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GeneBe

rs3761847

Variant summary

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

The ENST00000540010.1(TRAF1):c.-366+1153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,006 control chromosomes in the GnomAD database, including 21,763 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 0.53 ( 21716 hom., cov: 31)
Exomes 𝑓: 0.66 ( 47 hom. )

Consequence

TRAF1
ENST00000540010.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0210
Variant links:
Genes affected
TRAF1 (HGNC:12031): (TNF receptor associated factor 1) The protein encoded by this gene is a member of the TNF receptor (TNFR) associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from various receptors of the TNFR superfamily. This protein and TRAF2 form a heterodimeric complex, which is required for TNF-alpha-mediated activation of MAPK8/JNK and NF-kappaB. The protein complex formed by this protein and TRAF2 also interacts with inhibitor-of-apoptosis proteins (IAPs), and thus mediates the anti-apoptotic signals from TNF receptors. The expression of this protein can be induced by Epstein-Barr virus (EBV). EBV infection membrane protein 1 (LMP1) is found to interact with this and other TRAF proteins; this interaction is thought to link LMP1-mediated B lymphocyte transformation to the signal transduction from TNFR family receptors. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

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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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAF1NM_001190945.2 linkuse as main transcriptc.-366+1153C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAF1ENST00000540010.1 linkuse as main transcriptc.-366+1153C>T intron_variant 1 P1Q13077-1

Frequencies

GnomAD3 genomes
AF:
0.529
AC:
80181
AN:
151694
Hom.:
21701
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.405
Gnomad AMI
AF:
0.455
Gnomad AMR
AF:
0.599
Gnomad ASJ
AF:
0.663
Gnomad EAS
AF:
0.523
Gnomad SAS
AF:
0.701
Gnomad FIN
AF:
0.543
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.566
Gnomad OTH
AF:
0.574
GnomAD4 exome
AF:
0.660
AC:
128
AN:
194
Hom.:
47
Cov.:
0
AF XY:
0.638
AC XY:
74
AN XY:
116
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.756
Gnomad4 OTH exome
AF:
0.656
GnomAD4 genome
AF:
0.529
AC:
80233
AN:
151812
Hom.:
21716
Cov.:
31
AF XY:
0.534
AC XY:
39598
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.405
Gnomad4 AMR
AF:
0.600
Gnomad4 ASJ
AF:
0.663
Gnomad4 EAS
AF:
0.524
Gnomad4 SAS
AF:
0.702
Gnomad4 FIN
AF:
0.543
Gnomad4 NFE
AF:
0.566
Gnomad4 OTH
AF:
0.574
Alfa
AF:
0.574
Hom.:
50748
Bravo
AF:
0.525
Asia WGS
AF:
0.614
AC:
2134
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
1.7
Dann
Benign
0.76

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.

Other links and lift over

dbSNP: rs3761847; hg19: chr9-123690239; COSMIC: COSV65868031; API