chr12:48272895:A>G Detail (hg19) (VDR)

Information

Genome

Assembly Position
hg19 chr12:48,272,895-48,272,895
hg38 chr12:47,879,112-47,879,112 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001017535.1:c.2T>C NP_001017535.1:p.?
NM_000376.2:c.2T>C NP_000367.1:p.?
NM_001017536.1:c.152T>C NP_001017536.1:p.Met51Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.638
ToMMo:0.634
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.545

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601769 OMIM
HGNC 12679 HGNC
Ensembl ENSG00000111424 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv45750520 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-02-17 criteria provided, single submitter not specified germline Detail
Benign 2021-12-05 criteria provided, multiple submitters, no conflicts Vitamin D-dependent rickets type II with alopecia germline unknown Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2023-04-20 no assertion criteria provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.371 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.013 colorectal cancer Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C... BeFree 24075799 Detail
0.020 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.012 colorectal carcinoma Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and C... BeFree 24075799 Detail
0.008 coronary artery disease The aim of this study was to investigate the association between FokI (rs2228570... BeFree 19563249 Detail
0.014 breast carcinoma Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441... BeFree 19124512 Detail
0.066 Malignant neoplasm of breast Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441... BeFree 19124512 Detail
0.061 Osteoporosis, Postmenopausal The present study investigated the effect of two single nucleotide polymorphisms... BeFree 25764158 Detail
<0.001 Acute Q fever Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 ... BeFree 25577174 Detail
0.001 Diabetes Mellitus, Insulin-Dependent A total of 9, 5, 3, and 7 studies were finally included in the analyses for the ... BeFree 23209686 Detail
0.126 Hypertensive disease Our findings suggest that VDR genetic polymorphism rs2228570 is significantly as... BeFree 25196087 Detail
0.018 hepatitis B We conclude that the VDR rs2228570 and DBP rs7041 polymorphisms may contribute t... BeFree 25541958 Detail
0.030 multiple sclerosis The aim of this study is to measure plasma levels of OPG and RANKL as well as to... BeFree 22805623 Detail
<0.001 diabetes mellitus Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;... BeFree 25899017 Detail
0.002 Diabetes Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;... BeFree 25899017 Detail
<0.001 Diabetes Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;... BeFree 25899017 Detail
<0.001 mitral valve stenosis The aim of this study is to measure plasma levels of OPG and RANKL as well as to... BeFree 22805623 Detail
0.003 Malignant neoplasm of breast For example, breast cancer risk was associated with the GC rs7041 TT genotype (a... BeFree 21693626 Detail
0.002 diabetes mellitus Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;... BeFree 25899017 Detail
0.016 Malignant neoplasm of ovary [This pooled analysis provides further evidence that the VDR rs2228570 polymorph... GAD 20473893 Detail
<0.001 breast carcinoma For example, breast cancer risk was associated with the GC rs7041 TT genotype (a... BeFree 21693626 Detail
0.016 Malignant neoplasm of ovary The association of invasive ovarian carcinoma risk with the functional polymorph... BeFree 20473893 Detail
0.002 ovarian carcinoma The association of invasive ovarian carcinoma risk with the functional polymorph... BeFree 20473893 Detail
0.003 Epithelial ovarian cancer The association of invasive ovarian carcinoma risk with the functional polymorph... BeFree 20473893 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000376.3(VDR):c.2T>C (p.Met1Thr) AND not specified ClinVar Detail
NM_000376.3(VDR):c.2T>C (p.Met1Thr) AND Vitamin D-dependent rickets type II with alopecia ClinVar Detail
NM_000376.3(VDR):c.2T>C (p.Met1Thr) AND not provided ClinVar Detail
NM_000376.3(VDR):c.2T>C (p.Met1Thr) AND Periodontitis ClinVar Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit... DisGeNET Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Unadjusted and adjusted hazard ratios for all-cause mortality (469 events) and CRC-specific mortalit... DisGeNET Detail
The aim of this study was to investigate the association between FokI (rs2228570) and BsmI (rs154441... DisGeNET Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228... DisGeNET Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228... DisGeNET Detail
The present study investigated the effect of two single nucleotide polymorphisms (SNPs) of the vitam... DisGeNET Detail
Single nucleotide polymorphisms (SNPs) in the IFNG (rs2430561/rs1861493), STAT1 (rs1914408), and VDR... DisGeNET Detail
A total of 9, 5, 3, and 7 studies were finally included in the analyses for the associations between... DisGeNET Detail
Our findings suggest that VDR genetic polymorphism rs2228570 is significantly associated with the de... DisGeNET Detail
We conclude that the VDR rs2228570 and DBP rs7041 polymorphisms may contribute to increased suscepti... DisGeNET Detail
The aim of this study is to measure plasma levels of OPG and RANKL as well as to analyze VDR FokI po... DisGeNET Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;0.01), SBP (OR 1.022... DisGeNET Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;0.01), SBP (OR 1.022... DisGeNET Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;0.01), SBP (OR 1.022... DisGeNET Detail
The aim of this study is to measure plasma levels of OPG and RANKL as well as to analyze VDR FokI po... DisGeNET Detail
For example, breast cancer risk was associated with the GC rs7041 TT genotype (age-adjusted odds rat... DisGeNET Detail
Logistic analysis confirmed that diabetes duration (odds ratio (OR) 1.108, P&lt;0.01), SBP (OR 1.022... DisGeNET Detail
[This pooled analysis provides further evidence that the VDR rs2228570 polymorphism might influence ... DisGeNET Detail
For example, breast cancer risk was associated with the GC rs7041 TT genotype (age-adjusted odds rat... DisGeNET Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r... DisGeNET Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r... DisGeNET Detail
The association of invasive ovarian carcinoma risk with the functional polymorphism rs2228570 (aka r... DisGeNET Detail

Overlapped Transcript Coordinates

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

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2228570 dbSNP
Genome
hg19
Position
chr12:48,272,895-48,272,895
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1186
Mean of sample read depth (HGVD)
29.32
Standard deviation of sample read depth (HGVD)
14.05
Number of reference allele (HGVD)
858
Number of alternative allele (HGVD)
1514
Allele Frequency (HGVD)
0.6382799325463744
Gene Symbol (HGVD)
VDR
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))
rs2228570
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6337
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10620
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
4682
East Asian Heterozygous Counts (ExAC)
2144
East Asian Homozygous Counts (ExAC)
1269
East Asian Allele Frequency (ExAC)
0.544798696765185
Chromosome Counts in All Race (ExAC)
121098
Allele Counts in All Race (ExAC)
77207
Heterozygous Counts in All Race (ExAC)
27103
Homozygous Counts in All Race (ExAC)
25052
Allele Frequency in All Race (ExAC)
0.6375580108672315
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