chr12:47908762:C>T Detail (hg38) (VDR)

Information

Genome

Assembly Position
hg19 chr12:48,302,545-48,302,545 View the variant detail on this assembly version.
hg38 chr12:47,908,762-47,908,762

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000395324.6:c.-83-25988G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.401
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
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 tgv45751218 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
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
<0.001 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 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 Non-small cell lung carcinoma We evaluated the relationship between circulating 25-hydroxyvitamin D levels; VD... BeFree 18936471 Detail
Annotation

Annotations

DescrptionSourceLinks
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
In a post-hoc analysis of our previous prospective cohort study, VDR polymorphisms including Cdx2 G/... 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
We evaluated the relationship between circulating 25-hydroxyvitamin D levels; VDR polymorphisms, inc... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs11568820 dbSNP
Genome
hg38
Position
chr12:47,908,762-47,908,762
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))
rs11568820
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.401
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6721
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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