chr22:19919576:C>A Detail (hg38) (TXNRD2)

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Information

Genome

Assembly	Position
hg19	chr22:19,907,099-19,907,099 View the variant detail on this assembly version.
hg38	chr22:19,919,576-19,919,576

Summary

Links

Type	Database	ID	Link
Gene	MIM	606448	OMIM
	HGNC	18155	HGNC
	Ensembl	ENSG00000184470	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv65378785	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2015-03-11	criteria provided, single submitter		germline	Detail
Benign	2016-09-23	criteria provided, single submitter	not specified	germline	Detail
Benign	2024-02-01	criteria provided, single submitter	Primary dilated cardiomyopathy	germline	Detail
Benign	2021-12-05	criteria provided, single submitter	Glucocorticoid deficiency 5	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	Kashin-Beck Disease	In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs180066...	BeFree	24058403	Detail
<0.001	Kashin-Beck Disease	In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs180066...	BeFree	24058403	Detail
0.009	Malignant neoplasm of breast	For TXNRD2 A66S [AS versus AA: odds ratio (OR), 1.05; 95% confidence intervals (...	BeFree	16424062	Detail
0.002	breast carcinoma	For TXNRD2 A66S [AS versus AA: odds ratio (OR), 1.05; 95% confidence intervals (...	BeFree	16424062	Detail

Annotation

Descrption	Source	Links
NM_006440.5(TXNRD2):c.196G>T (p.Ala66Ser) AND Cardiovascular phenotype	ClinVar	Detail
NM_006440.5(TXNRD2):c.196G>T (p.Ala66Ser) AND not specified	ClinVar	Detail
NM_006440.5(TXNRD2):c.196G>T (p.Ala66Ser) AND Primary dilated cardiomyopathy	ClinVar	Detail
NM_006440.5(TXNRD2):c.196G>T (p.Ala66Ser) AND Glucocorticoid deficiency 5	ClinVar	Detail
In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs1800668 and rs3811699), Tr...	DisGeNET	Detail
In this study, we showed that single SNPs in the genes GPX1 (rs1050450, rs1800668 and rs3811699), Tr...	DisGeNET	Detail
For TXNRD2 A66S [AS versus AA: odds ratio (OR), 1.05; 95% confidence intervals (95% CI), 0.96-1.15; ...	DisGeNET	Detail
For TXNRD2 A66S [AS versus AA: odds ratio (OR), 1.05; 95% confidence intervals (95% CI), 0.96-1.15; ...	DisGeNET	Detail

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs5748469 dbSNP
Genome: hg38
Position: chr22:19,919,576-19,919,576
Variant Type: snv
Reference Allele: C
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1199
Mean of sample read depth (HGVD): 59.95
Standard deviation of sample read depth (HGVD): 28.41
Number of reference allele (HGVD): 373
Number of alternative allele (HGVD): 2025
Allele Frequency (HGVD): 0.8444537114261885
Gene Symbol (HGVD): TXNRD2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs5748469
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.8487
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 14223
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16758
East Asian Chromosome Counts (ExAC): 1312
East Asian Allele Counts (ExAC): 1042
East Asian Heterozygous Counts (ExAC): 234
East Asian Homozygous Counts (ExAC): 404
East Asian Allele Frequency (ExAC): 0.7942073170731707
Chromosome Counts in All Race (ExAC): 30356
Allele Counts in All Race (ExAC): 13493
Heterozygous Counts in All Race (ExAC): 8023
Homozygous Counts in All Race (ExAC): 2735
Allele Frequency in All Race (ExAC): 0.44449202793516934

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