{"_id":"chr13:g.77566230C>T","_version":2,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"T","anc":"C","annotype":["CodingTranscript","RegulatoryFeature","Intergenic","Intergenic"],"bstatistic":401,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.0,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.976,"tssaflnk":0.008,"tssbiv":0.0,"tx":0.0,"txflnk":0.008,"txwk":0.0,"znfrpts":0.0},"chrom":13,"consdetail":["synonymous","regulatory","downstream","downstream"],"consequence":["SYNONYMOUS","REGULATORY","DOWNSTREAM","DOWNSTREAM"],"consscore":[5,4,1,1],"cpg":0.29,"dna":{"helt":1.75,"mgw":0.22,"prot":-2.67,"roll":0.37},"encode":{"exp":10.13,"h3k27ac":27.16,"h3k4me1":4.0,"h3k4me3":137.0,"nucleo":0.0,"occ":2,"p_val":{"comb":16.0,"ctcf":1.51,"dnas":14.8,"faire":3.89,"mycp":4.78,"polii":16.0},"sig":{"ctcf":0.1,"dnase":0.39,"faire":0.03,"myc":0.15,"polii":0.44}},"exon":"1/4","fitcons":0.007796,"gc":0.75,"gene":[{"ccds_id":"CCDS9456.1","cds":{"cdna_pos":1436,"cds_pos":144,"rel_cdna_pos":0.35,"rel_cds_pos":0.12},"feature_id":"ENST00000377453","gene_id":"ENSG00000102805","genename":"CLN5","prot":{"protpos":48,"rel_prot_pos":0.12}},{"feature_id":"ENSR00000056063"},{"feature_id":"ENST00000485797","gene_id":"ENSG00000005812","genename":"FBXL3"},{"feature_id":"ENST00000436565","gene_id":"ENSG00000228002","genename":"DHX9P1"}],"gerp":{"n":4.06,"s":1.07},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":511,"min_dist_tss":22,"mutindex":-2,"naa":"S","oaa":"S","phast_cons":{"mammalian":0.037,"primate":0.025,"vertebrate":0.016},"phred":11.34,"phylop":{"mammalian":0.33,"primate":0.451,"vertebrate":0.394},"pos":77566230,"rawscore":1.123694,"ref":"C","segway":"TSS","tf":{"bs":61,"bs_peaks":126,"bs_peaks_max":289.2916},"type":"SNV"},"chrom":"13","clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":140496,"alt":"T","chrom":"13","cytogenic":"13q22.3","gene":{"id":"1203","symbol":"CLN5"},"hg19":{"end":77566230,"start":77566230},"hg38":{"end":76992095,"start":76992095},"hgvs":{"coding":["LRG_692t1:c.144C>T","NM_001366624.2:c.-4C>T","NM_006493.4:c.-4C>T"],"genomic":["LRG_692:g.5172C>T","NC_000013.10:g.77566230C>T","NC_000013.11:g.76992095C>T","NG_009064.1:g.5172C>T"]},"rcv":[{"accession":"RCV000124330","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"CN169374"},"name":"not specified","synonyms":["AllHighlyPenetrant"]},"last_evaluated":"2013-05-29","number_submitters":1,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, single submitter"},{"accession":"RCV000360042","clinical_significance":"Uncertain significance","conditions":{"identifiers":{"medgen":"CN239251"},"name":"Neuronal Ceroid-Lipofuscinosis, Dominant/Recessive"},"last_evaluated":"2016-06-14","number_submitters":1,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, single submitter"},{"accession":"RCV000711258","clinical_significance":"Likely benign","conditions":{"identifiers":{"medgen":"C3661900"},"name":"not provided","synonyms":["none provided","RECLASSIFIED - ADRA2C POLYMORPHISM","RECLASSIFIED - ADRB1 POLYMORPHISM"]},"last_evaluated":"2018-03-05","number_submitters":1,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, single submitter"},{"accession":"RCV001081887","clinical_significance":"Benign","conditions":{"identifiers":{"medgen":"C0027877","mondo":"MONDO:0016295","omim":"PS256730","orphanet":"79263"},"name":"Neuronal ceroid lipofuscinosis","synonyms":["Ceroid storage disease"]},"last_evaluated":"2025-01-13","number_submitters":1,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, single submitter"},{"accession":"RCV001111457","clinical_significance":"Conflicting interpretations of pathogenicity","conditions":{"identifiers":{"medgen":"C1850442","mondo":"MONDO:0009745","omim":"256731","orphanet":"228360"},"name":"Neuronal ceroid lipofuscinosis 5 (CLN5)","synonyms":["CEROID LIPOFUSCINOSIS, NEURONAL, 5, VARIABLE AGE AT ONSET","Neuronal ceroid lipofuscinosis Finnish variant","NEURONAL CEROID LIPOFUSCINOSIS, LATE INFANTILE, FINNISH VARIANT","CLN5-Related Neuronal Ceroid-Lipofuscinosis"]},"last_evaluated":"2021-05-18","number_submitters":3,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, conflicting interpretations"},{"accession":"RCV002316354","clinical_significance":"Likely benign","conditions":{"identifiers":{"medgen":"C0950123","mesh":"D030342"},"name":"Inborn genetic diseases"},"last_evaluated":"2016-09-01","number_submitters":1,"origin":"germline","preferred_name":"NM_006493.4(CLN5):c.-4C>T","review_status":"criteria provided, single submitter"}],"ref":"C","rsid":"rs587780896","type":"single nucleotide variant","variant_id":136793},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"C","freq":{"dbgap_popfreq":0.999,"exac":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"T","freq":{"dbgap_popfreq":0.001,"exac":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"T","chrom":"13","dbsnp_build":156,"gene":{"geneid":1203,"is_pseudo":false,"name":"CLN5 intracellular trafficking protein","rnas":[{"hgvs":"NM_001366624.2:c.-4=","protein_product":{"refseq":"NP_001353553.1"},"refseq":"NM_001366624.2","so":[{"accession":"SO:0001623","name":"5_prime_UTR_variant"}]},{"hgvs":"NM_006493.4:c.-4=","protein_product":{"refseq":"NP_006484.2"},"refseq":"NM_006493.4","so":[{"accession":"SO:0001623","name":"5_prime_UTR_variant"}]}],"strand":"+","symbol":"CLN5"},"hg19":{"end":77566230,"start":77566230},"ref":"C","rsid":"rs587780896","vartype":"snv"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":24,"ac_adj":24,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":8,"ac_fin":0,"ac_het":24,"ac_hom":0,"ac_male":16,"ac_nfe":16,"ac_oth":0,"ac_sas":8},"af":0.0001994,"alleles":"T","alt":"T","an":{"an":120358,"an_adj":102946,"an_afr":7064,"an_amr":10594,"an_eas":7896,"an_female":42678,"an_fin":4990,"an_male":60268,"an_nfe":56170,"an_oth":712,"an_sas":15520},"baseqranksum":-2.114,"chrom":13,"clippingranksum":0.015,"culprit":"InbreedingCoeff","fs":0.522,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":16,"het_oth":0,"het_sas":8},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0057,"mq":{"mq":59.72,"mq0":0,"mqranksum":-0.037},"ncc":1212,"pos":77566230,"qd":12.17,"readposranksum":0.656,"ref":"C","type":"snp","vqslod":1.78},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":22,"ac_adj":22,"ac_afr":0,"ac_amr":0,"ac_eas":0,"ac_female":7,"ac_fin":0,"ac_het":22,"ac_hom":0,"ac_male":15,"ac_nfe":14,"ac_oth":0,"ac_sas":8},"af":0.0002079,"alleles":"T","alt":"T","an":{"an":105800,"an_adj":93036,"an_afr":6326,"an_amr":10364,"an_eas":7382,"an_female":38564,"an_fin":4990,"an_male":54472,"an_nfe":47954,"an_oth":576,"an_sas":15444},"baseqranksum":-2.114,"chrom":13,"clippingranksum":0.015,"culprit":"InbreedingCoeff","fs":0.522,"het":{"het_afr":0,"het_amr":0,"het_eas":0,"het_fin":0,"het_nfe":14,"het_oth":0,"het_sas":8},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0057,"mq":{"mq":59.72,"mq0":0,"mqranksum":-0.037},"ncc":1212,"pos":77566230,"qd":12.17,"readposranksum":0.656,"ref":"C","type":"snp","vqslod":1.78},"geno2mp":{"_license":"http://bit.ly/2QyGCIN","hpo_count":6},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":71,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":0,"ac_amr_female":0,"ac_amr_male":0,"ac_asj":50,"ac_asj_female":24,"ac_asj_male":26,"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":30,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":41,"ac_nfe":5,"ac_nfe_bgr":0,"ac_nfe_est":0,"ac_nfe_female":0,"ac_nfe_male":5,"ac_nfe_nwe":0,"ac_nfe_onf":3,"ac_nfe_seu":2,"ac_nfe_swe":0,"ac_oth":1,"ac_oth_female":1,"ac_oth_male":0,"ac_sas":15,"ac_sas_female":5,"ac_sas_male":10},"af":{"af":0.00030229,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0,"af_amr_female":0.0,"af_amr_male":0.0,"af_asj":0.0051557,"af_asj_female":0.00512821,"af_asj_male":0.00518135,"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":0.000284382,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":0.000316891,"af_nfe":0.0000489505,"af_nfe_bgr":0.0,"af_nfe_est":0.0,"af_nfe_female":0.0,"af_nfe_male":0.000085147,"af_nfe_nwe":0.0,"af_nfe_onf":0.000110359,"af_nfe_seu":0.000185357,"af_nfe_swe":0.0,"af_oth":0.000172951,"af_oth_female":0.000370096,"af_oth_male":0.0,"af_sas":0.000493876,"af_sas_female":0.000670961,"af_sas_male":0.0004363},"alleles":"T","alt":"T","an":{"an":234874,"an_afr":14196,"an_afr_female":8406,"an_afr_male":5790,"an_amr":34150,"an_amr_female":20020,"an_amr_male":14130,"an_asj":9698,"an_asj_female":4680,"an_asj_male":5018,"an_eas":17644,"an_eas_female":8870,"an_eas_jpn":36,"an_eas_kor":3814,"an_eas_male":8774,"an_eas_oea":13794,"an_female":105492,"an_fin":20888,"an_fin_female":9940,"an_fin_male":10948,"an_male":129382,"an_nfe":102144,"an_nfe_bgr":2440,"an_nfe_est":188,"an_nfe_female":43422,"an_nfe_male":58722,"an_nfe_nwe":35930,"an_nfe_onf":27184,"an_nfe_seu":10790,"an_nfe_swe":25612,"an_oth":5782,"an_oth_female":2702,"an_oth_male":3080,"an_sas":30372,"an_sas_female":7452,"an_sas_male":22920},"baseqranksum":-0.735,"chrom":"13","clippingranksum":0.213,"dp":6994264,"fs":1.101,"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":0.0065,"mq":{"mq":59.34,"mqranksum":0.372},"pab_max":1.0,"pos":77566230,"qd":12.15,"readposranksum":0.662,"ref":"C","rf":0.939363,"rsid":"rs587780896","sor":0.661,"type":"snp","vqslod":2.72,"vqsr_culprit":"MQ"},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":4,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":0,"ac_amr_female":0,"ac_amr_male":0,"ac_asj":3,"ac_asj_female":1,"ac_asj_male":2,"ac_eas":0,"ac_eas_female":0,"ac_eas_male":0,"ac_female":1,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":3,"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":1,"ac_oth_female":0,"ac_oth_male":1},"af":{"af":0.000127551,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0,"af_amr_female":0.0,"af_amr_male":0.0,"af_asj":0.0103448,"af_asj_female":0.0125,"af_asj_male":0.00952381,"af_eas":0.0,"af_eas_female":0.0,"af_eas_male":0.0,"af_female":0.0000718597,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":0.000171979,"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":0.000919118,"af_oth_female":0.0,"af_oth_male":0.00190114},"alleles":"T","alt":"T","an":{"an":31360,"an_afr":8688,"an_afr_female":3674,"an_afr_male":5014,"an_amr":848,"an_amr_female":414,"an_amr_male":434,"an_asj":290,"an_asj_female":80,"an_asj_male":210,"an_eas":1558,"an_eas_female":536,"an_eas_male":1022,"an_female":13916,"an_fin":3472,"an_fin_female":1846,"an_fin_male":1626,"an_male":17444,"an_nfe":15416,"an_nfe_est":4582,"an_nfe_female":6804,"an_nfe_male":8612,"an_nfe_nwe":8592,"an_nfe_onf":2136,"an_nfe_seu":106,"an_oth":1088,"an_oth_female":562,"an_oth_male":526},"baseqranksum":-0.167,"chrom":"13","clippingranksum":-0.441,"dp":628927,"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":0.364},"pab_max":1.0,"pos":77566230,"qd":12.1,"readposranksum":0.079,"ref":"C","rf":0.965407,"rsid":"rs587780896","sor":0.735,"type":"snp","vqslod":15.56,"vqsr_culprit":"MQ"},"hg19":{"end":77566230,"start":77566230},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"2800","position":"172"},"cds":{"length":"1224","position":"144"},"effect":"synonymous_variant","feature_id":"NM_006493.2","feature_type":"transcript","gene_id":"CLN5","genename":"CLN5","hgvs_c":"c.144C>T","hgvs_p":"p.Ser48Ser","protein":{"length":"407","position":"48"},"putative_impact":"LOW","rank":"1","total":"4","transcript_biotype":"protein_coding"}},"vcf":{"alt":"T","position":"77566230","ref":"C"},"wellderly":{"_license":"http://bit.ly/2VE6gj7","alleles":[{"allele":"T","freq":0.000415973},{"allele":"C","freq":0.999584027}],"alt":"T","chrom":"13","genotypes":[{"count":1201,"freq":0.9991680532445923,"genotype":"C/C"},{"count":1,"freq":0.0008319467554076539,"genotype":"C/T"}],"hg19":{"end":77566230,"start":77566230},"pos":"77566230","ref":"C","vartype":"snp"}}