rs7852970
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
NM_021138.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.92
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]
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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 | UniProt |
---|---|---|---|---|---|---|---|
TRAF2 | NM_021138.4 | c.*68G>A | 3_prime_UTR_variant | 11/11 | ENST00000247668.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF2 | ENST00000247668.7 | c.*68G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_021138.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.578 AC: 87851AN: 152010Hom.: 25699 Cov.: 34
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GnomAD3 exomes AF: 0.590 AC: 138229AN: 234216Hom.: 41534 AF XY: 0.601 AC XY: 76599AN XY: 127348
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GnomAD4 exome AF: 0.593 AC: 843291AN: 1421166Hom.: 252406 Cov.: 25 AF XY: 0.597 AC XY: 422903AN XY: 708676
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GnomAD4 genome ? AF: 0.578 AC: 87891AN: 152128Hom.: 25706 Cov.: 34 AF XY: 0.582 AC XY: 43265AN XY: 74376
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at