Variant 6-149377880-A-T 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_001292034.3(TAB2):c.103-138A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 711,318 control chromosomes in the GnomAD database, including 278,373 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.87 ( 57836 hom., cov: 33)

Exomes 𝑓: 0.89 ( 220537 hom. )

Consequence

TAB2
NM_001292034.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

TAB2 (HGNC:17075): (TGF-beta activated kinase 1 (MAP3K7) binding protein 2) The protein encoded by this gene is an activator of MAP3K7/TAK1, which is required for for the IL-1 induced activation of nuclear factor kappaB and MAPK8/JNK. This protein forms a kinase complex with TRAF6, MAP3K7 and TAB1, and it thus serves as an adaptor that links MAP3K7 and TRAF6. This protein, along with TAB1 and MAP3K7, also participates in the signal transduction induced by TNFSF11/RANKl through the activation of the receptor activator of NF-kappaB (TNFRSF11A/RANK), which may regulate the development and function of osteoclasts. Studies of the related mouse protein indicate that it functions to protect against liver damage caused by chemical stressors. Mutations in this gene cause congenital heart defects, multiple types, 2 (CHTD2). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

TAB2 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=-1.02).

BP6

Variant 6-149377880-A-T is Benign according to our data. Variant chr6-149377880-A-T is described in ClinVar as [Benign]. Clinvar id is 1174413.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAB2	NM_001292034.3 linkuse as main transcript	c.103-138A>T		intron_variant		ENST00000637181.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAB2	ENST00000637181.2 linkuse as main transcript	c.103-138A>T		intron_variant		1	NM_001292034.3	P1	Q9NYJ8-1

Frequencies

GnomAD3 genomes

AF:

0.871

AC:

132522

AN:

152118

Hom.:

57799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.888

Gnomad ASJ

AF:

0.940

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.914

Gnomad FIN

AF:

0.871

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.888

Gnomad OTH

AF:

0.890

GnomAD4 exome

AF:

0.888

AC:

496284

AN:

559082

Hom.:

220537

AF XY:

0.890

AC XY:

262417

AN XY:

294782

show subpopulations

Gnomad4 AFR exome

AF:

0.820

Gnomad4 AMR exome

AF:

0.893

Gnomad4 ASJ exome

AF:

0.938

Gnomad4 EAS exome

AF:

0.840

Gnomad4 SAS exome

AF:

0.921

Gnomad4 FIN exome

AF:

0.873

Gnomad4 NFE exome

AF:

0.887

Gnomad4 OTH exome

AF:

0.900

GnomAD4 genome

AF:

0.871

AC:

132609

AN:

152236

Hom.:

57836

Cov.:

AF XY:

0.871

AC XY:

64834

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.824

Gnomad4 AMR

AF:

0.888

Gnomad4 ASJ

AF:

0.940

Gnomad4 EAS

AF:

0.887

Gnomad4 SAS

AF:

0.913

Gnomad4 FIN

AF:

0.871

Gnomad4 NFE

AF:

0.888

Gnomad4 OTH

AF:

0.892

Alfa

AF:

0.884

Hom.:

7401

Bravo

AF:

0.871

Asia WGS

AF:

0.882

AC:

3061

AN:

3468

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

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.27

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.

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