Variant chr9-136925969-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021138.4(TRAF2):c.*68G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 1,573,294 control chromosomes in the GnomAD database, including 278,112 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 25706 hom., cov: 34)

Exomes 𝑓: 0.59 ( 252406 hom. )

Consequence

TRAF2
NM_021138.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.92

Variant links:

Genes affected

TRAF2 (HGNC:12032): (TNF receptor associated factor 2) The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from members of the TNF receptor superfamily. This protein directly interacts with TNF receptors, and forms a heterodimeric complex with TRAF1. This protein is required for TNF-alpha-mediated activation of MAPK8/JNK and NF-kappaB. The protein complex formed by this protein and TRAF1 interacts with the inhibitor-of-apoptosis proteins (IAPs), and functions as a mediator of the anti-apoptotic signals from TNF receptors. The interaction of this protein with TRADD, a TNF receptor associated apoptotic signal transducer, ensures the recruitment of IAPs for the direct inhibition of caspase activation. BIRC2/c-IAP1, an apoptosis inhibitor possessing ubiquitin ligase activity, can unbiquitinate and induce the degradation of this protein, and thus potentiate TNF-induced apoptosis. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of only one transcript has been determined. [provided by RefSeq, Jul 2008]

TRAF2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAF2	NM_021138.4 linkuse as main transcript	c.*68G>A		3_prime_UTR_variant	11/11	ENST00000247668.7	NP_066961.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAF2	ENST00000247668.7 linkuse as main transcript	c.*68G>A		3_prime_UTR_variant	11/11	1	NM_021138.4	ENSP00000247668	P1	Q12933-1

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87851

AN:

152010

Hom.:

25699

Cov.:

show subpopulations

Gnomad AFR

AF:

0.514

Gnomad AMI

AF:

0.606

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.661

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.646

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.586

GnomAD3 exomes

AF:

0.590

AC:

138229

AN:

234216

Hom.:

41534

AF XY:

0.601

AC XY:

76599

AN XY:

127348

show subpopulations

Gnomad AFR exome

AF:

0.518

Gnomad AMR exome

AF:

0.417

Gnomad ASJ exome

AF:

0.665

Gnomad EAS exome

AF:

0.712

Gnomad SAS exome

AF:

0.660

Gnomad FIN exome

AF:

0.652

Gnomad NFE exome

AF:

0.597

Gnomad OTH exome

AF:

0.605

GnomAD4 exome

AF:

0.593

AC:

843291

AN:

1421166

Hom.:

252406

Cov.:

AF XY:

0.597

AC XY:

422903

AN XY:

708676

show subpopulations

Gnomad4 AFR exome

AF:

0.504

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.664

Gnomad4 EAS exome

AF:

0.735

Gnomad4 SAS exome

AF:

0.663

Gnomad4 FIN exome

AF:

0.649

Gnomad4 NFE exome

AF:

0.587

Gnomad4 OTH exome

AF:

0.602

GnomAD4 genome

AF:

0.578

AC:

87891

AN:

152128

Hom.:

25706

Cov.:

AF XY:

0.582

AC XY:

43265

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.513

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.661

Gnomad4 EAS

AF:

0.709

Gnomad4 SAS

AF:

0.684

Gnomad4 FIN

AF:

0.646

Gnomad4 NFE

AF:

0.602

Gnomad4 OTH

AF:

0.591

Alfa

AF:

0.579

Hom.:

18464

Bravo

AF:

0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.097

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over