chr6:396321:C>T Detail (hg38) (IRF4)

Information

Genome

Assembly Position
hg19 chr6:396,321-396,321 View the variant detail on this assembly version.
hg38 chr6:396,321-396,321

HGVS

Type Transcript Protein
RefSeq NM_001195286.1:c.492+386C>T
NM_002460.3:c.492+386C>T
NR_046000.2:c.492+386C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Affects
Review star
Show details
Links
Type Database ID Link
Gene MIM 601900 OMIM
HGNC 6119 HGNC
Ensembl ENSG00000137265 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24012462 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Affects 2015-07-21 no assertion criteria provided Skin/hair/eye pigmentation, variation in, 8 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.122 progressive supranuclear palsy [Identification of common variants influencing risk of the tauopathy progressive... GAD 21685912 Detail
<0.001 Spot pigmented We identified genome-wide significant association with pigmented spots at three ... BeFree 25705849 Detail
0.006 Nevus [SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but expla... GAD 20647408 Detail
<0.001 Spot pigmented We identified genome-wide significant association with pigmented spots at three ... BeFree 25705849 Detail
<0.001 Lymphoma, Non-Hodgkin Analysis of joint effects between eye and hair color with the IRF4 rs12203592 SN... BeFree 19396635 Detail
<0.001 Experimental Organism Basal Cell Carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.284 melanoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
<0.001 Lymphoma, Large-Cell, Follicular Analysis of joint effects between eye and hair color with the IRF4 rs12203592 SN... BeFree 19396635 Detail
0.005 Experimental Organism Basal Cell Carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
<0.001 Spot pigmented We identified genome-wide significant association with pigmented spots at three ... BeFree 25705849 Detail
0.014 Malignant neoplasm of skin Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.003 squamous cell carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
<0.001 squamous cell carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.020 melanoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
<0.001 Malignant neoplasm of skin Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.120 skin carcinoma As for the number of NMSCs, we identified two independent SNPs on chr6 and one S... GWASCAT 23548203 Detail
<0.001 Experimental Organism Basal Cell Carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.011 melanoma [SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but expla... GAD 20647408 Detail
<0.001 Malignant neoplasm of skin Association of interferon regulatory factor 4 gene polymorphisms rs12203592 and ... BeFree 24906573 Detail
0.006 squamous cell carcinoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
0.011 melanoma Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T all... BeFree 21270109 Detail
<0.001 melanoma In combined analysis of melanoma case-control data from Australia, the UK, and S... BeFree 20602913 Detail
0.125 melanoma Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated wit... BeFree 23537197 Detail
0.122 Freckles Web-based, participant-driven studies yield novel genetic associations for commo... GWASCAT 20585627 Detail
0.122 progressive supranuclear palsy Identification of common variants influencing risk of the tauopathy progressive ... GWASCAT 21685912 Detail
0.011 melanoma Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated wit... BeFree 23537197 Detail
0.120 Skin/hair/eye pigmentation, variation in, 8 NA CLINVAR Detail
0.002 Sunburn [SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but expla... GAD 20647408 Detail
0.007 Skin Neoplasms [SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but expla... GAD 20647408 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002460.4(IRF4):c.492+386C>T AND Skin/hair/eye pigmentation, variation in, 8 ClinVar Detail
[Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy.... DisGeNET Detail
We identified genome-wide significant association with pigmented spots at three genetic loci: IRF4 (... DisGeNET Detail
[SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but explain only a small prop... DisGeNET Detail
We identified genome-wide significant association with pigmented spots at three genetic loci: IRF4 (... DisGeNET Detail
Analysis of joint effects between eye and hair color with the IRF4 rs12203592 SNP did not reveal sta... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Analysis of joint effects between eye and hair color with the IRF4 rs12203592 SNP did not reveal sta... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
We identified genome-wide significant association with pigmented spots at three genetic loci: IRF4 (... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14:... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
[SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but explain only a small prop... DisGeNET Detail
Association of interferon regulatory factor 4 gene polymorphisms rs12203592 and rs872071 with skin c... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
Along with two known pigmentation loci, MC1R and OCA2, the IRF4 rs12203592 T allele was associated w... DisGeNET Detail
In combined analysis of melanoma case-control data from Australia, the UK, and Sweden, the rs1220359... DisGeNET Detail
Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated with melanoma susceptib... DisGeNET Detail
Web-based, participant-driven studies yield novel genetic associations for common traits. DisGeNET Detail
Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. DisGeNET Detail
Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated with melanoma susceptib... DisGeNET Detail
NA DisGeNET Detail
[SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but explain only a small prop... DisGeNET Detail
[SNPs on chromosome 6, 9 and 22 were shown to be associated with nevi, but explain only a small prop... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs12203592 dbSNP
Genome
hg38
Position
chr6:396,321-396,321
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))
rs12203592
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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