chr3:119815306:C>T Detail (hg38) (NR1I2)

Information

Genome

Assembly Position
hg19 chr3:119,534,153-119,534,153 View the variant detail on this assembly version.
hg38 chr3:119,815,306-119,815,306

HGVS

Type Transcript Protein
RefSeq NM_022002.2:c.1055-17C>T
NM_003889.3:c.938-17C>T
NM_033013.2:c.827-17C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.456
ToMMo:0.460
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.469

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 603065 OMIM
HGNC 7968 HGNC
Ensembl ENSG00000144852 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv13935214 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
0.007 Crohn Disease Genomic DNA from 2823 individuals of Caucasian origin including 859 patients wit... BeFree 21830270 Detail
Annotation

Annotations

DescrptionSourceLinks
Genomic DNA from 2823 individuals of Caucasian origin including 859 patients with Crohn's disease (C... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr3:119,815,306-119,815,306
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
58.73
Standard deviation of sample read depth (HGVD)
27.72
Number of reference allele (HGVD)
910
Number of alternative allele (HGVD)
764
Allele Frequency (HGVD)
0.45639187574671447
Gene Symbol (HGVD)
NR1I2
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))
rs2276707
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4596
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7703
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
4050
East Asian Heterozygous Counts (ExAC)
2188
East Asian Homozygous Counts (ExAC)
931
East Asian Allele Frequency (ExAC)
0.4694019471488178
Chromosome Counts in All Race (ExAC)
121164
Allele Counts in All Race (ExAC)
29589
Heterozygous Counts in All Race (ExAC)
21291
Homozygous Counts in All Race (ExAC)
4137
Allele Frequency in All Race (ExAC)
0.24420619986134495
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