chr9-136928090-C-T

Variant names:

• chr9-136928090-C-T
• rs908831
• ENST00000850853.1:c.*2189C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000850853.1(TRAF2):​c.*2189C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,884 control chromosomes in the GnomAD database, including 30,665 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 0.63 (30665 hom., cov: 31)
• Consequence: TRAF2 ENST00000850853.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAF2	ENST00000850853.1	c.*2189C>T		3_prime_UTR_variant	Exon 11 of 11			ENSP00000520942.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96056 AN: 151766 Hom.: 30653 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.639

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.633 AC: 96123 AN: 151884 Hom.: 30665 Cov.: 31 AF XY: 0.637 AC XY: 47318 AN XY: 74250

African (AFR) AF: 0.633 AC: 26188 AN: 41378

American (AMR) AF: 0.540 AC: 8243 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2326 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4391 AN: 5166

South Asian (SAS) AF: 0.750 AC: 3605 AN: 4808

European-Finnish (FIN) AF: 0.660 AC: 6953 AN: 10540

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42290 AN: 67954

Other (OTH) AF: 0.644 AC: 1358 AN: 2108

Alfa AF: 0.580 Hom.: 4462

Bravo AF: 0.620

Asia WGS AF: 0.766 AC: 2662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs908831; hg19: chr9-139822542;