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rs5029939

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001270508.2(TNFAIP3):c.296-259C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,196 control chromosomes in the GnomAD database, including 2,826 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 2826 hom., cov: 33)

Consequence

TNFAIP3
NM_001270508.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0240
Variant links:
Genes affected
TNFAIP3 (HGNC:11896): (TNF alpha induced protein 3) This gene was identified as a gene whose expression is rapidly induced by the tumor necrosis factor (TNF). The protein encoded by this gene is a zinc finger protein and ubiqitin-editing enzyme, and has been shown to inhibit NF-kappa B activation as well as TNF-mediated apoptosis. The encoded protein, which has both ubiquitin ligase and deubiquitinase activities, is involved in the cytokine-mediated immune and inflammatory responses. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TNFAIP3NM_001270508.2 linkuse as main transcriptc.296-259C>G intron_variant ENST00000612899.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TNFAIP3ENST00000612899.5 linkuse as main transcriptc.296-259C>G intron_variant 5 NM_001270508.2 P1

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19152
AN:
152078
Hom.:
2816
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.362
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0732
Gnomad ASJ
AF:
0.0441
Gnomad EAS
AF:
0.0425
Gnomad SAS
AF:
0.0321
Gnomad FIN
AF:
0.0167
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0313
Gnomad OTH
AF:
0.111
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.126
AC:
19200
AN:
152196
Hom.:
2826
Cov.:
33
AF XY:
0.122
AC XY:
9092
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.362
Gnomad4 AMR
AF:
0.0732
Gnomad4 ASJ
AF:
0.0441
Gnomad4 EAS
AF:
0.0430
Gnomad4 SAS
AF:
0.0317
Gnomad4 FIN
AF:
0.0167
Gnomad4 NFE
AF:
0.0313
Gnomad4 OTH
AF:
0.110
Alfa
AF:
0.0797
Hom.:
211
Bravo
AF:
0.140
Asia WGS
AF:
0.0510
AC:
180
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
1.8
Dann
Benign
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5029939; hg19: chr6-138195723; API