{"_id":"chr5:g.96786547T>G","_version":1,"chrom":"5","clingen":{"caid":"CA360489561"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"S","codon_degeneracy":[0,0],"codonpos":[2,2],"pos":[561,561],"ref":"Y","refcodon":["TAC","TAC"]},"alphamissense":{"pred":["B","B"],"rankscore":0.17573,"score":[0.101,0.094]},"alt":"G","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":["principal3","alternative2"],"bayesdel":{"add_af":{"pred":"T","rankscore":0.20812,"score":-0.199954},"no_af":{"pred":"T","rankscore":0.19789,"score":-0.524997}},"bstatistic":{"converted_rankscore":0.26808,"score":891.0},"cadd":{"phred":19.31,"raw_rankscore":0.33343,"raw_score":2.572657},"chagyrskaya_neandertal":["T","T"],"chrom":"5","clinpred":{"pred":"D","rankscore":0.33121,"score":0.513372182846069},"dann":{"rankscore":0.23344,"score":0.9352560012900805},"denisova":["T","T"],"deogen2":{"pred":"T","rankscore":0.64215,"score":0.269913},"eigen":{"phred_coding":1.424358,"raw_coding":-0.381177192344602,"raw_coding_rankscore":0.2614},"eigen-pc":{"phred_coding":1.645334,"raw_coding":-0.261538908703907,"raw_coding_rankscore":0.29376},"ensembl":{"geneid":["ENSG00000164307","ENSG00000164307"],"proteinid":["ENSP00000296754","ENSP00000406304"],"transcriptid":["ENST00000296754","ENST00000443439"]},"esm1b":{"pred":["T","T"],"rankscore":0.45341,"score":[-5.889,-5.842]},"fathmm":{"converted_rankscore":0.01297,"pred":["T","T"],"score":[5.02,5.02]},"fathmm-mkl":{"coding_group":"AEFGBCI","coding_pred":"D","coding_rankscore":0.4458,"coding_score":0.85447},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.36724,"coding_score":0.246501},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.89359,"score":0.724815},"h1-hesc":{"confidence_value":0,"rankscore":0.75317,"score":0.709663},"huvec":{"confidence_value":0,"rankscore":0.83352,"score":0.714379},"integrated":{"confidence_value":0,"rankscore":0.61202,"score":0.706298}},"gencode_basic":["Y","Y"],"genename":["ERAP1","ERAP1"],"genocanyon":{"rankscore":0.35288,"score":0.997118351080628},"gerp":{"91_mammals":{"rankscore":0.78007,"score":4.09}},"gerp++":{"nr":5.34,"rs":1.24,"rs_rankscore":0.20416},"gmvp":{"rankscore":0.78055,"score":0.7810414746927083},"hg18":{"end":96148007,"start":96148007},"hg19":{"end":96122251,"start":96122251},"hg38":{"end":96786547,"start":96786547},"hgvsc":"c.1682A>C","hgvsp":["p.Y561S","p.Tyr561Ser"],"list-s2":{"pred":["T","T"],"rankscore":0.28847,"score":[0.680032,0.680032]},"lrt":{"converted_rankscore":0.26107,"omega":0.424851,"pred":"N","score":0.025339},"m-cap":{"pred":"T","rankscore":0.246,"score":0.009385},"metalr":{"pred":"T","rankscore":0.0147,"score":0.0045},"metarnn":{"pred":["T","T"],"rankscore":0.33413,"score":[0.18169302,0.18169302]},"metasvm":{"pred":"T","rankscore":0.32903,"score":-0.9888},"mpc":{"rankscore":0.12212,"score":0.108328303191},"mutationassessor":{"pred":["L","L"],"rankscore":0.34214,"score":[1.37,1.37]},"mutationtaster":{"aae":["Y561S","Y561S","Y561S"],"converted_rankscore":0.322,"model":["simple_aae","simple_aae","simple_aae"],"pred":["D","D","D"],"score":[0.559424,0.559424,0.559424]},"mutformer":{"rankscore":0.55479,"score":0.03408702},"mutpred":{"aa_change":["Y561S","Y561S"],"accession":["Q9NZ08","Q9NZ08"],"pred":[{"mechanism":"Gain of disorder","p_val":0.0101},{"mechanism":"Gain of disorder","p_val":0.0101}],"rankscore":0.6473,"score":[0.537,0.537]},"mvp":{"rankscore":0.17676,"score":[0.180583059064,0.180583059064]},"phactboost":{"rankscore":0.22313,"score":0.00810881315319755},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.38829,"score":0.824},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.43718,"score":2.35},"17way_primate":{"rankscore":0.47794,"score":0.609},"470way_mammalian":{"rankscore":0.35974,"score":3.014}},"polyphen2":{"hdiv":{"pred":["B","B"],"rankscore":0.13644,"score":[0.002,0.006]},"hvar":{"pred":["B","B"],"rankscore":0.1009,"score":[0.004,0.003]}},"primateai":{"pred":"T","rankscore":0.29514,"score":0.432240247726},"provean":{"converted_rankscore":0.75615,"pred":["D","D"],"score":[-4.19,-4.19]},"ref":"T","reliability_index":10,"revel":{"rankscore":0.20419,"score":[0.07,0.07]},"sift":{"converted_rankscore":0.17701,"pred":["T","T"],"score":[0.24,0.243]},"sift4g":{"converted_rankscore":0.26883,"pred":["T","T"],"score":[0.208,0.211]},"siphy_29way":{"logodds_rankscore":0.20255,"logodds_score":6.2885,"pi":{"a":0.2571,"c":0.0,"g":0.2665,"t":0.4764}},"tsl":[1,1],"uniprot":[{"acc":"Q9NZ08-2","entry":"ERAP1_HUMAN"},{"acc":"Q9NZ08","entry":"ERAP1_HUMAN"}],"varity":{"er":{"rankscore":0.44728,"score":0.20554006},"er_loo":{"rankscore":0.44727,"score":0.20554006},"r":{"rankscore":0.55233,"score":0.32710797},"r_loo":{"rankscore":0.55233,"score":0.32710797}},"vep_canonical":"YES","vest4":{"rankscore":0.3114,"score":[0.275,0.272]},"vindijia_neandertal":["T","T"]},"hg38":{"end":96786547,"start":96786547},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"5584","position":"2029"},"cds":{"length":"2847","position":"1682"},"effect":"missense_variant&splice_region_variant","feature_id":"NM_016442.3","feature_type":"transcript","gene_id":"ERAP1","genename":"ERAP1","hgvs_c":"c.1682A>C","hgvs_p":"p.Tyr561Ser","protein":{"length":"948","position":"561"},"putative_impact":"MODERATE","rank":"12","total":"20","transcript_biotype":"protein_coding"},{"cdna":{"length":"5085","position":"2029"},"cds":{"length":"2826","position":"1682"},"effect":"missense_variant&splice_region_variant","feature_id":"NM_001040458.1","feature_type":"transcript","gene_id":"ERAP1","genename":"ERAP1","hgvs_c":"c.1682A>C","hgvs_p":"p.Tyr561Ser","protein":{"length":"941","position":"561"},"putative_impact":"MODERATE","rank":"12","total":"19","transcript_biotype":"protein_coding"},{"cdna":{"length":"4843","position":"1787"},"cds":{"length":"2826","position":"1682"},"effect":"missense_variant&splice_region_variant","feature_id":"NM_001198541.1","feature_type":"transcript","gene_id":"ERAP1","genename":"ERAP1","hgvs_c":"c.1682A>C","hgvs_p":"p.Tyr561Ser","protein":{"length":"941","position":"561"},"putative_impact":"MODERATE","rank":"12","total":"19","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"96786547","ref":"T"}}