dbSNP rs2307859: TNFAIP3:c.296-15_296-13delCCT (chr6-137874824-TCTC-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001270508.2(TNFAIP3):c.296-15_296-13delCCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 1,603,882 control chromosomes in the GnomAD database, including 322,124 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 23464 hom., cov: 0)

Exomes 𝑓: 0.64 ( 298660 hom. )

Consequence

TNFAIP3
NM_001270508.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.282

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 6-137874824-TCTC-T is Benign according to our data. Variant chr6-137874824-TCTC-T is described in ClinVar as [Benign]. Clinvar id is 993326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP3	NM_001270508.2 link	c.296-15_296-13delCCT		intron_variant	Intron 2 of 8	ENST00000612899.5	NP_001257437.1	P21580

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP3	ENST00000612899.5 link	c.296-20_296-18delCTC		intron_variant	Intron 2 of 8	5	NM_001270508.2	ENSP00000481570.1		P21580

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

77779

AN:

151574

Hom.:

23466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.570

Gnomad EAS

AF:

0.850

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.548

GnomAD3 exomes

AF:

0.615

AC:

151478

AN:

246108

Hom.:

48869

AF XY:

0.626

AC XY:

83189

AN XY:

132970

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.566

Gnomad ASJ exome

AF:

0.585

Gnomad EAS exome

AF:

0.854

Gnomad SAS exome

AF:

0.658

Gnomad FIN exome

AF:

0.637

Gnomad NFE exome

AF:

0.642

Gnomad OTH exome

AF:

0.627

GnomAD4 exome

AF:

0.635

AC:

922830

AN:

1452188

Hom.:

298660

AF XY:

0.638

AC XY:

459894

AN XY:

721190

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.567

Gnomad4 ASJ exome

AF:

0.581

Gnomad4 EAS exome

AF:

0.857

Gnomad4 SAS exome

AF:

0.661

Gnomad4 FIN exome

AF:

0.640

Gnomad4 NFE exome

AF:

0.645

Gnomad4 OTH exome

AF:

0.614

GnomAD4 genome

AF:

0.513

AC:

77781

AN:

151694

Hom.:

23464

Cov.:

AF XY:

0.517

AC XY:

38342

AN XY:

74092

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.560

Gnomad4 ASJ

AF:

0.570

Gnomad4 EAS

AF:

0.850

Gnomad4 SAS

AF:

0.666

Gnomad4 FIN

AF:

0.645

Gnomad4 NFE

AF:

0.646

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.581

Hom.:

5013

Bravo

AF:

0.494

Asia WGS

AF:

0.675

AC:

2345

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 30, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 79% of patients studied by a panel of primary immunodeficiencies. Number of patients: 76. Only high quality variants are reported. -

Autoinflammatory syndrome, familial, Behcet-like

Benign:1

Sep 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autoinflammatory syndrome, familial, Behcet-like 1

Benign:1

Nov 26, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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