{"_id":"chr4:g.72316953G>A","_version":2,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"A","anc":"G","annotype":"CodingTranscript","bstatistic":661,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.0,"het":0.0,"quies":0.787,"reprpc":0.0,"reprpcwk":0.016,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.055,"txflnk":0.0,"txwk":0.142,"znfrpts":0.0},"chrom":4,"consdetail":"synonymous","consequence":"SYNONYMOUS","consscore":5,"cpg":0.05,"dna":{"helt":-1.55,"mgw":-0.55,"prot":0.65,"roll":-1.21},"encode":{"exp":40.99,"h3k27ac":3.28,"h3k4me1":2.52,"h3k4me3":2.0,"nucleo":2.4},"exon":"11/25","fitcons":0.577471,"gc":0.49,"gene":{"ccds_id":"CCDS47071.1","cds":{"cdna_pos":1374,"cds_pos":1257,"rel_cdna_pos":0.18,"rel_cds_pos":0.38},"feature_id":"ENST00000425175","gene_id":"ENSG00000080493","genename":"SLC4A4","prot":{"domain":"ndomain","protpos":419,"rel_prot_pos":0.38}},"gerp":{"n":6.08,"rs":512.8,"rs_pval":1.17522e-103,"s":-6.97},"isderived":"TRUE","isknownvariant":"FALSE","istv":"FALSE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":22072,"min_dist_tss":112183,"mutindex":79,"naa":"T","oaa":"T","phast_cons":{"mammalian":0.383,"primate":0.795,"vertebrate":0.47},"phred":13.52,"phylop":{"mammalian":-1.825,"primate":-0.808,"vertebrate":-0.881},"pos":72316953,"rawscore":1.537979,"ref":"G","segway":"TF0","type":"SNV"},"chrom":"4","clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":299386,"alt":"A","chrom":"4","cytogenic":"4q13.3","gene":{"id":"8671","symbol":"SLC4A4"},"hg19":{"end":72316953,"start":72316953},"hg38":{"end":71451236,"start":71451236},"hgvs":{"coding":["NM_001098484.3:c.1257G>A","NM_001134742.2:c.1257G>A","NM_003759.4:c.1125G>A"],"genomic":["NC_000004.11:g.72316953G>A","NC_000004.12:g.71451236G>A","NG_012653.1:g.268951G>A"],"protein":["NP_001091954.1:p.Thr419=","NP_001128214.1:p.Thr419=","NP_003750.1:p.Thr375=","NP_003750.1:p.Thr375="]},"rcv":{"accession":"RCV000291593","clinical_significance":"Uncertain significance","conditions":{"identifiers":{"medgen":"C1970309","mondo":"MONDO:0011422","omim":"604278"},"name":"Autosomal recessive proximal renal tubular acidosis (PRTAO)","synonyms":["RTA, PROXIMAL, AUTOSOMAL RECESSIVE","RENAL TUBULAR ACIDOSIS, PROXIMAL, WITH OCULAR ABNORMALITIES AND MENTAL RETARDATION","RENAL TUBULAR ACIDOSIS, PROXIMAL, WITH OCULAR ABNORMALITIES AND IMPAIRED INTELLECTUAL DEVELOPMENT","PROXIMAL RENAL TUBULAR ACIDOSIS-OCULAR ANOMALY SYNDROME"]},"last_evaluated":"2018-01-12","number_submitters":1,"origin":"germline","preferred_name":"NM_001098484.3(SLC4A4):c.1257G>A (p.Thr419=)","review_status":"criteria provided, single submitter"},"ref":"G","rsid":"rs201149572","type":"single nucleotide variant","variant_id":349543},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"dbgap_popfreq":1.0,"exac":1.0,"gnomad":1.0,"gnomad_exomes":1.0,"topmed":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"exac":0.0,"gnomad":0.0,"gnomad_exomes":0.0,"topmed":0.0}}],"alt":"A","chrom":"4","dbsnp_build":156,"gene":{"geneid":8671,"is_pseudo":false,"name":"solute carrier family 4 member 4","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1398,"seq_id":"NM_001098484.3"},"hgvs":"NM_001098484.3:c.1257=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":418,"seq_id":"NP_001091954.1"}}},"protein_product":{"refseq":"NP_001091954.1"},"refseq":"NM_001098484.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1892,"seq_id":"NM_001134742.2"},"hgvs":"NM_001134742.2:c.1257=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":418,"seq_id":"NP_001128214.1"}}},"protein_product":{"refseq":"NP_001128214.1"},"refseq":"NM_001134742.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1351,"seq_id":"NM_003759.4"},"hgvs":"NM_003759.4:c.1125=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":374,"seq_id":"NP_003750.1"}}},"protein_product":{"refseq":"NP_003750.1"},"refseq":"NM_003759.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":2081,"seq_id":"XM_011532390.3"},"hgvs":"XM_011532390.3:c.699=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":232,"seq_id":"XP_011530692.1"}}},"protein_product":{"refseq":"XP_011530692.1"},"refseq":"XM_011532390.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1044,"seq_id":"XM_017008792.2"},"hgvs":"XM_017008792.2:c.1032=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":343,"seq_id":"XP_016864281.1"}}},"protein_product":{"refseq":"XP_016864281.1"},"refseq":"XM_017008792.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1344,"seq_id":"XM_017008793.2"},"hgvs":"XM_017008793.2:c.741=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":246,"seq_id":"XP_016864282.1"}}},"protein_product":{"refseq":"XP_016864282.1"},"refseq":"XM_017008793.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1427,"seq_id":"XM_024454267.2"},"hgvs":"XM_024454267.2:c.1350=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":449,"seq_id":"XP_024310035.1"}}},"protein_product":{"refseq":"XP_024310035.1"},"refseq":"XM_024454267.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1529,"seq_id":"XM_024454268.2"},"hgvs":"XM_024454268.2:c.1272=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":423,"seq_id":"XP_024310036.1"}}},"protein_product":{"refseq":"XP_024310036.1"},"refseq":"XM_024454268.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1447,"seq_id":"XM_024454269.2"},"hgvs":"XM_024454269.2:c.1272=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":423,"seq_id":"XP_024310037.1"}}},"protein_product":{"refseq":"XP_024310037.1"},"refseq":"XM_024454269.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1260,"seq_id":"XM_024454270.2"},"hgvs":"XM_024454270.2:c.1257=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":418,"seq_id":"XP_024310038.1"}}},"protein_product":{"refseq":"XP_024310038.1"},"refseq":"XM_024454270.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":1380,"seq_id":"XM_024454271.2"},"hgvs":"XM_024454271.2:c.1257=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":418,"seq_id":"XP_024310039.1"}}},"protein_product":{"refseq":"XP_024310039.1"},"refseq":"XM_024454271.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":2694,"seq_id":"XM_024454272.2"},"hgvs":"XM_024454272.2:c.1257=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":418,"seq_id":"XP_024310040.1"}}},"protein_product":{"refseq":"XP_024310040.1"},"refseq":"XM_024454272.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACG","inserted_sequence":"ACG","position":2582,"seq_id":"XM_047416348.1"},"hgvs":"XM_047416348.1:c.600=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":199,"seq_id":"XP_047272304.1"}}},"protein_product":{"refseq":"XP_047272304.1"},"refseq":"XM_047416348.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]}],"strand":"+","symbol":"SLC4A4"},"hg19":{"end":72316953,"start":72316953},"ref":"G","rsid":"rs201149572","vartype":"snv"},"exac":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":6,"ac_adj":6,"ac_afr":0,"ac_amr":1,"ac_eas":0,"ac_female":3,"ac_fin":0,"ac_het":6,"ac_hom":0,"ac_male":3,"ac_nfe":5,"ac_oth":0,"ac_sas":0},"af":0.00004942,"alleles":"A","alt":"A","an":{"an":121412,"an_adj":121234,"an_afr":10404,"an_amr":11514,"an_eas":8612,"an_female":54044,"an_fin":6610,"an_male":67190,"an_nfe":66690,"an_oth":908,"an_sas":16496},"baseqranksum":0.121,"chrom":4,"clippingranksum":0.288,"culprit":"FS","fs":0.0,"het":{"het_afr":0,"het_amr":1,"het_eas":0,"het_fin":0,"het_nfe":5,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0003,"mq":{"mq":59.6,"mq0":0,"mqranksum":-0.714},"ncc":17,"pos":72316953,"qd":12.12,"readposranksum":-0.283,"ref":"G","type":"snp","vqslod":1.51},"exac_nontcga":{"_license":"http://bit.ly/2H9c4hg","ac":{"ac":5,"ac_adj":5,"ac_afr":0,"ac_amr":1,"ac_eas":0,"ac_female":2,"ac_fin":0,"ac_het":5,"ac_hom":0,"ac_male":3,"ac_nfe":4,"ac_oth":0,"ac_sas":0},"af":0.00004708,"alleles":"A","alt":"A","an":{"an":106210,"an_adj":106042,"an_afr":9064,"an_amr":11152,"an_eas":7824,"an_female":45794,"an_fin":6610,"an_male":60248,"an_nfe":54306,"an_oth":694,"an_sas":16392},"baseqranksum":0.121,"chrom":4,"clippingranksum":0.288,"culprit":"FS","fs":0.0,"het":{"het_afr":0,"het_amr":1,"het_eas":0,"het_fin":0,"het_nfe":4,"het_oth":0,"het_sas":0},"hom":{"hom_afr":0,"hom_amr":0,"hom_eas":0,"hom_fin":0,"hom_nfe":0,"hom_oth":0,"hom_sas":0},"inbreedingcoeff":-0.0003,"mq":{"mq":59.6,"mq0":0,"mqranksum":-0.714},"ncc":17,"pos":72316953,"qd":12.12,"readposranksum":-0.283,"ref":"G","type":"snp","vqslod":1.51},"geno2mp":{"_license":"http://bit.ly/2QyGCIN","hpo_count":1},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":17,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":1,"ac_amr_female":0,"ac_amr_male":1,"ac_asj":14,"ac_asj_female":7,"ac_asj_male":7,"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":7,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":10,"ac_nfe":1,"ac_nfe_bgr":0,"ac_nfe_est":0,"ac_nfe_female":0,"ac_nfe_male":1,"ac_nfe_nwe":1,"ac_nfe_onf":0,"ac_nfe_seu":0,"ac_nfe_swe":0,"ac_oth":1,"ac_oth_female":0,"ac_oth_male":1,"ac_sas":0,"ac_sas_female":0,"ac_sas_male":0},"af":{"af":0.0000677037,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0000289352,"af_amr_female":0.0,"af_amr_male":0.0000699007,"af_asj":0.00138944,"af_asj_female":0.00142915,"af_asj_male":0.00135187,"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":0.0000606575,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":0.0000736963,"af_nfe":8.81477e-6,"af_nfe_bgr":0.0,"af_nfe_est":0.0,"af_nfe_female":0.0,"af_nfe_male":0.0000157694,"af_nfe_nwe":0.0000237959,"af_nfe_onf":0.0,"af_nfe_seu":0.0,"af_nfe_swe":0.0,"af_oth":0.000163132,"af_oth_female":0.0,"af_oth_male":0.000311721,"af_sas":0.0,"af_sas_female":0.0,"af_sas_male":0.0},"alleles":"A","alt":"A","an":{"an":251094,"an_afr":16254,"an_afr_female":10070,"an_afr_male":6184,"an_amr":34560,"an_amr_female":20254,"an_amr_male":14306,"an_asj":10076,"an_asj_female":4898,"an_asj_male":5178,"an_eas":18370,"an_eas_female":9310,"an_eas_jpn":152,"an_eas_kor":3794,"an_eas_male":9060,"an_eas_oea":14424,"an_female":115402,"an_fin":21644,"an_fin_female":10372,"an_fin_male":11272,"an_male":135692,"an_nfe":113446,"an_nfe_bgr":2668,"an_nfe_est":242,"an_nfe_female":50032,"an_nfe_male":63414,"an_nfe_nwe":42024,"an_nfe_onf":30894,"an_nfe_seu":11490,"an_nfe_swe":26128,"an_oth":6130,"an_oth_female":2922,"an_oth_male":3208,"an_sas":30614,"an_sas_female":7544,"an_sas_male":23070},"baseqranksum":0.789,"chrom":"4","clippingranksum":0.303,"dp":11325929,"fs":0.529,"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":59.57,"mqranksum":0.089},"pab_max":1.0,"pos":72316953,"qd":11.52,"readposranksum":0.287,"ref":"G","rf":0.93954,"rsid":"rs201149572","sor":0.665,"type":"snp","vqslod":3.87,"vqsr_culprit":"QD"},"hg19":{"end":72316953,"start":72316953},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"7596","position":"1374"},"cds":{"length":"3285","position":"1257"},"effect":"synonymous_variant","feature_id":"NM_001134742.1","feature_type":"transcript","gene_id":"SLC4A4","genename":"SLC4A4","hgvs_c":"c.1257G>A","hgvs_p":"p.Thr419Thr","protein":{"length":"1094","position":"419"},"putative_impact":"LOW","rank":"11","total":"25","transcript_biotype":"protein_coding"},{"cdna":{"length":"7693","position":"1374"},"cds":{"length":"3240","position":"1257"},"effect":"synonymous_variant","feature_id":"NM_001098484.2","feature_type":"transcript","gene_id":"SLC4A4","genename":"SLC4A4","hgvs_c":"c.1257G>A","hgvs_p":"p.Thr419Thr","protein":{"length":"1079","position":"419"},"putative_impact":"LOW","rank":"11","total":"26","transcript_biotype":"protein_coding"},{"cdna":{"length":"7640","position":"1321"},"cds":{"length":"3108","position":"1125"},"effect":"synonymous_variant","feature_id":"NM_003759.3","feature_type":"transcript","gene_id":"SLC4A4","genename":"SLC4A4","hgvs_c":"c.1125G>A","hgvs_p":"p.Thr375Thr","protein":{"length":"1035","position":"375"},"putative_impact":"LOW","rank":"8","total":"23","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"A","position":"72316953","ref":"G"}}