{"_id":"chr22:g.19880628G>A","_version":2,"chrom":"22","clingen":{"caid":"CA10103774"},"clinvar":{"_license":"http://bit.ly/2SQdcI0","allele_id":377388,"alt":"A","chrom":"22","cytogenic":"22q11.21","gene":{"id":"10587","symbol":"TXNRD2"},"hg19":{"end":19868151,"start":19868151},"hg38":{"end":19880628,"start":19880628},"hgvs":{"coding":["LRG_417t1:c.1176C>T","NM_001352300.2:c.1173C>T","NM_001352301.2:c.1086C>T","NM_001352302.2:c.888C>T","NM_006440.5:c.1176C>T"],"genomic":["LRG_417:g.66209C>T","NC_000022.10:g.19868151G>A","NC_000022.11:g.19880628G>A","NG_011835.1:g.66209C>T"],"non-coding":"NR_147957.2:n.1134C>T","protein":["","NP_001339229.1:p.Tyr391=","NP_001339230.1:p.Tyr362=","NP_001339231.1:p.Tyr296=","NP_006431.2:p.Tyr392="]},"rcv":[{"accession":"RCV000442676","clinical_significance":"Likely benign","conditions":{"identifiers":{"medgen":"CN169374"},"name":"not specified","synonyms":["AllHighlyPenetrant"]},"last_evaluated":"2016-10-06","number_submitters":1,"origin":"germline","preferred_name":"NM_006440.5(TXNRD2):c.1176C>T (p.Tyr392=)","review_status":"criteria provided, single submitter"},{"accession":"RCV000619724","clinical_significance":"Likely benign","conditions":{"identifiers":{"medgen":"CN230736"},"name":"Cardiovascular phenotype"},"last_evaluated":"2016-12-29","number_submitters":1,"origin":"germline","preferred_name":"NM_006440.5(TXNRD2):c.1176C>T (p.Tyr392=)","review_status":"criteria provided, single submitter"},{"accession":"RCV002059952","clinical_significance":"Likely benign","conditions":{"identifiers":{"efo":"EFO_0000407","human_phenotype_ontology":"HP:0200130","medgen":"C0007193","mesh":"D002311","mondo":"MONDO:0005021"},"name":"Primary dilated cardiomyopathy (DCM)","synonyms":["Dilated Cardiomyopathy"]},"last_evaluated":"2024-02-05","number_submitters":1,"origin":"germline","preferred_name":"NM_006440.5(TXNRD2):c.1176C>T (p.Tyr392=)","review_status":"criteria provided, single submitter"}],"ref":"G","rsid":"rs544242322","type":"single nucleotide variant","variant_id":389670},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"G","freq":{"dbgap_popfreq":1.0,"exac":1.0,"gnomad":1.0,"gnomad_exomes":1.0,"prjeb36033":0.972,"sgdp_prj":0.5,"topmed":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"exac":0.0,"gnomad":0.0,"gnomad_exomes":0.0,"prjeb36033":0.028,"sgdp_prj":0.5,"topmed":0.0}}],"alt":"A","chrom":"22","dbsnp_build":156,"gene":{"geneid":10587,"is_pseudo":false,"name":"thioredoxin reductase 2","rnas":[{"protein_product":{"refseq":"NP_001269441.1"},"refseq":"NM_001282512.3","so":[{"accession":"SO:0002152","name":"genic_downstream_transcript_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TAC","inserted_sequence":"TAC","position":1185,"seq_id":"NM_001352300.2"},"hgvs":"NM_001352300.2:c.1173=","protein":{"variant":{"spdi":{"deleted_sequence":"Y","inserted_sequence":"Y","position":390,"seq_id":"NP_001339229.1"}}},"protein_product":{"refseq":"NP_001339229.1"},"refseq":"NM_001352300.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TAC","inserted_sequence":"TAC","position":1267,"seq_id":"NM_001352301.2"},"hgvs":"NM_001352301.2:c.1086=","protein":{"variant":{"spdi":{"deleted_sequence":"Y","inserted_sequence":"Y","position":361,"seq_id":"NP_001339230.1"}}},"protein_product":{"refseq":"NP_001339230.1"},"refseq":"NM_001352301.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TAC","inserted_sequence":"TAC","position":1267,"seq_id":"NM_001352302.2"},"hgvs":"NM_001352302.2:c.888=","protein":{"variant":{"spdi":{"deleted_sequence":"Y","inserted_sequence":"Y","position":295,"seq_id":"NP_001339231.1"}}},"protein_product":{"refseq":"NP_001339231.1"},"refseq":"NM_001352302.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"protein_product":{"refseq":"NP_001339232.1"},"refseq":"NM_001352303.2","so":[{"accession":"SO:0002152","name":"genic_downstream_transcript_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"TAC","inserted_sequence":"TAC","position":1188,"seq_id":"NM_006440.5"},"hgvs":"NM_006440.5:c.1176=","protein":{"variant":{"spdi":{"deleted_sequence":"Y","inserted_sequence":"Y","position":391,"seq_id":"NP_006431.2"}}},"protein_product":{"refseq":"NP_006431.2"},"refseq":"NM_006440.5","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"C","inserted_sequence":"C","position":1133,"seq_id":"NR_147957.2"},"hgvs":"NR_147957.2:n.1134=","refseq":"NR_147957.2","so":[{"accession":"SO:0001619","name":"non_coding_transcript_variant"}]}],"strand":"-","symbol":"TXNRD2"},"hg38":{"end":19880628,"start":19880628},"ref":"G","rsid":"rs544242322","vartype":"snv"},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":6,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"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":2,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":4,"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":6,"ac_sas_female":2,"ac_sas_male":4},"af":{"af":0.0000241361,"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":0.0,"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":0.0000176432,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":0.0000295788,"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":0.000196091,"af_sas_female":0.000265534,"af_sas_male":0.000173415},"alleles":"A","alt":"A","an":{"an":248590,"an_afr":15400,"an_afr_female":9242,"an_afr_male":6158,"an_amr":34494,"an_amr_female":20220,"an_amr_male":14274,"an_asj":10036,"an_asj_female":4864,"an_asj_male":5172,"an_eas":17968,"an_eas_female":9122,"an_eas_jpn":134,"an_eas_kor":3818,"an_eas_male":8846,"an_eas_oea":14016,"an_female":113358,"an_fin":21526,"an_fin_female":10294,"an_fin_male":11232,"an_male":135232,"an_nfe":112526,"an_nfe_bgr":2658,"an_nfe_est":234,"an_nfe_female":49232,"an_nfe_male":63294,"an_nfe_nwe":41840,"an_nfe_onf":30398,"an_nfe_seu":11360,"an_nfe_swe":26036,"an_oth":6042,"an_oth_female":2852,"an_oth_male":3190,"an_sas":30598,"an_sas_female":7532,"an_sas_male":23066},"baseqranksum":2.48,"chrom":"22","clippingranksum":0.196,"dp":11025535,"fs":1.784,"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":0.0014,"mq":{"mq":59.72,"mqranksum":0.388},"pab_max":1.0,"pos":19880628,"qd":13.06,"readposranksum":0.405,"ref":"G","rf":0.934067,"rsid":"rs544242322","sor":0.561,"type":"snp","vqslod":1.36,"vqsr_culprit":"FS"},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":9,"ac_afr":6,"ac_afr_xx":5,"ac_afr_xy":1,"ac_ami":0,"ac_ami_xx":0,"ac_ami_xy":0,"ac_amr":1,"ac_amr_xx":0,"ac_amr_xy":1,"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":1,"ac_nfe_xx":0,"ac_nfe_xy":1,"ac_oth":0,"ac_oth_xx":0,"ac_oth_xy":0,"ac_sas":1,"ac_sas_xx":0,"ac_sas_xy":1,"ac_xx":5,"ac_xy":4},"af":{"af":0.0000591576,"af_afr":0.000144851,"af_afr_xx":0.000225856,"af_afr_xy":0.0000518565,"af_ami":0.0,"af_ami_xx":0.0,"af_ami_xy":0.0,"af_amr":0.0000654279,"af_amr_xx":0.0,"af_amr_xy":0.000117758,"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":0.0000146994,"af_nfe_xx":0.0,"af_nfe_xy":0.0000348772,"af_oth":0.0,"af_oth_xx":0.0,"af_oth_xy":0.0,"af_sas":0.000207211,"af_sas_xx":0.0,"af_sas_xy":0.000273224,"af_xx":0.0000642376,"af_xy":0.0000538358},"alleles":"A","alt":"A","an":{"an":152136,"an_afr":41422,"an_afr_xx":22138,"an_afr_xy":19284,"an_ami":912,"an_ami_xx":470,"an_ami_xy":442,"an_amr":15284,"an_amr_xx":6792,"an_amr_xy":8492,"an_asj":3472,"an_asj_xx":1868,"an_asj_xy":1604,"an_eas":5188,"an_eas_xx":2276,"an_eas_xy":2912,"an_fin":10596,"an_fin_xx":2572,"an_fin_xy":8024,"an_mid":316,"an_mid_xx":164,"an_mid_xy":152,"an_nfe":68030,"an_nfe_xx":39358,"an_nfe_xy":28672,"an_oth":2090,"an_oth_xx":1032,"an_oth_xy":1058,"an_sas":4826,"an_sas_xx":1166,"an_sas_xy":3660,"an_xx":77836,"an_xy":74300},"as_fs":0.515317,"as_mq":{"as_mq":59.986,"as_mqranksum":-0.196},"as_pab_max":1.0,"as_qd":13.2122,"as_readposranksum":0.313,"as_sor":0.718136,"as_vqslod":5.3106,"chrom":"22","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":-0.0000591278,"pos":19880628,"ref":"G","rsid":"rs544242322","type":"snp"},"hg38":{"end":19880628,"start":19880628},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"2119","position":"1365"},"cds":{"length":"1575","position":"1176"},"effect":"synonymous_variant","feature_id":"NM_006440.4","feature_type":"transcript","gene_id":"TXNRD2","genename":"TXNRD2","hgvs_c":"c.1176C>T","hgvs_p":"p.Tyr392Tyr","protein":{"length":"524","position":"392"},"putative_impact":"LOW","rank":"13","total":"18","transcript_biotype":"protein_coding"}},"vcf":{"alt":"A","position":"19880628","ref":"G"}}