chr12:47846052:C>T Detail (hg38) (VDR)

Information

Genome

Assembly Position
hg19 chr12:48,239,835-48,239,835 View the variant detail on this assembly version.
hg38 chr12:47,846,052-47,846,052

HGVS

Type Transcript Protein
RefSeq NM_001017535.1:c.1024+283G>A
NM_000376.2:c.1024+283G>A
NM_001017536.1:c.1174+283G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.110
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv45749377 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-03-29 criteria provided, single submitter not provided germline Detail
Likely risk allele 2022-07-14 no assertion criteria provided hepatocellular carcinoma 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
0.020 Diabetes Mellitus, Insulin-Dependent Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs115... BeFree 22960018 Detail
0.008 coronary artery disease The aim of this study was to investigate the association between FokI (rs2228570... BeFree 19563249 Detail
<0.001 hepatitis B After adjustment for gender, age at the RRT onset, RRT vintage, chronic glomerul... BeFree 25245883 Detail
0.014 breast carcinoma Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441... BeFree 19124512 Detail
<0.001 aortic valve stenosis Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within th... BeFree 24903972 Detail
0.018 Lupus Erythematosus, Systemic Three hundred and thirty-seven patients with SLE and 239 healthy controls were g... BeFree 22004974 Detail
0.066 Malignant neoplasm of breast Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs154441... BeFree 19124512 Detail
0.003 aortic valve stenosis Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within th... BeFree 24903972 Detail
0.003 kidney failure After adjustment for gender, age at the RRT onset, RRT vintage, chronic glomerul... BeFree 25245883 Detail
0.061 Osteoporosis, Postmenopausal The present study investigated the effect of two single nucleotide polymorphisms... BeFree 25764158 Detail
<0.001 Squamous cell carcinoma of the head and neck In a post-hoc analysis of our previous prospective cohort study, VDR polymorphis... BeFree 22242137 Detail
<0.001 Thyroid carcinoma Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for ... BeFree 19499989 Detail
<0.001 schizophrenia Four single-nucleotide polymorphisms (SNPs; rs10735810/FokI, rs1544410/BsmI, rs7... BeFree 16634022 Detail
<0.001 Epithelial ovarian cancer The association of ovarian cancer risk with polymorphisms in the vitamin D recep... BeFree 18086759 Detail
0.003 Epithelial ovarian cancer The association of ovarian cancer risk with polymorphisms in the vitamin D recep... BeFree 18086759 Detail
<0.001 Thyroid carcinoma Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for ... BeFree 19499989 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000376.3(VDR):c.1024+283G>A AND not provided ClinVar Detail
NM_000376.3(VDR):c.1024+283G>A AND Hepatocellular carcinoma ClinVar Detail
NM_000376.3(VDR):c.1024+283G>A AND Periodontitis ClinVar Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
Of the 1692 DAISY children genotyped for VDR rs1544410, VDR rs2228570, VDR rs11568820, PTPN2 rs18932... DisGeNET Detail
The aim of this study was to investigate the association between FokI (rs2228570) and BsmI (rs154441... DisGeNET Detail
After adjustment for gender, age at the RRT onset, RRT vintage, chronic glomerulonephritis as a caus... DisGeNET Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228... DisGeNET Detail
Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within the apoE gene, rs6254 ... DisGeNET Detail
Three hundred and thirty-seven patients with SLE and 239 healthy controls were genotyped for the VDR... DisGeNET Detail
Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI), and rs2228... DisGeNET Detail
Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within the apoE gene, rs6254 ... DisGeNET Detail
After adjustment for gender, age at the RRT onset, RRT vintage, chronic glomerulonephritis as a caus... DisGeNET Detail
The present study investigated the effect of two single nucleotide polymorphisms (SNPs) of the vitam... DisGeNET Detail
In a post-hoc analysis of our previous prospective cohort study, VDR polymorphisms including Cdx2 G/... DisGeNET Detail
Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for follicular) and HC (... DisGeNET Detail
Four single-nucleotide polymorphisms (SNPs; rs10735810/FokI, rs1544410/BsmI, rs7975232/ApaI, and rs7... DisGeNET Detail
The association of ovarian cancer risk with polymorphisms in the vitamin D receptor (VDR) gene, incl... DisGeNET Detail
The association of ovarian cancer risk with polymorphisms in the vitamin D receptor (VDR) gene, incl... DisGeNET Detail
Patients with thyroid carcinoma (n = 172) (n = 132 for papillary and n = 40 for follicular) and HC (... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1544410 dbSNP
Genome
hg38
Position
chr12:47,846,052-47,846,052
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs1544410
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1099
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1842
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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