{"_id":"chr12:g.103248918C>T","_version":2,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"T","anc":"C","annotype":"CodingTranscript","bstatistic":809,"chmm":{"bivflnk":0.0,"enh":0.008,"enhbiv":0.0,"het":0.031,"quies":0.787,"reprpc":0.008,"reprpcwk":0.126,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.008,"txflnk":0.0,"txwk":0.024,"znfrpts":0.0},"chrom":12,"consdetail":"synonymous","consequence":"SYNONYMOUS","consscore":5,"cpg":0.01,"dna":{"helt":1.29,"mgw":0.62,"prot":-2.97,"roll":1.2},"dst2splice":5,"dst2spltype":"DONOR","encode":{"exp":9.25,"h3k27ac":5.0,"h3k4me1":3.0,"h3k4me3":4.0,"nucleo":2.7},"exon":"6/13","fitcons":0.65045,"gc":0.5,"gene":{"ccds_id":"CCDS9092.1","cds":{"cdna_pos":1175,"cds_pos":702,"rel_cdna_pos":0.29,"rel_cds_pos":0.52},"feature_id":"ENST00000553106","gene_id":"ENSG00000171759","genename":"PAH","prot":{"domain":"ndomain","protpos":234,"rel_prot_pos":0.52}},"gerp":{"n":5.17,"rs":683.5,"rs_pval":2.62852e-107,"s":0.213},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":140,"min_dist_tss":62080,"mutindex":10,"naa":"L","oaa":"L","phast_cons":{"mammalian":0.997,"primate":0.647,"vertebrate":0.999},"phred":11.7,"phylop":{"mammalian":0.174,"primate":0.645,"vertebrate":0.262},"pos":103248918,"rawscore":1.190688,"ref":"C","segway":"R2","type":"SNV"},"chrom":"12","clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":1572387,"alt":"T","chrom":"12","cytogenic":"12q23.2","gene":{"id":"5053","symbol":"PAH"},"hg19":{"end":103248918,"start":103248918},"hg38":{"end":102855140,"start":102855140},"hgvs":{"coding":["NM_000277.3:c.702G>A","NM_001354304.2:c.702G>A"],"genomic":["NC_000012.11:g.103248918C>T","NC_000012.12:g.102855140C>T","NG_008690.2:g.108271G>A"],"protein":["NP_000268.1:p.Leu234=","NP_001341233.1:p.Leu234="]},"rcv":{"accession":"RCV002219138","clinical_significance":"Likely benign","conditions":{"identifiers":{"medgen":"C0031485","mondo":"MONDO:0009861","omim":"261600","orphanet":"716"},"name":"Phenylketonuria (PKU)","synonyms":["FOLLING DISEASE","OLIGOPHRENIA PHENYLPYRUVICA","Phenylketonurias"]},"last_evaluated":"2022-03-24","number_submitters":1,"origin":"germline","preferred_name":"NM_000277.3(PAH):c.702G>A (p.Leu234=)","review_status":"criteria provided, single submitter"},"ref":"C","rsid":"rs993558609","type":"single nucleotide variant","variant_id":1571594},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"C","freq":{"dbgap_popfreq":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"T","freq":{"dbgap_popfreq":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"T","chrom":"12","dbsnp_build":156,"gene":{"geneid":5053,"is_pseudo":false,"name":"phenylalanine hydroxylase","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"CTG","inserted_sequence":"CTG","position":813,"seq_id":"NM_000277.3"},"hgvs":"NM_000277.3:c.702=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":233,"seq_id":"NP_000268.1"}}},"protein_product":{"refseq":"NP_000268.1"},"refseq":"NM_000277.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"CTG","inserted_sequence":"CTG","position":1041,"seq_id":"NM_001354304.2"},"hgvs":"NM_001354304.2:c.702=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":233,"seq_id":"NP_001341233.1"}}},"protein_product":{"refseq":"NP_001341233.1"},"refseq":"NM_001354304.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"CTG","inserted_sequence":"CTG","position":813,"seq_id":"XM_017019370.2"},"hgvs":"XM_017019370.2:c.702=","protein":{"variant":{"spdi":{"deleted_sequence":"L","inserted_sequence":"L","position":233,"seq_id":"XP_016874859.1"}}},"protein_product":{"refseq":"XP_016874859.1"},"refseq":"XM_017019370.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]}],"strand":"-","symbol":"PAH"},"hg19":{"end":103248918,"start":103248918},"ref":"C","rsid":"rs993558609","vartype":"snv"},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":1,"ac_afr":1,"ac_afr_female":0,"ac_afr_male":1,"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_male":0,"ac_female":0,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":1,"ac_nfe":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_oth":0,"ac_oth_female":0,"ac_oth_male":0},"af":{"af":0.000031837,"af_afr":0.000114758,"af_afr_female":0.0,"af_afr_male":0.000198728,"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_male":0.0,"af_female":0.0,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":0.0000572213,"af_nfe":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_oth":0.0,"af_oth_female":0.0,"af_oth_male":0.0},"alleles":"T","alt":"T","an":{"an":31410,"an_afr":8714,"an_afr_female":3682,"an_afr_male":5032,"an_amr":848,"an_amr_female":414,"an_amr_male":434,"an_asj":290,"an_asj_female":80,"an_asj_male":210,"an_eas":1560,"an_eas_female":538,"an_eas_male":1022,"an_female":13934,"an_fin":3476,"an_fin_female":1846,"an_fin_male":1630,"an_male":17476,"an_nfe":15434,"an_nfe_est":4592,"an_nfe_female":6812,"an_nfe_male":8622,"an_nfe_nwe":8598,"an_nfe_onf":2138,"an_nfe_seu":106,"an_oth":1088,"an_oth_female":562,"an_oth_male":526},"baseqranksum":-1.65,"chrom":"12","clippingranksum":-0.025,"dp":679473,"fs":0.0,"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_male":0,"hom_female":0,"hom_fin":0,"hom_fin_female":0,"hom_fin_male":0,"hom_male":0,"hom_nfe":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_oth":0,"hom_oth_female":0,"hom_oth_male":0},"inbreedingcoeff":0.0001,"mq":{"mq":60.0,"mqranksum":-0.133},"pab_max":0.511376,"pos":103248918,"qd":9.17,"readposranksum":-0.527,"ref":"C","rf":0.873821,"rsid":"rs993558609","sor":0.765,"type":"snp","vqslod":13.25,"vqsr_culprit":"MQ"},"hg19":{"end":103248918,"start":103248918},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"2681","position":"1175"},"cds":{"length":"1359","position":"702"},"effect":"synonymous_variant","feature_id":"NM_000277.1","feature_type":"transcript","gene_id":"PAH","genename":"PAH","hgvs_c":"c.702G>A","hgvs_p":"p.Leu234Leu","protein":{"length":"452","position":"234"},"putative_impact":"LOW","rank":"6","total":"13","transcript_biotype":"protein_coding"}},"vcf":{"alt":"T","position":"103248918","ref":"C"}}