Variant chr6-149370219-T-G 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.102+120T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 933,332 control chromosomes in the GnomAD database, including 110,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 15182 hom., cov: 32)

Exomes 𝑓: 0.49 ( 95013 hom. )

Consequence

TAB2
NM_001292034.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.264

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=-0.6).

BP6

Variant 6-149370219-T-G is Benign according to our data. Variant chr6-149370219-T-G is described in ClinVar as [Benign]. Clinvar id is 1259650.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 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.102+120T>G		intron_variant		ENST00000637181.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAB2	ENST00000637181.2 linkuse as main transcript	c.102+120T>G		intron_variant		1	NM_001292034.3	P1	Q9NYJ8-1

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66430

AN:

151944

Hom.:

15187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.589

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.529

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.513

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.488

AC:

380895

AN:

781270

Hom.:

95013

AF XY:

0.487

AC XY:

198513

AN XY:

407962

show subpopulations

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.394

Gnomad4 ASJ exome

AF:

0.517

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.425

Gnomad4 FIN exome

AF:

0.464

Gnomad4 NFE exome

AF:

0.521

Gnomad4 OTH exome

AF:

0.476

GnomAD4 genome

AF:

0.437

AC:

66446

AN:

152062

Hom.:

15182

Cov.:

AF XY:

0.433

AC XY:

32220

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.314

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.529

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.413

Gnomad4 FIN

AF:

0.463

Gnomad4 NFE

AF:

0.513

Gnomad4 OTH

AF:

0.447

Alfa

AF:

0.504

Hom.:

37502

Bravo

AF:

0.427

Asia WGS

AF:

0.286

AC:

996

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

Sep 04, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

6.6

DANN

Benign

0.84

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