{"_id":"chr12:g.102855200T>C","_version":2,"chrom":"12","clingen":{"caid":"CA6748886"},"clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":1143129,"alt":"C","chrom":"12","cytogenic":"12q23.2","gene":{"id":"5053","symbol":"PAH"},"hg19":{"end":103248978,"start":103248978},"hg38":{"end":102855200,"start":102855200},"hgvs":{"coding":["NM_000277.3:c.642A>G","NM_001354304.2:c.642A>G"],"genomic":["NC_000012.11:g.103248978T>C","NC_000012.12:g.102855200T>C","NG_008690.2:g.108211A>G"],"protein":["NP_000268.1:p.Glu214=","NP_001341233.1:p.Glu214="]},"rcv":{"accession":"RCV001500105","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":"2024-08-28","number_submitters":1,"origin":"germline","preferred_name":"NM_000277.3(PAH):c.642A>G (p.Glu214=)","review_status":"criteria provided, single submitter"},"ref":"T","rsid":"rs373782868","type":"single nucleotide variant","variant_id":1157163},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"T","freq":{"dbgap_popfreq":1.0,"exac":1.0,"gnomad":1.0,"gnomad_exomes":1.0,"goesp":1.0,"topmed":1.0}},{"allele":"C","freq":{"dbgap_popfreq":0.0,"exac":0.0,"gnomad":0.0,"gnomad_exomes":0.0,"goesp":0.0,"topmed":0.0}}],"alt":"C","chrom":"12","dbsnp_build":156,"gene":{"geneid":5053,"is_pseudo":false,"name":"phenylalanine hydroxylase","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":753,"seq_id":"NM_000277.3"},"hgvs":"NM_000277.3:c.642=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":213,"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":"GAA","inserted_sequence":"GAA","position":981,"seq_id":"NM_001354304.2"},"hgvs":"NM_001354304.2:c.642=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":213,"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":"GAA","inserted_sequence":"GAA","position":753,"seq_id":"XM_017019370.2"},"hgvs":"XM_017019370.2:c.642=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":213,"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"},"hg38":{"end":102855200,"start":102855200},"ref":"T","rsid":"rs373782868","vartype":"snv"},"evs":{"_license":"http://bit.ly/2QAcvkh","allele_count":{"african_american":{"C":1,"T":4405},"all":{"C":1,"T":13005},"european_american":{"C":0,"T":8600}},"alt":"C","avg_sample_read":131,"chimp_allele":"T","chrom":12,"coding_dna_size":1359,"conservation":{"gerp":4.5,"phast_cons":1.0},"dbsnp_version":138,"estimated_age_kyrs":{"aa":"2.1+/-5.4"},"filter_status":"PASS","function_gvs":"coding-synonymous","gene":{"accession":"NM_000277.1","symbol":"PAH"},"genotype_count":{"african_american":{"CC":0,"CT":1,"TT":2202},"all_genotype":{"CC":0,"CT":1,"TT":6502},"european_american":{"CC":0,"CT":0,"TT":4300}},"hg19":{"end":103248978,"start":103248978},"hg38":{"end":102855200,"start":102855200},"hgvs":{"coding":"c.642A>G","protein":"p.(E214=)"},"ma_fin_percent":{"african_american":0.0227,"all":0.0077,"european_american":0.0},"on_illumina_human_exome_chip":"no","polyphen2":{"class":"u","score":"n"},"ref":"T","ref_base_ncbi":"T","rsid":"rs373782868"},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":4,"ac_afr":4,"ac_afr_female":3,"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_jpn":0,"ac_eas_kor":0,"ac_eas_male":0,"ac_eas_oea":0,"ac_female":3,"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":0.000015916,"af_afr":0.000246063,"af_afr_female":0.000297915,"af_afr_male":0.000161655,"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":0.000025974,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":7.36269e-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":"C","alt":"C","an":{"an":251320,"an_afr":16256,"an_afr_female":10070,"an_afr_male":6186,"an_amr":34590,"an_amr_female":20270,"an_amr_male":14320,"an_asj":10078,"an_asj_female":4898,"an_asj_male":5180,"an_eas":18386,"an_eas_female":9328,"an_eas_jpn":152,"an_eas_kor":3810,"an_eas_male":9058,"an_eas_oea":14424,"an_female":115500,"an_fin":21648,"an_fin_female":10374,"an_fin_male":11274,"an_male":135820,"an_nfe":113618,"an_nfe_bgr":2668,"an_nfe_est":242,"an_nfe_female":50096,"an_nfe_male":63522,"an_nfe_nwe":42132,"an_nfe_onf":30952,"an_nfe_seu":11496,"an_nfe_swe":26128,"an_oth":6128,"an_oth_female":2920,"an_oth_male":3208,"an_sas":30616,"an_sas_female":7544,"an_sas_male":23072},"baseqranksum":2.9,"chrom":"12","clippingranksum":-0.973,"dp":10378194,"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_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":59.68,"mqranksum":0.01},"pab_max":0.576431,"pos":102855200,"qd":13.59,"readposranksum":0.346,"ref":"T","rf":0.92965,"rsid":"rs373782868","sor":0.654,"type":"snp","vqslod":4.37,"vqsr_culprit":"FS"},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":3,"ac_afr":3,"ac_afr_xx":1,"ac_afr_xy":2,"ac_ami":0,"ac_ami_xx":0,"ac_ami_xy":0,"ac_amr":0,"ac_amr_xx":0,"ac_amr_xy":0,"ac_asj":0,"ac_asj_xx":0,"ac_asj_xy":0,"ac_eas":0,"ac_eas_xx":0,"ac_eas_xy":0,"ac_fin":0,"ac_fin_xx":0,"ac_fin_xy":0,"ac_mid":0,"ac_mid_xx":0,"ac_mid_xy":0,"ac_nfe":0,"ac_nfe_xx":0,"ac_nfe_xy":0,"ac_oth":0,"ac_oth_xx":0,"ac_oth_xy":0,"ac_sas":0,"ac_sas_xx":0,"ac_sas_xy":0,"ac_xx":1,"ac_xy":2},"af":{"af":0.0000197145,"af_afr":0.0000724148,"af_afr_xx":0.0000451671,"af_afr_xy":0.000103691,"af_ami":0.0,"af_ami_xx":0.0,"af_ami_xy":0.0,"af_amr":0.0,"af_amr_xx":0.0,"af_amr_xy":0.0,"af_asj":0.0,"af_asj_xx":0.0,"af_asj_xy":0.0,"af_eas":0.0,"af_eas_xx":0.0,"af_eas_xy":0.0,"af_fin":0.0,"af_fin_xx":0.0,"af_fin_xy":0.0,"af_mid":0.0,"af_mid_xx":0.0,"af_mid_xy":0.0,"af_nfe":0.0,"af_nfe_xx":0.0,"af_nfe_xy":0.0,"af_oth":0.0,"af_oth_xx":0.0,"af_oth_xy":0.0,"af_sas":0.0,"af_sas_xx":0.0,"af_sas_xy":0.0,"af_xx":0.0000128488,"af_xy":0.000026902},"alleles":"C","alt":"C","an":{"an":152172,"an_afr":41428,"an_afr_xx":22140,"an_afr_xy":19288,"an_ami":912,"an_ami_xx":470,"an_ami_xy":442,"an_amr":15276,"an_amr_xx":6786,"an_amr_xy":8490,"an_asj":3472,"an_asj_xx":1868,"an_asj_xy":1604,"an_eas":5204,"an_eas_xx":2280,"an_eas_xy":2924,"an_fin":10624,"an_fin_xx":2574,"an_fin_xy":8050,"an_mid":316,"an_mid_xx":164,"an_mid_xy":152,"an_nfe":68024,"an_nfe_xx":39348,"an_nfe_xy":28676,"an_oth":2090,"an_oth_xx":1032,"an_oth_xy":1058,"an_sas":4826,"an_sas_xx":1166,"an_sas_xy":3660,"an_xx":77828,"an_xy":74344},"as_fs":2.60061,"as_mq":{"as_mq":60.0,"as_mqranksum":-0.258},"as_pab_max":1.0,"as_qd":12.21,"as_readposranksum":0.31,"as_sor":0.790722,"as_vqslod":5.7314,"chrom":"12","hom":{"hom":0,"hom_afr":0,"hom_afr_xx":0,"hom_afr_xy":0,"hom_ami":0,"hom_ami_xx":0,"hom_ami_xy":0,"hom_amr":0,"hom_amr_xx":0,"hom_amr_xy":0,"hom_asj":0,"hom_asj_xx":0,"hom_asj_xy":0,"hom_eas":0,"hom_eas_xx":0,"hom_eas_xy":0,"hom_fin":0,"hom_fin_xx":0,"hom_fin_xy":0,"hom_mid":0,"hom_mid_xx":0,"hom_mid_xy":0,"hom_nfe":0,"hom_nfe_xx":0,"hom_nfe_xy":0,"hom_oth":0,"hom_oth_xx":0,"hom_oth_xy":0,"hom_sas":0,"hom_sas_xx":0,"hom_sas_xy":0,"hom_xx":0,"hom_xy":0},"inbreedingcoeff":-0.0000197887,"pos":102855200,"ref":"T","rsid":"rs373782868","type":"snp"},"hg38":{"end":102855200,"start":102855200},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"2681","position":"1115"},"cds":{"length":"1359","position":"642"},"effect":"synonymous_variant","feature_id":"NM_000277.1","feature_type":"transcript","gene_id":"PAH","genename":"PAH","hgvs_c":"c.642A>G","hgvs_p":"p.Glu214Glu","protein":{"length":"452","position":"214"},"putative_impact":"LOW","rank":"6","total":"13","transcript_biotype":"protein_coding"}},"vcf":{"alt":"C","position":"102855200","ref":"T"}}