Variant chrX-30855128-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_152787.5(TAB3):c.537G>A(p.Pro179=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00466 in 1,209,363 control chromosomes in the GnomAD database, including 9 homozygotes. There are 1,822 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., 114 hem., cov: 23)

Exomes 𝑓: 0.0047 ( 7 hom. 1708 hem. )

Consequence

TAB3
NM_152787.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.524

Variant links:

Genes affected

TAB3 (HGNC:30681): (TGF-beta activated kinase 1 (MAP3K7) binding protein 3) The product of this gene functions in the NF-kappaB signal transduction pathway. The encoded protein, and the similar and functionally redundant protein MAP3K7IP2/TAB2, forms a ternary complex with the protein kinase MAP3K7/TAK1 and either TRAF2 or TRAF6 in response to stimulation with the pro-inflammatory cytokines TNF or IL-1. Subsequent MAP3K7/TAK1 kinase activity triggers a signaling cascade leading to activation of the NF-kappaB transcription factor. The human genome contains a related pseudogene. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

TAB3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant X-30855128-C-T is Benign according to our data. Variant chrX-30855128-C-T is described in ClinVar as [Benign]. Clinvar id is 715889.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.524 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAB3	NM_152787.5 linkuse as main transcript	c.537G>A	p.Pro179=	synonymous_variant	6/11	ENST00000288422.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAB3	ENST00000288422.4 linkuse as main transcript	c.537G>A	p.Pro179=	synonymous_variant	6/11	5	NM_152787.5	P1	Q8N5C8-1

Frequencies

GnomAD3 genomes

AF:

0.00380

AC:

423

AN:

111341

Hom.:

Cov.:

AF XY:

0.00340

AC XY:

114

AN XY:

33577

show subpopulations

Gnomad AFR

AF:

0.000654

Gnomad AMI

AF:

0.00146

Gnomad AMR

AF:

0.00153

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000281

Gnomad SAS

AF:

0.00114

Gnomad FIN

AF:

0.00734

Gnomad MID

AF:

0.00840

Gnomad NFE

AF:

0.00620

Gnomad OTH

AF:

0.00468

GnomAD3 exomes

AF:

0.00333

AC:

611

AN:

183231

Hom.:

AF XY:

0.00334

AC XY:

226

AN XY:

67765

show subpopulations

Gnomad AFR exome

AF:

0.000304

Gnomad AMR exome

AF:

0.000802

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000722

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.00826

Gnomad NFE exome

AF:

0.00502

Gnomad OTH exome

AF:

0.00420

GnomAD4 exome

AF:

0.00474

AC:

5208

AN:

1097968

Hom.:

Cov.:

AF XY:

0.00470

AC XY:

1708

AN XY:

363322

show subpopulations

Gnomad4 AFR exome

AF:

0.000455

Gnomad4 AMR exome

AF:

0.000909

Gnomad4 ASJ exome

AF:

0.0000516

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00131

Gnomad4 FIN exome

AF:

0.00849

Gnomad4 NFE exome

AF:

0.00536

Gnomad4 OTH exome

AF:

0.00469

GnomAD4 genome

AF:

0.00380

AC:

423

AN:

111395

Hom.:

Cov.:

AF XY:

0.00339

AC XY:

114

AN XY:

33641

show subpopulations

Gnomad4 AFR

AF:

0.000652

Gnomad4 AMR

AF:

0.00153

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000281

Gnomad4 SAS

AF:

0.00115

Gnomad4 FIN

AF:

0.00734

Gnomad4 NFE

AF:

0.00621

Gnomad4 OTH

AF:

0.00462

Alfa

AF:

0.00411

Hom.:

Bravo

AF:

0.00303

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 03, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

0.79

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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