chr6:138195723:C>G Detail (hg19) (TNFAIP3)

Information

Genome

Assembly Position
hg19 chr6:138,195,723-138,195,723
hg38 chr6:137,874,586-137,874,586 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001270507.1:c.296-259C>G
NM_001270508.1:c.296-259C>G
NM_006290.3:c.296-259C>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.079
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 191163 OMIM
HGNC 11896 HGNC
Ensembl ENSG00000118503 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv27187466 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
0.268 Lupus Erythematosus, Systemic Single-marker analysis validated the association of BLK rs2736340 (P=4.25×10(-6)... BeFree 21905002 Detail
0.008 Autoimmune Diseases [Convincing associations between TNFAIP3 variants and autoimmune diseases have b... GAD 20511617 Detail
0.003 systemic scleroderma Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the Euro... BeFree 20511617 Detail
0.003 systemic scleroderma [Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the Eur... GAD 20511617 Detail
0.268 Lupus Erythematosus, Systemic [Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythe... GAD 19165918 Detail
0.268 Lupus Erythematosus, Systemic Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythem... GWASCAT 19165918 Detail
Annotation

Annotations

DescrptionSourceLinks
Single-marker analysis validated the association of BLK rs2736340 (P=4.25×10(-6)) as well as TNFSF4 ... DisGeNET Detail
[Convincing associations between TNFAIP3 variants and autoimmune diseases have been reported.] DisGeNET Detail
Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the European Caucasian popul... DisGeNET Detail
[Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the European Caucasian popu... DisGeNET Detail
[Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus.] DisGeNET Detail
Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5029939 dbSNP
Genome
hg19
Position
chr6:138,195,723-138,195,723
Variant Type
snv
Reference Allele
C
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))
rs5029939
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0791
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1326
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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