{"_id":"chr5:g.96122251T>A","_version":1,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","annotype":"CodingTranscript","bstatistic":598,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.031,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.488,"txflnk":0.0,"txwk":0.48,"znfrpts":0.0},"chrom":5,"consdetail":"missense,splice","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.03,"dna":{"helt":-2.66,"mgw":-0.21,"prot":2.77,"roll":-0.93},"dst2splice":3,"dst2spltype":"ACCEPTOR","encode":{"exp":278.01,"h3k27ac":8.0,"h3k4me1":1.92,"h3k4me3":2.52,"nucleo":1.0,"occ":3,"p_val":{"comb":0.85,"ctcf":0.0,"dnas":0.0,"faire":1.5,"mycp":0.0,"polii":0.0},"sig":{"ctcf":0.01,"dnase":0.01,"faire":0.02,"myc":0.0,"polii":0.0}},"exon":"12/20","fitcons":0.701516,"gc":0.36,"gene":{"ccds_id":"CCDS4085.1","cds":{"cdna_pos":1940,"cds_pos":1682,"rel_cdna_pos":0.35,"rel_cds_pos":0.59},"feature_id":"ENST00000296754","gene_id":"ENSG00000164307","genename":"ERAP1","prot":{"protpos":561,"rel_prot_pos":0.59}},"gerp":{"n":5.34,"rs":279.4,"rs_pval":2.51436e-50,"s":1.24},"grantham":22,"isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":548,"min_dist_tss":214,"mutindex":-18,"naa":"F","oaa":"Y","phast_cons":{"mammalian":0.985,"primate":0.805,"vertebrate":0.995},"phred":9.551,"phylop":{"mammalian":0.302,"primate":0.398,"vertebrate":0.575},"polyphen":{"cat":"benign","val":0.001},"pos":96122251,"rawscore":0.814083,"ref":"T","segway":"R1","sift":{"cat":"tolerated","val":0.74},"type":"SNV"},"chrom":"5","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"F","codon_degeneracy":[0,0],"codonpos":[2,2],"pos":[561,561],"ref":"Y","refcodon":["TAC","TAC"]},"alphamissense":{"pred":["B","B"],"rankscore":0.11749,"score":[0.0859,0.0882]},"alt":"A","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":["principal3","alternative2"],"bayesdel":{"add_af":{"pred":"T","rankscore":0.13726,"score":-0.253062},"no_af":{"pred":"T","rankscore":0.12703,"score":-0.601282}},"bstatistic":{"converted_rankscore":0.26808,"score":891.0},"chagyrskaya_neandertal":["T","T"],"chrom":"5","clinpred":{"pred":"T","rankscore":0.21192,"score":0.214631721377373},"dann":{"rankscore":0.18634,"score":0.8924735373595819},"denisova":["T","T"],"deogen2":{"pred":"T","rankscore":0.40279,"score":0.098704},"eigen":{"phred_coding":1.449757,"raw_coding":-0.369862810110999,"raw_coding_rankscore":0.26549},"eigen-pc":{"phred_coding":1.663001,"raw_coding":-0.253466613972937,"raw_coding_rankscore":0.29652},"ensembl":{"geneid":["ENSG00000164307","ENSG00000164307"],"proteinid":["ENSP00000296754","ENSP00000406304"],"transcriptid":["ENST00000296754","ENST00000443439"]},"esm1b":{"pred":["T","T"],"rankscore":0.25804,"score":[-4.135,-4.135]},"fathmm":{"converted_rankscore":0.01356,"pred":["T","T"],"score":[4.97,4.97]},"fathmm-mkl":{"coding_group":"AEFGBCI","coding_pred":"D","coding_rankscore":0.35152,"coding_score":0.71757},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.23388,"coding_score":0.119947},"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":0.51326,"score":0.5140459869374027},"hg18":{"end":96148007,"start":96148007},"hg19":{"end":96122251,"start":96122251},"hg38":{"end":96786547,"start":96786547},"hgvsc":"c.1682A>T","hgvsp":["p.Tyr561Phe","p.Y561F"],"list-s2":{"pred":["T","T"],"rankscore":0.4115,"score":[0.777822,0.777822]},"lrt":{"converted_rankscore":0.26107,"omega":0.424851,"pred":"N","score":0.025339},"m-cap":{"pred":"T","rankscore":0.08062,"score":0.003539},"metalr":{"pred":"T","rankscore":0.01542,"score":0.0047},"metarnn":{"pred":["T","T"],"rankscore":0.26538,"score":[0.13957846,0.13957846]},"metasvm":{"pred":"T","rankscore":0.36925,"score":-0.9713},"mpc":{"rankscore":0.0765,"score":0.0682964760759},"mutationassessor":{"pred":["L","L"],"rankscore":0.41913,"score":[1.64,1.64]},"mutationtaster":{"aae":["Y561F","Y561F","Y561F"],"converted_rankscore":0.27581,"model":["simple_aae","simple_aae","simple_aae"],"pred":["N","N","N"],"score":[0.907299,0.907299,0.907299]},"mutformer":{"rankscore":0.46135,"score":0.01491959},"mutpred":{"aa_change":["Y561F","Y561F"],"accession":["Q9NZ08","Q9NZ08"],"pred":[{"mechanism":"Loss of phosphorylation at Y561","p_val":0.0285},{"mechanism":"Loss of phosphorylation at Y561","p_val":0.0285}],"rankscore":0.52916,"score":[0.461,0.461]},"mvp":{"rankscore":0.08535,"score":[0.0920862733494,0.0920862733494]},"phactboost":{"rankscore":0.08432,"score":0.000777204689146661},"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":0.02946,"score":[0.0,0.0]},"hvar":{"pred":["B","B"],"rankscore":0.04355,"score":[0.001,0.001]}},"primateai":{"pred":"T","rankscore":0.27549,"score":0.417898505926},"provean":{"converted_rankscore":0.35991,"pred":["N","N"],"score":[-1.47,-1.47]},"ref":"T","reliability_index":10,"revel":{"rankscore":0.11576,"score":[0.043,0.043]},"sift":{"converted_rankscore":0.16848,"pred":["T","T"],"score":[0.255,0.259]},"sift4g":{"converted_rankscore":0.11335,"pred":["T","T"],"score":[0.496,0.504]},"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":0.09971,"score":0.05612487},"er_loo":{"rankscore":0.09971,"score":0.05612487},"r":{"rankscore":0.3254,"score":0.14117631},"r_loo":{"rankscore":0.3254,"score":0.14117631}},"vep_canonical":"YES","vest4":{"rankscore":0.21839,"score":[0.198,0.197]},"vindijia_neandertal":["T","T"]},"hg19":{"end":96122251,"start":96122251},"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>T","hgvs_p":"p.Tyr561Phe","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>T","hgvs_p":"p.Tyr561Phe","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>T","hgvs_p":"p.Tyr561Phe","protein":{"length":"941","position":"561"},"putative_impact":"MODERATE","rank":"12","total":"19","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"A","position":"96122251","ref":"T"}}