chr1:167420425:T>G Detail (hg19) (CD247)

Information

Genome

Assembly Position
hg19 chr1:167,420,425-167,420,425
hg38 chr1:167,451,188-167,451,188 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000734.3:c.59-10421A>C
NM_198053.2:c.59-10421A>C
Ensemble ENST00000700108.1:c.-536-6737A>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.128
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 186780 OMIM
HGNC 1677 HGNC
Ensembl ENSG00000198821 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3660393 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
0.257 systemic scleroderma Five single nucleotide polymorphisms, IRF5 (rs10488631, rs12537284, rs4728142), ... BeFree 22440820 Detail
0.246 systemic scleroderma Five single nucleotide polymorphisms, IRF5 (rs10488631, rs12537284, rs4728142), ... BeFree 22440820 Detail
0.246 systemic scleroderma [Identification of novel genetic markers associated with clinical phenotypes of ... GAD 21779181 Detail
0.246 systemic scleroderma Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for sys... GWASCAT 21750679 Detail
0.002 Sclerosis [Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for sy... GAD 21750679 Detail
0.246 systemic scleroderma [Genome-wide association study of systemic sclerosis identifies CD247 as a new s... GAD 20383147 Detail
0.246 systemic scleroderma Genome-wide association study of systemic sclerosis identifies CD247 as a new su... GWASCAT 20383147 Detail
0.004 Autoimmune Diseases Given the role of CD247 in the response of the T cells, its entailment in autoim... BeFree 23861880 Detail
Annotation

Annotations

DescrptionSourceLinks
Five single nucleotide polymorphisms, IRF5 (rs10488631, rs12537284, rs4728142), STAT4 (rs3821236), C... DisGeNET Detail
Five single nucleotide polymorphisms, IRF5 (rs10488631, rs12537284, rs4728142), STAT4 (rs3821236), C... DisGeNET Detail
[Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis t... DisGeNET Detail
Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis. DisGeNET Detail
[Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.] DisGeNET Detail
[Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.... DisGeNET Detail
Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus. DisGeNET Detail
Given the role of CD247 in the response of the T cells, its entailment in autoimmune diseases and in... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2056626 dbSNP
Genome
hg19
Position
chr1:167,420,425-167,420,425
Variant Type
snv
Reference Allele
T
Alternative Allele
G
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))
rs2056626
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1285
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2153
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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