{"_id":"chr17:g.62019103G>T","_version":2,"cadd":{"1000g":{"af":0.16,"afr":0.18,"amr":0.13,"asn":0.12,"eur":0.19},"_license":"http://bit.ly/2TIuab9","alt":"T","anc":"G","annotype":"CodingTranscript","bstatistic":259,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.575,"reprpc":0.031,"reprpcwk":0.213,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.079,"txflnk":0.0,"txwk":0.079,"znfrpts":0.016},"chrom":17,"consdetail":"synonymous","consequence":"SYNONYMOUS","consscore":5,"cpg":0.13,"dna":{"helt":0.91,"mgw":0.58,"prot":-1.42,"roll":7.23},"encode":{"exp":34.48,"h3k27ac":4.0,"h3k4me1":4.0,"h3k4me3":2.0,"nucleo":0.6,"occ":2,"p_val":{"comb":1.38,"ctcf":0.0,"dnas":2.15,"faire":0.0,"mycp":0.0,"polii":0.0},"sig":{"ctcf":0.02,"dnase":0.05,"faire":0.01,"myc":0.0,"polii":0.0}},"esp":{"af":0.175,"afr":0.133,"eur":0.196},"exon":"24/24","fitcons":0.722197,"gc":0.53,"gene":{"ccds_id":"CCDS45761.1","cds":{"cdna_pos":4616,"cds_pos":4539,"rel_cdna_pos":0.59,"rel_cds_pos":0.82},"feature_id":"ENST00000435607","gene_id":"ENSG00000007314","genename":"SCN4A","prot":{"domain":"ndomain","protpos":1513,"rel_prot_pos":0.82}},"gerp":{"n":3.9,"rs":2693.4,"rs_pval":0,"s":-0.348},"isderived":"TRUE","isknownvariant":"TRUE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":3189,"min_dist_tss":31176,"mutindex":91,"naa":"I","oaa":"I","phast_cons":{"mammalian":0.999,"primate":0.96,"vertebrate":0.999},"phred":8.437,"phylop":{"mammalian":0.096,"primate":-1.073,"vertebrate":0.402},"pos":62019103,"rawscore":0.641221,"ref":"G","segway":"R5","type":"SNV"},"chrom":"17","clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":98770,"alt":"T","chrom":"17","cytogenic":"17q23.3","gene":{"id":"106128904","symbol":"GH-LCR"},"hg19":{"end":62019103,"start":62019103},"hg38":{"end":63941743,"start":63941743},"hgvs":{"coding":"NM_000334.4:c.4539C>A","genomic":["NC_000017.10:g.62019103G>T","NC_000017.11:g.63941743G>T","NG_011699.1:g.36176C>A","NG_042788.1:g.24651G>T"],"protein":["NP_000325.4:p.(=)","NP_000325.4:p.Ile1513=","p.Ile1513Ile"]},"rcv":[{"accession":"RCV000078661","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"CN169374"},"name":"not specified","synonyms":["AllHighlyPenetrant"]},"last_evaluated":"2021-03-09","number_submitters":4,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, multiple submitters, no conflicts"},{"accession":"RCV000282735","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C0221055","mondo":"MONDO:0008195","omim":"168300","orphanet":"684"},"name":"Paramyotonia congenita of Von Eulenburg","synonyms":["PARALYSIS PERIODICA PARAMYOTONICA","Eulenburg disease","Myotonia congenita intermittens","Von Eulenburg paramyotonia congenita","Paramyotonia Congenita"]},"last_evaluated":"2018-01-12","number_submitters":1,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, single submitter"},{"accession":"RCV000289029","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C2931826","mondo":"MONDO:0018959","omim":"608390","orphanet":"99736"},"name":"Potassium-aggravated myotonia","synonyms":["MYOTONIA CONGENITA, ACETAZOLAMIDE-RESPONSIVE","MYOTONIA CONGENITA, ATYPICAL","SODIUM CHANNEL MUSCLE DISEASE"]},"last_evaluated":"2018-01-12","number_submitters":1,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, single submitter"},{"accession":"RCV000347637","clinical_significance":"Benign","conditions":{"identifiers":{"human_phenotype_ontology":"HP:0007215","medgen":"C0238357","mondo":"MONDO:0008224","omim":"170500","orphanet":"682"},"name":"Hyperkalemic periodic paralysis","synonyms":["Familial hyperkalemic periodic paralysis","Gamstorp disease"]},"last_evaluated":"2025-02-03","number_submitters":2,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, multiple submitters, no conflicts"},{"accession":"RCV000377718","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C3280112","mondo":"MONDO:0013620","omim":"614198","orphanet":"590"},"name":"Congenital myasthenic syndrome 16","synonyms":["Congenital myasthenic syndrome, acetazolamide-responsive"]},"last_evaluated":"2018-01-12","number_submitters":1,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, single submitter"},{"accession":"RCV000392374","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C2750061","mondo":"MONDO:0013234","omim":"613345","orphanet":"681"},"name":"Hypokalemic periodic paralysis, type 2 (HOKPP2)"},"last_evaluated":"2018-01-12","number_submitters":1,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, single submitter"},{"accession":"RCV001682760","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C3661900"},"name":"not provided","synonyms":["none provided","RECLASSIFIED - ADRA2C POLYMORPHISM","RECLASSIFIED - ADRB1 POLYMORPHISM"]},"last_evaluated":"2015-03-03","number_submitters":2,"origin":"germline","preferred_name":"NM_000334.4(SCN4A):c.4539C>A (p.Ile1513=)","review_status":"criteria provided, multiple submitters, no conflicts"}],"ref":"G","rsid":"rs56342400","type":"single nucleotide variant","variant_id":92863},"cosmic":{"_license":"http://bit.ly/2VMkY7R","alt":"A","chrom":"17","cosmic_id":"COSM148317","hg19":{"end":62019103,"start":62019103},"mut_freq":100.0,"mut_nt":"C>A","ref":"C","tumor_site":"stomach"},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"1000g":0.861,"alspac":0.814,"dbgap_popfreq":0.807,"estonian":0.821,"exac":0.836,"finrisk":0.855,"genome_dk":0.9,"gnomad":0.832,"gnomad_exomes":0.834,"goesp":0.825,"gonl":0.794,"korea1k":0.905,"korean":0.902,"mgp":0.811,"northernsweden":0.852,"qatari":0.773,"sgdp_prj":0.418,"siberian":0.455,"tommo":0.915,"topmed":0.835,"twinsuk":0.802,"vietnamese":0.883}},{"allele":"T","freq":{"1000g":0.139,"alspac":0.186,"dbgap_popfreq":0.193,"estonian":0.179,"exac":0.164,"finrisk":0.145,"genome_dk":0.1,"gnomad":0.168,"gnomad_exomes":0.166,"goesp":0.175,"gonl":0.206,"korea1k":0.095,"korean":0.098,"mgp":0.189,"northernsweden":0.148,"qatari":0.227,"sgdp_prj":0.582,"siberian":0.545,"tommo":0.085,"topmed":0.165,"twinsuk":0.198,"vietnamese":0.117}}],"alt":"T","chrom":"17","citations":[18414213,23757202,25741868],"dbsnp_build":156,"dbsnp_merges":{"date":"2010-08-16T13:01Z","rsid":"rs117146515","rv":132},"gene":{"geneid":6329,"is_pseudo":false,"name":"sodium voltage-gated channel alpha subunit 4","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"ATC","inserted_sequence":"ATC","position":4613,"seq_id":"NM_000334.4"},"hgvs":"NM_000334.4:c.4539=","protein":{"variant":{"spdi":{"deleted_sequence":"I","inserted_sequence":"I","position":1512,"seq_id":"NP_000325.4"}}},"protein_product":{"refseq":"NP_000325.4"},"refseq":"NM_000334.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]}],"strand":"-","symbol":"SCN4A"},"hg19":{"end":62019103,"start":62019103},"ref":"G","rsid":"rs56342400","vartype":"snv"},"emv":{"_license":"http://bit.ly/2RieoY1","egl_classification":"Benign","egl_classification_date":"07/05/2013","egl_protein":"p.I1513= | p.I1513=","egl_variant":"NM_000334.4:c.4539C>A","exon":"Ex24","gene":"SCN4A","hgvs":"NM_000334.4:c.4539C>A","variant_id":10806},"evs":{"_license":"http://bit.ly/2QAcvkh","allele_count":{"african_american":{"G":3819,"T":587},"all":{"G":10736,"T":2270},"european_american":{"G":6917,"T":1683}},"alt":"T","avg_sample_read":123,"chimp_allele":"A","chrom":17,"coding_dna_size":5511,"conservation":{"gerp":-0.3,"phast_cons":1.0},"dbsnp_version":129,"estimated_age_kyrs":{"aa":"246.8+/-255.3","ea":"304.6+/-307.0"},"filter_status":"PASS","function_gvs":"coding-synonymous","gene":{"accession":"NM_000334.4","symbol":"SCN4A"},"genotype_count":{"african_american":{"GG":1654,"TG":511,"TT":38},"all_genotype":{"GG":4425,"TG":1886,"TT":192},"european_american":{"GG":2771,"TG":1375,"TT":154}},"hg19":{"end":62019103,"start":62019103},"hg38":{"end":63941743,"start":63941743},"hgvs":{"coding":"c.4539C>A","protein":"p.(I1513=)"},"ma_fin_percent":{"african_american":13.3227,"all":17.4535,"european_american":19.5698},"on_illumina_human_exome_chip":"no","polyphen2":{"class":"u","score":"n"},"ref":"G","ref_base_ncbi":"G","rsid":"rs56342400"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":19855,"ac_adj":19843,"ac_afr":1357,"ac_amr":1606,"ac_eas":842,"ac_female":8588,"ac_fin":985,"ac_het":16443,"ac_hom":1700,"ac_male":11255,"ac_nfe":12711,"ac_oth":167,"ac_sas":2175},"af":0.164,"alleles":"T","alt":"T","an":{"an":121408,"an_adj":121082,"an_afr":10112,"an_amr":11572,"an_eas":8638,"an_female":53806,"an_fin":6614,"an_male":67276,"an_nfe":66734,"an_oth":902,"an_sas":16510},"baseqranksum":0.952,"chrom":17,"clippingranksum":-0.417,"culprit":"InbreedingCoeff","fs":1.127,"het":{"het_afr":1165,"het_amr":1382,"het_eas":742,"het_fin":829,"het_nfe":10343,"het_oth":133,"het_sas":1849},"hom":{"hom_afr":96,"hom_amr":112,"hom_eas":50,"hom_fin":78,"hom_nfe":1184,"hom_oth":17,"hom_sas":163},"inbreedingcoeff":0.0106,"mq":{"mq":59.63,"mq0":0,"mqranksum":0.11},"ncc":18,"pos":62019103,"qd":14.48,"readposranksum":0.489,"ref":"G","type":"snp","vqslod":4.48},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":17137,"ac_adj":17125,"ac_afr":1174,"ac_amr":1551,"ac_eas":782,"ac_female":7128,"ac_fin":985,"ac_het":14227,"ac_hom":1449,"ac_male":9997,"ac_nfe":10344,"ac_oth":130,"ac_sas":2159},"af":0.161,"alleles":"T","alt":"T","an":{"an":106206,"an_adj":105892,"an_afr":8774,"an_amr":11210,"an_eas":7854,"an_female":45566,"an_fin":6614,"an_male":60326,"an_nfe":54342,"an_oth":692,"an_sas":16406},"baseqranksum":0.952,"chrom":17,"clippingranksum":-0.417,"culprit":"InbreedingCoeff","fs":1.127,"het":{"het_afr":1006,"het_amr":1333,"het_eas":682,"het_fin":829,"het_nfe":8440,"het_oth":102,"het_sas":1835},"hom":{"hom_afr":84,"hom_amr":109,"hom_eas":50,"hom_fin":78,"hom_nfe":952,"hom_oth":14,"hom_sas":162},"inbreedingcoeff":0.0106,"mq":{"mq":59.63,"mq0":0,"mqranksum":0.11},"ncc":18,"pos":62019103,"qd":14.48,"readposranksum":0.489,"ref":"G","type":"snp","vqslod":4.48},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":41536,"ac_afr":2135,"ac_afr_female":1285,"ac_afr_male":850,"ac_amr":5037,"ac_amr_female":2917,"ac_amr_male":2120,"ac_asj":2120,"ac_asj_female":999,"ac_asj_male":1121,"ac_eas":1773,"ac_eas_female":869,"ac_eas_jpn":10,"ac_eas_kor":391,"ac_eas_male":904,"ac_eas_oea":1372,"ac_female":18733,"ac_fin":3431,"ac_fin_female":1642,"ac_fin_male":1789,"ac_male":22803,"ac_nfe":21904,"ac_nfe_bgr":557,"ac_nfe_est":42,"ac_nfe_female":9554,"ac_nfe_male":12350,"ac_nfe_nwe":8040,"ac_nfe_onf":6128,"ac_nfe_seu":2406,"ac_nfe_swe":4731,"ac_oth":1046,"ac_oth_female":506,"ac_oth_male":540,"ac_sas":4090,"ac_sas_female":961,"ac_sas_male":3129},"af":{"af":0.165523,"af_afr":0.133438,"af_afr_female":0.130909,"af_afr_male":0.137451,"af_amr":0.145637,"af_amr_female":0.14395,"af_amr_male":0.148024,"af_asj":0.210443,"af_asj_female":0.203961,"af_asj_male":0.216577,"af_eas":0.0965581,"af_eas_female":0.0933405,"af_eas_jpn":0.0657895,"af_eas_kor":0.10241,"af_eas_male":0.0998674,"af_eas_oea":0.0953307,"af_female":0.162683,"af_fin":0.158549,"af_fin_female":0.158372,"af_fin_male":0.158712,"af_male":0.167931,"af_nfe":0.192892,"af_nfe_bgr":0.208927,"af_nfe_est":0.173554,"af_nfe_female":0.190881,"af_nfe_male":0.194476,"af_nfe_nwe":0.190684,"af_nfe_onf":0.198381,"af_nfe_seu":0.209472,"af_nfe_swe":0.181209,"af_oth":0.171363,"af_oth_female":0.174603,"af_oth_male":0.168434,"af_sas":0.13359,"af_sas_female":0.127386,"af_sas_male":0.135619},"alleles":"T","alt":"T","an":{"an":250938,"an_afr":16000,"an_afr_female":9816,"an_afr_male":6184,"an_amr":34586,"an_amr_female":20264,"an_amr_male":14322,"an_asj":10074,"an_asj_female":4898,"an_asj_male":5176,"an_eas":18362,"an_eas_female":9310,"an_eas_jpn":152,"an_eas_kor":3818,"an_eas_male":9052,"an_eas_oea":14392,"an_female":115150,"an_fin":21640,"an_fin_female":10368,"an_fin_male":11272,"an_male":135788,"an_nfe":113556,"an_nfe_bgr":2666,"an_nfe_est":242,"an_nfe_female":50052,"an_nfe_male":63504,"an_nfe_nwe":42164,"an_nfe_onf":30890,"an_nfe_seu":11486,"an_nfe_swe":26108,"an_oth":6104,"an_oth_female":2898,"an_oth_male":3206,"an_sas":30616,"an_sas_female":7544,"an_sas_male":23072},"baseqranksum":1.66,"chrom":"17","clippingranksum":0.001,"dp":15713516,"fs":0.0,"hom":{"hom":3558,"hom_afr":154,"hom_afr_female":84,"hom_afr_male":70,"hom_amr":367,"hom_amr_female":217,"hom_amr_male":150,"hom_asj":202,"hom_asj_female":92,"hom_asj_male":110,"hom_eas":84,"hom_eas_female":37,"hom_eas_jpn":0,"hom_eas_kor":24,"hom_eas_male":47,"hom_eas_oea":60,"hom_female":1551,"hom_fin":279,"hom_fin_female":137,"hom_fin_male":142,"hom_male":2007,"hom_nfe":2083,"hom_nfe_bgr":59,"hom_nfe_est":2,"hom_nfe_female":887,"hom_nfe_male":1196,"hom_nfe_nwe":762,"hom_nfe_onf":603,"hom_nfe_seu":235,"hom_nfe_swe":422,"hom_oth":87,"hom_oth_female":38,"hom_oth_male":49,"hom_sas":302,"hom_sas_female":59,"hom_sas_male":243},"inbreedingcoeff":0.0081,"mq":{"mq":59.38,"mqranksum":0.163},"pab_max":1.0,"pos":62019103,"qd":15.06,"readposranksum":0.348,"ref":"G","rf":0.939363,"rsid":"rs56342400","sor":0.713,"type":"snp","vqslod":5.88,"vqsr_culprit":"FS"},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":5134,"ac_afr":1171,"ac_afr_female":488,"ac_afr_male":683,"ac_amr":115,"ac_amr_female":56,"ac_amr_male":59,"ac_asj":55,"ac_asj_female":12,"ac_asj_male":43,"ac_eas":144,"ac_eas_female":51,"ac_eas_male":93,"ac_female":2265,"ac_fin":542,"ac_fin_female":287,"ac_fin_male":255,"ac_male":2869,"ac_nfe":2908,"ac_nfe_est":825,"ac_nfe_female":1282,"ac_nfe_male":1626,"ac_nfe_nwe":1616,"ac_nfe_onf":443,"ac_nfe_seu":24,"ac_oth":199,"ac_oth_female":89,"ac_oth_male":110},"af":{"af":0.163973,"af_afr":0.134722,"af_afr_female":0.133043,"af_afr_male":0.135947,"af_amr":0.135613,"af_amr_female":0.135266,"af_amr_male":0.135945,"af_asj":0.189655,"af_asj_female":0.15,"af_asj_male":0.204762,"af_eas":0.0929032,"af_eas_female":0.0951493,"af_eas_male":0.091716,"af_female":0.163208,"af_fin":0.156286,"af_fin_female":0.155809,"af_fin_male":0.156827,"af_male":0.164582,"af_nfe":0.189101,"af_nfe_est":0.180921,"af_nfe_female":0.189141,"af_nfe_male":0.18907,"af_nfe_nwe":0.188477,"af_nfe_onf":0.207203,"af_nfe_seu":0.226415,"af_oth":0.183579,"af_oth_female":0.158929,"af_oth_male":0.209924},"alleles":"T","alt":"T","an":{"an":31310,"an_afr":8692,"an_afr_female":3668,"an_afr_male":5024,"an_amr":848,"an_amr_female":414,"an_amr_male":434,"an_asj":290,"an_asj_female":80,"an_asj_male":210,"an_eas":1550,"an_eas_female":536,"an_eas_male":1014,"an_female":13878,"an_fin":3468,"an_fin_female":1842,"an_fin_male":1626,"an_male":17432,"an_nfe":15378,"an_nfe_est":4560,"an_nfe_female":6778,"an_nfe_male":8600,"an_nfe_nwe":8574,"an_nfe_onf":2138,"an_nfe_seu":106,"an_oth":1084,"an_oth_female":560,"an_oth_male":524},"baseqranksum":2.51,"chrom":"17","clippingranksum":-0.02,"dp":652228,"fs":0.0,"hom":{"hom":418,"hom_afr":75,"hom_afr_female":35,"hom_afr_male":40,"hom_amr":8,"hom_amr_female":4,"hom_amr_male":4,"hom_asj":3,"hom_asj_female":0,"hom_asj_male":3,"hom_eas":6,"hom_eas_female":2,"hom_eas_male":4,"hom_female":181,"hom_fin":50,"hom_fin_female":25,"hom_fin_male":25,"hom_male":237,"hom_nfe":257,"hom_nfe_est":67,"hom_nfe_female":111,"hom_nfe_male":146,"hom_nfe_nwe":142,"hom_nfe_onf":46,"hom_nfe_seu":2,"hom_oth":19,"hom_oth_female":4,"hom_oth_male":15},"inbreedingcoeff":0.0019,"mq":{"mq":60.0,"mqranksum":-0.027},"pab_max":1.0,"pos":62019103,"qd":14.63,"readposranksum":0.348,"ref":"G","rf":0.970717,"rsid":"rs56342400","sor":0.683,"type":"snp","vqslod":21.29,"vqsr_culprit":"MQ"},"hg19":{"end":62019103,"start":62019103},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"7805","position":"4616"},"cds":{"length":"5511","position":"4539"},"effect":"synonymous_variant","feature_id":"NM_000334.4","feature_type":"transcript","gene_id":"SCN4A","genename":"SCN4A","hgvs_c":"c.4539C>A","hgvs_p":"p.Ile1513Ile","protein":{"length":"1836","position":"1513"},"putative_impact":"LOW","rank":"24","total":"24","transcript_biotype":"protein_coding"}},"vcf":{"alt":"T","position":"62019103","ref":"G"},"wellderly":{"_license":"http://bit.ly/2VE6gj7","alleles":[{"allele":"T","freq":0.198419},{"allele":"G","freq":0.801581}],"alt":"T","chrom":"17","genotypes":[{"count":771,"freq":0.6414309484193012,"genotype":"G/G"},{"count":385,"freq":0.32029950083194675,"genotype":"G/T"},{"count":46,"freq":0.03826955074875208,"genotype":"T/T"}],"hg19":{"end":62019103,"start":62019103},"pos":"62019103","ref":"G","vartype":"snp"}}