chr6:138196066:T>G Detail (hg19) (TNFAIP3)

Information

Genome

Assembly Position
hg19 chr6:138,196,066-138,196,066
hg38 chr6:137,874,929-137,874,929 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001270507.1:c.380T>G NP_001257436.1:p.Phe127Cys
NM_001270508.1:c.380T>G NP_001257437.1:p.Phe127Cys
NM_006290.3:c.380T>G NP_006281.1:p.Phe127Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.068
ToMMo:0.079
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.040

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
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 tgv27187493 TogoVar
COSMIC COSM1685340 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided 2013-09-19 no assertion provided not specified germline Detail
Benign Likely benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2023-11-29 criteria provided, single submitter Autoinflammatory syndrome, familial, Behcet-like 1 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Lupus Erythematosus, Systemic Association of rs2230926 G allele with SLE was replicated in Japanese (allelic a... BeFree 20617138 Detail
0.268 Lupus Erythematosus, Systemic Genome-wide association study in a Chinese Han population identifies nine new su... GWASCAT 19838193 Detail
0.003 arthritis Interestingly, rs2230926 of TNFAIP3 was also associated with arthritis, ANA and ... BeFree 19774492 Detail
0.168 rheumatoid arthritis TNFAIP3 rs2230926 polymorphisms in rheumatoid arthritis of southern Chinese Han ... BeFree 25674272 Detail
0.268 Lupus Erythematosus, Systemic [Genome-wide association study in a Chinese Han population identifies nine new s... GAD 19838193 Detail
0.268 Lupus Erythematosus, Systemic There are two nonsynonymous coding polymorphisms in the deubiquitinating (DUB) d... BeFree 20483768 Detail
0.268 Lupus Erythematosus, Systemic Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, C... GWASCAT 23273568 Detail
0.129 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.006 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.248 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.123 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
<0.001 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.168 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.123 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.268 Lupus Erythematosus, Systemic Associations of TNFAIP3 rs2230926 (p=1.43 × 10(-3)) and TNIP1 rs10036748 (p=4.33... BeFree 23911423 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001270508.2(TNFAIP3):c.380T>G (p.Phe127Cys) AND not specified ClinVar Detail
NM_001270508.2(TNFAIP3):c.380T>G (p.Phe127Cys) AND not provided ClinVar Detail
NM_001270508.2(TNFAIP3):c.380T>G (p.Phe127Cys) AND Autoinflammatory syndrome, familial, Behcet-like ... ClinVar Detail
Association of rs2230926 G allele with SLE was replicated in Japanese (allelic association P = .033,... DisGeNET Detail
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci fo... DisGeNET Detail
Interestingly, rs2230926 of TNFAIP3 was also associated with arthritis, ANA and some other subphenot... DisGeNET Detail
TNFAIP3 rs2230926 polymorphisms in rheumatoid arthritis of southern Chinese Han population: a case-c... DisGeNET Detail
[Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci f... DisGeNET Detail
There are two nonsynonymous coding polymorphisms in the deubiquitinating (DUB) domain of TNFAIP3: F1... DisGeNET Detail
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Associations of TNFAIP3 rs2230926 (p=1.43 × 10(-3)) and TNIP1 rs10036748 (p=4.33 × 10(-3)) with SLE ... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2230926 dbSNP
Genome
hg19
Position
chr6:138,196,066-138,196,066
Variant Type
snv
Reference Allele
T
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1201
Mean of sample read depth (HGVD)
49.23
Standard deviation of sample read depth (HGVD)
23.57
Number of reference allele (HGVD)
2238
Number of alternative allele (HGVD)
164
Allele Frequency (HGVD)
0.06827643630308076
Gene Symbol (HGVD)
TNFAIP3
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))
rs2230926
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
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
348
East Asian Heterozygous Counts (ExAC)
332
East Asian Homozygous Counts (ExAC)
8
East Asian Allele Frequency (ExAC)
0.04025913928736696
Chromosome Counts in All Race (ExAC)
121386
Allele Counts in All Race (ExAC)
7438
Heterozygous Counts in All Race (ExAC)
5888
Homozygous Counts in All Race (ExAC)
775
Allele Frequency in All Race (ExAC)
0.06127560015158255
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