{"_id":"chr5:g.1201911G>A","_version":2,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"G","annotype":"CodingTranscript","bstatistic":964,"chmm":{"bivflnk":0.008,"enh":0.008,"enhbiv":0.008,"het":0.0,"quies":0.228,"reprpc":0.173,"reprpcwk":0.48,"tssa":0.008,"tssaflnk":0.024,"tssbiv":0.008,"tx":0.0,"txflnk":0.0,"txwk":0.031,"znfrpts":0.0},"chrom":5,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.15,"dna":{"helt":-2.1,"mgw":0.04,"prot":1.45,"roll":-0.8},"encode":{"exp":24.84,"h3k27ac":8.48,"h3k4me1":16.64,"h3k4me3":8.8,"nucleo":0.5,"occ":2,"p_val":{"comb":5.85,"ctcf":1.54,"dnas":7.09,"faire":0.0,"mycp":1.87,"polii":0.0},"sig":{"ctcf":0.14,"dnase":0.22,"faire":0.01,"myc":0.11,"polii":0.02}},"exon":"1/12","fitcons":0.527649,"gc":0.68,"gene":{"ccds_id":"CCDS34130.1","cds":{"cdna_pos":202,"cds_pos":146,"rel_cdna_pos":0.04,"rel_cds_pos":0.08},"feature_id":"ENST00000304460","gene_id":"ENSG00000174358","genename":"SLC6A19","prot":{"domain":"tmhmm","protpos":49,"rel_prot_pos":0.08}},"gerp":{"n":4.41,"rs":599.6,"rs_pval":3.32345e-107,"s":2.53},"grantham":194,"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":21475,"min_dist_tss":201,"mutindex":-39,"naa":"Y","oaa":"C","phast_cons":{"mammalian":0.997,"primate":0.006,"vertebrate":1.0},"phred":23.2,"phylop":{"mammalian":0.429,"primate":0.457,"vertebrate":2.058},"polyphen":{"cat":"probably_damaging","val":1},"pos":1201911,"rawscore":3.647624,"ref":"G","segway":"GM1","sift":{"cat":"deleterious","val":0},"type":"SNV"},"chrom":"5","clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":204445,"alt":"A","chrom":"5","cytogenic":"5p15.33","gene":{"id":"340024","symbol":"SLC6A19"},"hg19":{"end":1201911,"start":1201911},"hg38":{"end":1201796,"start":1201796},"hgvs":{"coding":"NM_001003841.3:c.146G>A","genomic":["NC_000005.10:g.1201796G>A","NC_000005.9:g.1201911G>A","NG_008282.1:g.5202G>A"],"protein":"NP_001003841.1:p.Cys49Tyr"},"rcv":{"accession":"RCV000190382","clinical_significance":"not provided","conditions":{"identifiers":{"medgen":"C3661900"},"name":"not provided","synonyms":["none provided"]},"number_submitters":1,"origin":"not provided","preferred_name":"NM_001003841.3(SLC6A19):c.146G>A (p.Cys49Tyr)","review_status":"no assertion provided"},"ref":"G","rsid":"rs796064507","type":"single nucleotide variant","variant_id":208186},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"Y","codon_degeneracy":0,"codonpos":2,"pos":49,"ref":"C","refcodon":"TGC"},"alphamissense":{"pred":"P","rankscore":0.83119,"score":0.9054},"alt":"A","altai_neandertal":["G","G"],"ancestral_allele":"G","appris":"principal1","bayesdel":{"add_af":{"pred":"D","rankscore":0.83592,"score":0.307987},"no_af":{"pred":"D","rankscore":0.8338,"score":0.204625}},"bstatistic":{"converted_rankscore":0.0917,"score":958.0},"cds_strand":"+","chagyrskaya_neandertal":["G","G"],"chrom":"5","clinpred":{"pred":"D","rankscore":0.90962,"score":0.997189581394196},"clinvar":{"clinvar_id":"208186","clnsig":"not_provided","hgvs":"NC_000005.10:g.1201796G>A","medgen":"CN517202","review":"no_classification_provided","trait":"not_provided","var_source":"ClinGen:CA248449"},"dann":{"rankscore":0.30596,"score":0.9665255107568678},"denisova":["G","G"],"deogen2":{"pred":"D","rankscore":0.88985,"score":0.640857},"eigen":{"phred_coding":5.765733,"raw_coding":0.584112596034566,"raw_coding_rankscore":0.72183},"eigen-pc":{"phred_coding":4.854263,"raw_coding":0.464882526334832,"raw_coding_rankscore":0.65679},"ensembl":{"geneid":"ENSG00000174358","proteinid":"ENSP00000305302","transcriptid":"ENST00000304460"},"esm1b":{"pred":"D","rankscore":0.8916,"score":-12.951},"eve":{"class10_pred":"U","class20_pred":"U","class25_pred":"U","class30_pred":"P","class40_pred":"P","class50_pred":"P","class60_pred":"P","class70_pred":"P","class75_pred":"P","class80_pred":"P","class90_pred":"P","rankscore":0.91223,"score":0.8445175434584113},"fathmm":{"converted_rankscore":0.74053,"pred":"T","score":-0.82},"fathmm-mkl":{"coding_group":"AEFDGBCI","coding_pred":"D","coding_rankscore":0.39986,"coding_score":0.80316},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.82347,"coding_score":0.889423},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.14657,"score":0.547309},"h1-hesc":{"confidence_value":3,"rankscore":0.00348,"score":0.056198},"huvec":{"confidence_value":0,"rankscore":0.41899,"score":0.613276},"integrated":{"confidence_value":0,"rankscore":0.06694,"score":0.428477}},"gencode_basic":"Y","genename":"SLC6A19","genocanyon":{"rankscore":0.74766,"score":0.999996914482635},"gerp":{"91_mammals":{"rankscore":0.11184,"score":-2.12}},"gerp++":{"nr":4.41,"rs":2.53,"rs_rankscore":0.29594},"gmvp":{"rankscore":0.87735,"score":0.8776801359410421},"hg18":{"end":1254911,"start":1254911},"hg19":{"end":1201911,"start":1201911},"hg38":{"end":1201796,"start":1201796},"hgvsc":"c.146G>A","hgvsp":["p.Cys49Tyr","p.C49Y"],"list-s2":{"pred":"D","rankscore":0.84889,"score":0.959904},"lrt":{"converted_rankscore":0.8433,"omega":0.0,"pred":"D","score":0.0},"m-cap":{"pred":"D","rankscore":0.76854,"score":0.09792},"metalr":{"pred":"D","rankscore":0.86051,"score":0.6068},"metarnn":{"pred":"D","rankscore":0.90157,"score":0.90792537},"metasvm":{"pred":"D","rankscore":0.87807,"score":0.3158},"mpc":{"rankscore":0.75857,"score":1.04290875018},"mutationassessor":{"pred":"H","rankscore":0.95014,"score":3.75},"mutationtaster":{"aae":"C49Y","converted_rankscore":0.53665,"model":"simple_aae","pred":"D","score":0.999972},"mutformer":{"rankscore":0.96207,"score":0.98606735},"mutpred":{"aa_change":"C49Y","accession":"Q695T7","pred":{"mechanism":"Gain of helix","p_val":0.1736},"rankscore":0.83869,"score":0.702},"mvp":{"rankscore":0.75417,"score":0.756380454418},"phactboost":{"rankscore":0.86137,"score":0.983298123649144},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.76049,"score":0.996},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.72865,"score":6.326},"17way_primate":{"rankscore":0.7674,"score":0.676},"470way_mammalian":{"rankscore":0.76855,"score":8.245}},"polyphen2":{"hdiv":{"pred":"D","rankscore":0.77913,"score":0.999},"hvar":{"pred":"D","rankscore":0.74454,"score":0.979}},"primateai":{"pred":"D","rankscore":0.94445,"score":0.883633136749},"provean":{"converted_rankscore":0.71397,"pred":"D","score":-3.77},"ref":"G","reliability_index":10,"revel":{"rankscore":0.91879,"score":0.761},"rsid":"rs796064507","sift":{"converted_rankscore":0.7849,"pred":"D","score":0.001},"sift4g":{"converted_rankscore":0.83351,"pred":"D","score":0.001},"siphy_29way":{"logodds_rankscore":0.64281,"logodds_score":14.0546,"pi":{"a":0.0,"c":0.2884,"g":0.7116,"t":0.0}},"tsl":1,"uniprot":{"acc":"Q695T7","entry":"S6A19_HUMAN"},"varity":{"er":{"rankscore":0.99738,"score":0.9772345},"er_loo":{"rankscore":0.99739,"score":0.9772345},"r":{"rankscore":0.98778,"score":0.9758532},"r_loo":{"rankscore":0.98778,"score":0.9758532}},"vep_canonical":"YES","vest4":{"rankscore":0.91162,"score":0.91},"vindijia_neandertal":["G","G"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alt":"A","chrom":"5","dbsnp_build":156,"gene":{"geneid":340024,"is_pseudo":false,"name":"solute carrier family 6 member 19","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"TGC","inserted_sequence":"TGC","position":200,"seq_id":"NM_001003841.3"},"hgvs":"NM_001003841.3:c.146=","protein":{"variant":{"spdi":{"deleted_sequence":"C","inserted_sequence":"C","position":48,"seq_id":"NP_001003841.1"}}},"protein_product":{"refseq":"NP_001003841.1"},"refseq":"NM_001003841.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]}],"strand":"+","symbol":"SLC6A19"},"hg19":{"end":1201911,"start":1201911},"ref":"G","rsid":"rs796064507","vartype":"snv"},"hg19":{"end":1201911,"start":1201911},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"5172","position":"202"},"cds":{"length":"1905","position":"146"},"effect":"missense_variant","feature_id":"NM_001003841.2","feature_type":"transcript","gene_id":"SLC6A19","genename":"SLC6A19","hgvs_c":"c.146G>A","hgvs_p":"p.Cys49Tyr","protein":{"length":"634","position":"49"},"putative_impact":"MODERATE","rank":"1","total":"12","transcript_biotype":"protein_coding"}},"vcf":{"alt":"A","position":"1201911","ref":"G"}}