Variant rs5029948 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001270508.2(TNFAIP3):c.805+26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 1,590,148 control chromosomes in the GnomAD database, including 2,288 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 376 hom., cov: 32)

Exomes 𝑓: 0.047 ( 1912 hom. )

Consequence

TNFAIP3
NM_001270508.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0420

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]

TNFAIP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 6-137876192-C-T is Benign according to our data. Variant chr6-137876192-C-T is described in ClinVar as [Benign]. Clinvar id is 1250083.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFAIP3	NM_001270508.2 linkuse as main transcript	c.805+26C>T		intron_variant		ENST00000612899.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP3	ENST00000612899.5 linkuse as main transcript	c.805+26C>T		intron_variant		5	NM_001270508.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0608

AC:

9254

AN:

152202

Hom.:

370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0474

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.000961

Gnomad SAS

AF:

0.0393

Gnomad FIN

AF:

0.00613

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0482

Gnomad OTH

AF:

0.0587

GnomAD3 exomes

AF:

0.0429

AC:

10311

AN:

240434

Hom.:

320

AF XY:

0.0427

AC XY:

5552

AN XY:

129976

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.0288

Gnomad ASJ exome

AF:

0.0733

Gnomad EAS exome

AF:

0.000897

Gnomad SAS exome

AF:

0.0443

Gnomad FIN exome

AF:

0.00787

Gnomad NFE exome

AF:

0.0483

Gnomad OTH exome

AF:

0.0477

GnomAD4 exome

AF:

0.0469

AC:

67450

AN:

1437830

Hom.:

1912

Cov.:

AF XY:

0.0469

AC XY:

33573

AN XY:

715516

show subpopulations

Gnomad4 AFR exome

AF:

0.108

Gnomad4 AMR exome

AF:

0.0307

Gnomad4 ASJ exome

AF:

0.0756

Gnomad4 EAS exome

AF:

0.000658

Gnomad4 SAS exome

AF:

0.0452

Gnomad4 FIN exome

AF:

0.00913

Gnomad4 NFE exome

AF:

0.0481

Gnomad4 OTH exome

AF:

0.0534

GnomAD4 genome

AF:

0.0609

AC:

9275

AN:

152318

Hom.:

376

Cov.:

AF XY:

0.0575

AC XY:

4281

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.0474

Gnomad4 ASJ

AF:

0.0784

Gnomad4 EAS

AF:

0.000963

Gnomad4 SAS

AF:

0.0391

Gnomad4 FIN

AF:

0.00613

Gnomad4 NFE

AF:

0.0482

Gnomad4 OTH

AF:

0.0624

Alfa

AF:

0.0570

Hom.:

Bravo

AF:

0.0659

Asia WGS

AF:

0.0630

AC:

218

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.18

DANN

Benign

0.24

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over