"XP_047296265.1"}}},"protein_product":{"refseq":"XP_047296265.1"},"refseq":"XM_047440309.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2832,"seq_id":"XM_047440310.1"},"hgvs":"XM_047440310.1:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"XP_047296266.1"}}},"protein_product":{"refseq":"XP_047296266.1"},"refseq":"XM_047440310.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":2374,"seq_id":"XM_047440311.1"},"hgvs":"XM_047440311.1:c.1952=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":650,"seq_id":"XP_047296267.1"}}},"protein_product":{"refseq":"XP_047296267.1"},"refseq":"XM_047440311.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":1957,"seq_id":"XM_047440312.1"},"hgvs":"XM_047440312.1:c.1805=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":601,"seq_id":"XP_047296268.1"}}},"protein_product":{"refseq":"XP_047296268.1"},"refseq":"XM_047440312.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TCA","inserted_sequence":"TCA","position":1730,"seq_id":"XM_047440313.1"},"hgvs":"XM_047440313.1:c.1409=","protein":{"variant":{"spdi":{"deleted_sequence":"S","inserted_sequence":"S","position":469,"seq_id":"XP_047296269.1"}}},"protein_product":{"refseq":"XP_047296269.1"},"refseq":"XM_047440313.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"refseq":"XR_007067469.1","so":[{"accession":"SO:0002152","name":"genic_downstream_transcript_variant"}]}],"strand":"-","symbol":"GPCPD1"},"hg19":{"end":5528374,"start":5528374},"ref":"G","rsid":"rs777014844","vartype":"snv"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":1,"ac_adj":1,"ac_afr":0,"ac_amr":0,"ac_eas":1,"ac_female":0,"ac_fin":0,"ac_het":1,"ac_hom":0,"ac_male":1,"ac_nfe":0,"ac_oth":0,"ac_sas":0},"af":8.236e-6,"alleles":"A","alt":"A","an":{"an":121412,"an_adj":121062,"an_afr":10356,"an_amr":11546,"an_eas":8640,"an_female":53896,"an_fin":6612,"an_male":67166,"an_nfe":66564,"an_oth":908,"an_sas":16436},"baseqranksum":-4.985,"chrom":20,"clippingranksum":0.342,"culprit":"MQRankSum","fs":3.628,"het":{"het_afr":0,"het_amr":0,"het_eas":1,"het_fin":0,"het_nfe":0,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.51,"mq0":0,"mqranksum":1.72},"ncc":2,"pos":5528374,"qd":13.06,"readposranksum":1.44,"ref":"G","type":"snp","vqslod":0.147},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":1,"ac_adj":1,"ac_afr":0,"ac_amr":0,"ac_eas":1,"ac_female":0,"ac_fin":0,"ac_het":1,"ac_hom":0,"ac_male":1,"ac_nfe":0,"ac_oth":0,"ac_sas":0},"af":9.415e-6,"alleles":"A","alt":"A","an":{"an":106210,"an_adj":106030,"an_afr":9056,"an_amr":11194,"an_eas":7864,"an_female":45804,"an_fin":6612,"an_male":60226,"an_nfe":54278,"an_oth":694,"an_sas":16332},"baseqranksum":-4.985,"chrom":20,"clippingranksum":0.342,"culprit":"MQRankSum","fs":3.628,"het":{"het_afr":0,"het_amr":0,"het_eas":1,"het_fin":0,"het_nfe":0,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0001,"mq":{"mq":59.51,"mq0":0,"mqranksum":1.72},"ncc":2,"pos":5528374,"qd":13.06,"readposranksum":1.44,"ref":"G","type":"snp","vqslod":0.147},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":1,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":0,"ac_amr_female":0,"ac_amr_male":0,"ac_asj":0,"ac_asj_female":0,"ac_asj_male":0,"ac_eas":1,"ac_eas_female":0,"ac_eas_jpn":0,"ac_eas_kor":0,"ac_eas_male":1,"ac_eas_oea":1,"ac_female":0,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":1,"ac_nfe":0,"ac_nfe_bgr":0,"ac_nfe_est":0,"ac_nfe_female":0,"ac_nfe_male":0,"ac_nfe_nwe":0,"ac_nfe_onf":0,"ac_nfe_seu":0,"ac_nfe_swe":0,"ac_oth":0,"ac_oth_female":0,"ac_oth_male":0,"ac_sas":0,"ac_sas_female":0,"ac_sas_male":0},"af":{"af":3.98654e-6,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0,"af_amr_female":0.0,"af_amr_male":0.0,"af_asj":0.0,"af_asj_female":0.0,"af_asj_male":0.0,"af_eas":0.000054407,"af_eas_female":0.0,"af_eas_jpn":0.0,"af_eas_kor":0.0,"af_eas_male":0.000110375,"af_eas_oea":0.0000693674,"af_female":0.0,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":7.37757e-6,"af_nfe":0.0,"af_nfe_bgr":0.0,"af_nfe_est":0.0,"af_nfe_female":0.0,"af_nfe_male":0.0,"af_nfe_nwe":0.0,"af_nfe_onf":0.0,"af_nfe_seu":0.0,"af_nfe_swe":0.0,"af_oth":0.0,"af_oth_female":0.0,"af_oth_male":0.0,"af_sas":0.0,"af_sas_female":0.0,"af_sas_male":0.0},"alleles":"A","alt":"A","an":{"an":250844,"an_afr":16248,"an_afr_female":10064,"an_afr_male":6184,"an_amr":34448,"an_amr_female":20194,"an_amr_male":14254,"an_asj":10072,"an_asj_female":4898,"an_asj_male":5174,"an_eas":18380,"an_eas_female":9320,"an_eas_jpn":152,"an_eas_kor":3812,"an_eas_male":9060,"an_eas_oea":14416,"an_female":115298,"an_fin":21638,"an_fin_female":10368,"an_fin_male":11270,"an_male":135546,"an_nfe":113362,"an_nfe_bgr":2668,"an_nfe_est":242,"an_nfe_female":49996,"an_nfe_male":63366,"an_nfe_nwe":41984,"an_nfe_onf":30868,"an_nfe_seu":11468,"an_nfe_swe":26132,"an_oth":6108,"an_oth_female":2918,"an_oth_male":3190,"an_sas":30588,"an_sas_female":7540,"an_sas_male":23048},"baseqranksum":-2.463,"chrom":"20","clippingranksum":1.07,"dp":7775681,"fs":3.359,"hom":{"hom":0,"hom_afr":0,"hom_afr_female":0,"hom_afr_male":0,"hom_amr":0,"hom_amr_female":0,"hom_amr_male":0,"hom_asj":0,"hom_asj_female":0,"hom_asj_male":0,"hom_eas":0,"hom_eas_female":0,"hom_eas_jpn":0,"hom_eas_kor":0,"hom_eas_male":0,"hom_eas_oea":0,"hom_female":0,"hom_fin":0,"hom_fin_female":0,"hom_fin_male":0,"hom_male":0,"hom_nfe":0,"hom_nfe_bgr":0,"hom_nfe_est":0,"hom_nfe_female":0,"hom_nfe_male":0,"hom_nfe_nwe":0,"hom_nfe_onf":0,"hom_nfe_seu":0,"hom_nfe_swe":0,"hom_oth":0,"hom_oth_female":0,"hom_oth_male":0,"hom_sas":0,"hom_sas_female":0,"hom_sas_male":0},"inbreedingcoeff":0.0002,"mq":{"mq":58.89,"mqranksum":0.97},"pab_max":1.0,"pos":5528374,"qd":13.04,"readposranksum":-0.523,"ref":"G","rf":0.82491,"rsid":"rs777014844","sor":0.515,"type":"snp","vqslod":-1.061,"vqsr_culprit":"FS"},"hg19":{"end":5528374,"start":5528374},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"5459","position":"2165"},"cds":{"length":"2019","position":"1952"},"effect":"missense_variant","feature_id":"NM_019593.3","feature_type":"transcript","gene_id":"GPCPD1","genename":"GPCPD1","hgvs_c":"c.1952C>T","hgvs_p":"p.Ser651Leu","protein":{"length":"672","position":"651"},"putative_impact":"MODERATE","rank":"20","total":"20","transcript_biotype":"protein_coding"}},"vcf":{"alt":"A","position":"5528374","ref":"G"}},{"_id":"chr1:g.11147870G>A","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"G","annotype":"CodingTranscript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.906,"txflnk":0.0,"txwk":0.087,"znfrpts":0.0},"chrom":1,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.03,"dna":{"helt":-2.4,"mgw":0.1,"prot":1.39,"roll":-0.56},"dst2splice":14,"dst2spltype":"DONOR","encode":{"exp":247.55,"h3k27ac":4.0,"h3k4me1":2.0,"h3k4me3":1.0,"nucleo":2.2},"exon":"8/25","fitcons":0.701516,"gc":0.4,"gene":{"ccds_id":"CCDS30584.1","cds":{"cdna_pos":982,"cds_pos":932,"rel_cdna_pos":0.35,"rel_cds_pos":0.35},"feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10","prot":{"domain":"ndomain","protpos":311,"rel_prot_pos":0.35}},"gerp":{"n":6.17,"rs":333.2,"rs_pval":3.65172e-38,"s":5.22},"grantham":64,"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":21192,"min_dist_tss":12025,"mutindex":2,"naa":"V","oaa":"A","phast_cons":{"mammalian":0.978,"primate":0.949,"vertebrate":0.997},"phred":33,"phylop":{"mammalian":2.938,"primate":0.651,"vertebrate":3.295},"polyphen":{"cat":"probably_damaging","val":0.985},"pos":11147870,"rawscore":6.947718,"ref":"G","segway":"GE0","sift":{"cat":"deleterious","val":0},"type":"SNV"},"chrom":"1","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"V","codon_degeneracy":[0,0],"codonpos":[2,2],"pos":[311,311],"ref":"A","refcodon":["GCA","GCA"]},"alfa":{"african":{"ac":0,"af":0.0,"an":2898},"african_american":{"ac":0,"af":0.0,"an":2784},"african_others":{"ac":0,"af":0.0,"an":114},"asian":{"ac":0,"af":0.0,"an":112},"east_asian":{"ac":0,"af":0.0,"an":86},"european":{"ac":0,"af":0.0,"an":9690},"latin_american_1":{"ac":0,"af":0.0,"an":146},"latin_american_2":{"ac":0,"af":0.0,"an":610},"other":{"ac":0,"af":0.0,"an":496},"other_asian":{"ac":0,"af":0.0,"an":26},"south_asian":{"ac":0,"af":0.0,"an":98},"total":{"ac":0,"af":0.0,"an":14050}},"alphamissense":{"pred":["P","P"],"rankscore":0.90447,"score":[0.9763,0.9744]},"alt":"A","altai_neandertal":["G","G"],"ancestral_allele":"G","appris":"principal1","bayesdel":{"add_af":{"pred":"D","rankscore":0.85106,"score":0.329181},"no_af":{"pred":"D","rankscore":0.84911,"score":0.235069}},"bstatistic":{"converted_rankscore":0.81939,"score":413.0},"chagyrskaya_neandertal":["G","G"],"chrom":"1","clinpred":{"pred":"D","rankscore":0.85995,"score":0.994604789662408},"dann":{"rankscore":0.99042,"score":0.9992513284297346},"denisova":["G","G"],"deogen2":{"pred":"D","rankscore":0.94044,"score":0.776017},"eigen":{"phred_coding":15.48749,"raw_coding":1.04752235038793,"raw_coding_rankscore":0.9703},"eigen-pc":{"phred_coding":17.69647,"raw_coding":0.980509774627628,"raw_coding_rankscore":0.98214},"ensembl":{"geneid":["ENSG00000171824","ENSG00000171824"],"proteinid":["ENSP00000307307","ENSP00000366135"],"transcriptid":["ENST00000304457","ENST00000376936"]},"esm1b":{"pred":["D","D"],"rankscore":0.94643,"score":[-14.512,-14.527]},"fathmm":{"converted_rankscore":0.74896,"pred":["T","T"],"score":[-0.9,-0.9]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.97031,"coding_score":0.99522},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.77118,"coding_score":0.854169},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.89359,"score":0.724815},"h1-hesc":{"confidence_value":0,"rankscore":0.87919,"score":0.724815},"huvec":{"confidence_value":0,"rankscore":0.83352,"score":0.714379},"integrated":{"confidence_value":0,"rankscore":0.73137,"score":0.706548}},"gencode_basic":["Y","Y"],"genename":["EXOSC10","EXOSC10"],"genocanyon":{"rankscore":0.39042,"score":0.999296886801962},"gerp++":{"nr":6.17,"rs":5.22,"rs_rankscore":0.72285},"gmvp":{"rankscore":0.87661,"score":0.8769496789600049},"hg18":{"end":11070457,"start":11070457},"hg19":{"end":11147870,"start":11147870},"hg38":{"end":11087813,"start":11087813},"hgvsc":"c.932C>T","hgvsp":["p.A311V","p.Ala311Val"],"interpro":{"domain":"3'-5' exonuclease domain|3'-5' exonuclease domain"},"list-s2":{"pred":["D","D"],"rankscore":0.84033,"score":[0.957604,0.957038]},"lrt":{"converted_rankscore":0.8433,"omega":0.045014,"pred":"D","score":0.0},"m-cap":{"pred":"D","rankscore":0.67109,"score":0.057848},"metalr":{"pred":"D","rankscore":0.89771,"score":0.7028},"metarnn":{"pred":["D","D"],"rankscore":0.90643,"score":[0.9127948,0.9127948]},"metasvm":{"pred":"D","rankscore":0.9206,"score":0.6123},"mpc":{"rankscore":0.6668,"score":0.809751422137},"mutationassessor":{"pred":["H","H"],"rankscore":0.94653,"score":[3.705,3.705]},"mutationtaster":{"aae":["A311V","A311V","A311V"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae","simple_aae"],"pred":["D","D","D"],"score":[1.0,1.0,1.0]},"mutformer":{"rankscore":0.68302,"score":0.11863223},"mutpred":{"aa_change":["A311V","A311V"],"accession":["Q01780","Q01780"],"pred":[{"mechanism":"Gain of relative solvent accessibility","p_val":0.1571},{"mechanism":"Gain of relative solvent accessibility","p_val":0.1571}],"rankscore":0.8953,"score":[0.768,0.768]},"mvp":{"rankscore":0.93456,"score":[0.935233630009,0.935233630009]},"phactboost":{"rankscore":0.8193,"score":0.961674160523807},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.63387,"score":0.988},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.86956,"score":7.923},"17way_primate":{"rankscore":0.7674,"score":0.676},"470way_mammalian":{"rankscore":0.81106,"score":9.621}},"polyphen2":{"hdiv":{"pred":["D","D"],"rankscore":0.90584,"score":[0.999,1.0]},"hvar":{"pred":["D","D"],"rankscore":0.78936,"score":[0.982,0.99]}},"primateai":{"pred":"T","rankscore":0.59823,"score":0.648850083351},"provean":{"converted_rankscore":0.73267,"pred":["D","D"],"score":[-3.93,-3.93]},"ref":"G","reliability_index":10,"revel":{"rankscore":0.89192,"score":[0.7,0.7]},"rsid":"rs1483916848","sift":{"converted_rankscore":0.7849,"pred":["D","D"],"score":[0.001,0.002]},"sift4g":{"converted_rankscore":0.76473,"pred":["D","D"],"score":[0.003,0.003]},"siphy_29way":{"logodds_rankscore":0.90464,"logodds_score":18.402,"pi":{"a":0.0,"c":0.1276,"g":0.8724,"t":0.0}},"tsl":[1,1],"uniprot":[{"acc":"Q01780-2","entry":"EXOSX_HUMAN"},{"acc":"Q01780","entry":"EXOSX_HUMAN"}],"varity":{"er":{"rankscore":0.79404,"score":0.6478401},"er_loo":{"rankscore":0.79405,"score":0.6478401},"r":{"rankscore":0.85072,"score":0.81780094},"r_loo":{"rankscore":0.85073,"score":0.81780094}},"vep_canonical":"YES","vest4":{"rankscore":0.89465,"score":[0.89,0.895]},"vindijia_neandertal":["G","G"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"dbgap_popfreq":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"A","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"GCA","inserted_sequence":"GCA","position":968,"seq_id":"NM_001001998.3"},"hgvs":"NM_001001998.3:c.932=","protein":{"variant":{"spdi":{"deleted_sequence":"A","inserted_sequence":"A","position":310,"seq_id":"NP_001001998.1"}}},"protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GCA","inserted_sequence":"GCA","position":968,"seq_id":"NM_002685.4"},"hgvs":"NM_002685.4:c.932=","protein":{"variant":{"spdi":{"deleted_sequence":"A","inserted_sequence":"A","position":310,"seq_id":"NP_002676.1"}}},"protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GCA","inserted_sequence":"GCA","position":968,"seq_id":"XM_005263475.3"},"hgvs":"XM_005263475.3:c.932=","protein":{"variant":{"spdi":{"deleted_sequence":"A","inserted_sequence":"A","position":310,"seq_id":"XP_005263532.2"}}},"protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001986","name":"upstream_transcript_variant"},{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147870,"start":11147870},"ref":"G","rsid":"rs1483916848","vartype":"snv"},"hg19":{"end":11147870,"start":11147870},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"effect":"structural_interaction_variant","feature_id":"3SAF:A_311-A_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:B_311-B_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_311-A_331:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_311-A_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:B_311-B_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:A_311-A_331:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:A_311-A_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_311-B_331:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_311-B_332:NM_001001998.2","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:A_311-A_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAF:B_311-B_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_311-A_331:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:A_311-A_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAG:B_311-B_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:A_311-A_331:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:A_311-A_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_311-B_331:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3SAH:B_311-B_332:NM_002685.3","feature_type":"interaction","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","putative_impact":"HIGH","rank":"8","total":"24","transcript_biotype":"protein_coding"},{"cdna":{"length":"2842","position":"1011"},"cds":{"length":"2658","position":"932"},"effect":"missense_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","hgvs_p":"p.Ala311Val","protein":{"length":"885","position":"311"},"putative_impact":"MODERATE","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"2767","position":"1011"},"cds":{"length":"2583","position":"932"},"effect":"missense_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.932C>T","hgvs_p":"p.Ala311Val","protein":{"length":"860","position":"311"},"putative_impact":"MODERATE","rank":"8","total":"24","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"A","position":"11147870","ref":"G"}},{"_id":"chr1:g.11147886T>C","_score":1.14209415e-8,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"C","anc":"T","annotype":"CodingTranscript","bstatistic":334,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.008,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.906,"txflnk":0.0,"txwk":0.087,"znfrpts":0.0},"chrom":1,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.03,"dna":{"helt":-3.85,"mgw":-0.33,"prot":3.33,"roll":0.13},"encode":{"exp":314.2,"h3k27ac":3.84,"h3k4me1":2.56,"h3k4me3":1.52,"nucleo":1.5},"exon":"8/25","fitcons":0.701516,"gc":0.39,"gene":{"ccds_id":"CCDS30584.1","cds":{"cdna_pos":966,"cds_pos":916,"rel_cdna_pos":0.34,"rel_cds_pos":0.34},"feature_id":"ENST00000376936","gene_id":"ENSG00000171824","genename":"EXOSC10","prot":{"domain":"ndomain","protpos":306,"rel_prot_pos":0.35}},"gerp":{"n":6.17,"rs":333.2,"rs_pval":3.65172e-38,"s":2.57},"grantham":23,"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":21208,"min_dist_tss":12009,"mutindex":-36,"naa":"D","oaa":"N","phast_cons":{"mammalian":0.015,"primate":0.983,"vertebrate":0.035},"phred":9.802,"phylop":{"mammalian":0.196,"primate":0.53,"vertebrate":0.365},"polyphen":{"cat":"benign","val":0.102},"pos":11147886,"rawscore":0.855557,"ref":"T","segway":"GE0","sift":{"cat":"tolerated","val":0.5},"type":"SNV"},"chrom":"1","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"D","codon_degeneracy":[0,0],"codonpos":[1,1],"pos":[306,306],"ref":"N","refcodon":["AAT","AAT"]},"alfa":{"african":{"ac":0,"af":0.0,"an":2294},"african_american":{"ac":0,"af":0.0,"an":2210},"african_others":{"ac":0,"af":0.0,"an":84},"asian":{"ac":0,"af":0.0,"an":108},"east_asian":{"ac":0,"af":0.0,"an":84},"european":{"ac":0,"af":0.0,"an":6962},"latin_american_1":{"ac":0,"af":0.0,"an":146},"latin_american_2":{"ac":0,"af":0.0,"an":610},"other":{"ac":0,"af":0.0,"an":466},"other_asian":{"ac":0,"af":0.0,"an":24},"south_asian":{"ac":0,"af":0.0,"an":94},"total":{"ac":0,"af":0.0,"an":10680}},"alphamissense":{"pred":["B","B"],"rankscore":0.09868,"score":[0.083,0.0843]},"alt":"C","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.19255,"score":-0.210879},"no_af":{"pred":"T","rankscore":0.18229,"score":-0.54069}},"bstatistic":{"converted_rankscore":0.81939,"score":413.0},"chagyrskaya_neandertal":["T","T"],"chrom":"1","clinpred":{"pred":"T","rankscore":0.09157,"score":0.0736723941471746},"dann":{"rankscore":0.3376,"score":0.9739888645284804},"denisova":["T","T"],"deogen2":{"pred":"T","rankscore":0.54594,"score":0.19117},"eigen":{"phred_coding":0.6943469,"raw_coding":-0.773335944062011,"raw_coding_rankscore":0.14008},"eigen-pc":{"phred_coding":0.9117899,"raw_coding":-0.691594476798813,"raw_coding_rankscore":0.17169},"ensembl":{"geneid":["ENSG00000171824","ENSG00000171824"],"proteinid":["ENSP00000307307","ENSP00000366135"],"transcriptid":["ENST00000304457","ENST00000376936"]},"esm1b":{"pred":["T","T"],"rankscore":0.50464,"score":[-6.523,-6.502]},"fathmm":{"converted_rankscore":0.66113,"pred":["T","T"],"score":[-0.2,-0.2]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"N","coding_rankscore":0.25861,"coding_score":0.37875},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.32785,"coding_score":0.201174},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.89359,"score":0.724815},"h1-hesc":{"confidence_value":0,"rankscore":0.87919,"score":0.724815},"huvec":{"confidence_value":0,"rankscore":0.83352,"score":0.714379},"integrated":{"confidence_value":0,"rankscore":0.73137,"score":0.706548}},"gencode_basic":["Y","Y"],"genename":["EXOSC10","EXOSC10"],"genocanyon":{"rankscore":0.15798,"score":0.0787769855251484},"gerp":{"91_mammals":{"rankscore":0.52066,"score":2.85}},"gerp++":{"nr":6.17,"rs":2.57,"rs_rankscore":0.29928},"gmvp":{"rankscore":0.21412,"score":0.21496335541500347},"hg18":{"end":11070473,"start":11070473},"hg19":{"end":11147886,"start":11147886},"hg38":{"end":11087829,"start":11087829},"hgvsc":"c.916A>G","hgvsp":["p.N306D","p.Asn306Asp"],"interpro":{"domain":"3'-5' exonuclease domain|3'-5' exonuclease domain"},"list-s2":{"pred":["D","D"],"rankscore":0.66782,"score":[0.905809,0.905809]},"lrt":{"converted_rankscore":0.21598,"omega":0.563162,"pred":"N","score":0.069556},"m-cap":{"pred":"T","rankscore":0.33248,"score":0.013668},"metalr":{"pred":"T","rankscore":0.39462,"score":0.1092},"metarnn":{"pred":["T","T"],"rankscore":0.21117,"score":[0.112563014,0.112563014]},"metasvm":{"pred":"T","rankscore":0.26541,"score":-1.0112},"mpc":{"rankscore":0.31682,"score":0.292617977072},"mutationassessor":{"pred":["N","N"],"rankscore":0.09567,"score":[0.22,0.22]},"mutationtaster":{"aae":["N306D","N306D","N306D"],"converted_rankscore":0.08975,"model":["simple_aae","simple_aae","simple_aae"],"pred":["N","N","N"],"score":[1.0,1.0,1.0]},"mutformer":{"rankscore":0.1583,"score":0.00102775},"mutpred":{"aa_change":["N306D","N306D"],"accession":["Q01780","Q01780"],"pred":[{"mechanism":"Loss of helix","p_val":0.079},{"mechanism":"Loss of helix","p_val":0.079}],"rankscore":0.49157,"score":[0.438,0.438]},"mvp":{"rankscore":0.54254,"score":[0.546000776237,0.546000776237]},"phactboost":{"rankscore":0.18166,"score":0.00454703187030825},"phastcons":{"100way_vertebrate":{"rankscore":0.20612,"score":0.033},"17way_primate":{"rankscore":0.85391,"score":0.998},"470way_mammalian":{"rankscore":0.21063,"score":0.026}},"phylop":{"100way_vertebrate":{"rankscore":0.36876,"score":1.647},"17way_primate":{"rankscore":0.62972,"score":0.665},"470way_mammalian":{"rankscore":0.20256,"score":0.634}},"polyphen2":{"hdiv":{"pred":["B","B"],"rankscore":0.24253,"score":[0.062,0.076]},"hvar":{"pred":["B","B"],"rankscore":0.33484,"score":[0.062,0.139]}},"primateai":{"pred":"T","rankscore":0.05931,"score":0.268385469913},"provean":{"converted_rankscore":0.34397,"pred":["N","N"],"score":[-1.39,-1.39]},"ref":"T","reliability_index":10,"revel":{"rankscore":0.05988,"score":[0.027,0.027]},"rsid":"rs1640579969","sift":{"converted_rankscore":0.08018,"pred":["T","T"],"score":[0.527,0.489]},"sift4g":{"converted_rankscore":0.19304,"pred":["T","T"],"score":[0.335,0.317]},"siphy_29way":{"logodds_rankscore":0.15346,"logodds_score":5.3523,"pi":{"a":0.0,"c":0.1461,"g":0.2823,"t":0.5716}},"tsl":[1,1],"uniprot":[{"acc":"Q01780-2","entry":"EXOSX_HUMAN"},{"acc":"Q01780","entry":"EXOSX_HUMAN"}],"varity":{"er":{"rankscore":0.10031,"score":0.056291845},"er_loo":{"rankscore":0.10031,"score":0.056291845},"r":{"rankscore":0.10539,"score":0.054723065},"r_loo":{"rankscore":0.10539,"score":0.054723065}},"vep_canonical":"YES","vest4":{"rankscore":0.37093,"score":[0.33,0.274]},"vindijia_neandertal":["T","T"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"T","freq":{"dbgap_popfreq":1.0,"topmed":1.0}},{"allele":"C","freq":{"dbgap_popfreq":0.0,"topmed":0.0}}],"alt":"C","chrom":"1","dbsnp_build":156,"gene":{"geneid":5394,"is_pseudo":false,"name":"exosome component 10","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"AAT","inserted_sequence":"AAT","position":953,"seq_id":"NM_001001998.3"},"hgvs":"NM_001001998.3:c.916=","protein":{"variant":{"spdi":{"deleted_sequence":"N","inserted_sequence":"N","position":305,"seq_id":"NP_001001998.1"}}},"protein_product":{"refseq":"NP_001001998.1"},"refseq":"NM_001001998.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"AAT","inserted_sequence":"AAT","position":953,"seq_id":"NM_002685.4"},"hgvs":"NM_002685.4:c.916=","protein":{"variant":{"spdi":{"deleted_sequence":"N","inserted_sequence":"N","position":305,"seq_id":"NP_002676.1"}}},"protein_product":{"refseq":"NP_002676.1"},"refseq":"NM_002685.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"AAT","inserted_sequence":"AAT","position":953,"seq_id":"XM_005263475.3"},"hgvs":"XM_005263475.3:c.916=","protein":{"variant":{"spdi":{"deleted_sequence":"N","inserted_sequence":"N","position":305,"seq_id":"XP_005263532.2"}}},"protein_product":{"refseq":"XP_005263532.2"},"refseq":"XM_005263475.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"protein_product":{"refseq":"XP_047278617.1"},"refseq":"XM_047422661.1","so":[{"accession":"SO:0001986","name":"upstream_transcript_variant"},{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]},{"protein_product":{"refseq":"XP_047278619.1"},"refseq":"XM_047422663.1","so":[{"accession":"SO:0002153","name":"genic_upstream_transcript_variant"}]}],"strand":"-","symbol":"EXOSC10"},"hg19":{"end":11147886,"start":11147886},"ref":"T","rsid":"rs1640579969","vartype":"snv"},"hg19":{"end":11147886,"start":11147886},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"2842","position":"995"},"cds":{"length":"2658","position":"916"},"effect":"missense_variant","feature_id":"NM_001001998.2","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.916A>G","hgvs_p":"p.Asn306Asp","protein":{"length":"885","position":"306"},"putative_impact":"MODERATE","rank":"8","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"2767","position":"995"},"cds":{"length":"2583","position":"916"},"effect":"missense_variant","feature_id":"NM_002685.3","feature_type":"transcript","gene_id":"EXOSC10","genename":"EXOSC10","hgvs_c":"c.916A>G","hgvs_p":"p.Asn306Asp","protein":{"length":"860","position":"306"},"putative_impact":"MODERATE","rank":"8","total":"24","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"C","position":"11147886","ref":"T"}}]}