chr12:47845054:C>A Detail (hg38) (VDR)

Information

Genome

Assembly Position
hg19 chr12:48,238,837-48,238,837 View the variant detail on this assembly version.
hg38 chr12:47,845,054-47,845,054

HGVS

Type Transcript Protein
RefSeq NM_001017535.1:c.1025-49G>T
NM_000376.2:c.1025-49G>T
NM_001017536.1:c.1175-49G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.319
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.278

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 tgv45749360 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-08-16 criteria provided, single submitter not provided germline Detail
Benign 2021-12-05 criteria provided, single submitter Vitamin D-dependent rickets type II with alopecia germline Detail
Likely pathogenic 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
0.001 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 Detail
<0.001 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 Detail
0.004 melanoma In our hospital-based case-control study including 305 melanoma patients and 370... BeFree 22576141 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
0.030 multiple sclerosis An association of two single-nucleotide polymorphisms (SNPs) of the vitamin D re... BeFree 19758194 Detail
0.018 asthma Although the susceptibility of VDR gene variants with asthma could not be confir... BeFree 19622139 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.1025-49G>T AND not provided ClinVar Detail
NM_000376.3(VDR):c.1025-49G>T AND Vitamin D-dependent rickets type II with alopecia ClinVar Detail
NM_000376.3(VDR):c.1025-49G>T AND Hepatocellular carcinoma ClinVar Detail
NM_000376.3(VDR):c.1025-49G>T AND Periodontitis ClinVar Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
In our hospital-based case-control study including 305 melanoma patients and 370 healthy controls si... DisGeNET Detail
A total of 9, 5, 3, and 7 studies were finally included in the analyses for the associations between... DisGeNET Detail
An association of two single-nucleotide polymorphisms (SNPs) of the vitamin D receptor (VDR) gene, A... DisGeNET Detail
Although the susceptibility of VDR gene variants with asthma could not be confirmed for all SNPs tes... 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
rs7975232 dbSNP
Genome
hg38
Position
chr12:47,845,054-47,845,054
Variant Type
snv
Reference Allele
C
Alternative Allele
A
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))
rs7975232
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3193
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5352
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8592
East Asian Allele Counts (ExAC)
2387
East Asian Heterozygous Counts (ExAC)
1765
East Asian Homozygous Counts (ExAC)
311
East Asian Allele Frequency (ExAC)
0.277816573556797
Chromosome Counts in All Race (ExAC)
120724
Allele Counts in All Race (ExAC)
62616
Heterozygous Counts in All Race (ExAC)
29114
Homozygous Counts in All Race (ExAC)
16751
Allele Frequency in All Race (ExAC)
0.518670686855969
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