rs3761847
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001190945.2(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
NM_001190945.2 intron
NM_001190945.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0210
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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.529 AC: 80181AN: 151694Hom.: 21701 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
80181
AN:
151694
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome AF: 0.660 AC: 128AN: 194Hom.: 47 Cov.: 0 AF XY: 0.638 AC XY: 74AN XY: 116 show subpopulations
GnomAD4 exome
AF:
AC:
128
AN:
194
Hom.:
Cov.:
0
AF XY:
AC XY:
74
AN XY:
116
Gnomad4 AFR exome
AF:
AC:
0
AN:
2
Gnomad4 AMR exome
AF:
AC:
2
AN:
2
Gnomad4 ASJ exome
AF:
AC:
4
AN:
4
Gnomad4 EAS exome
AF:
AC:
0
AN:
2
Gnomad4 SAS exome
AF:
AC:
2
AN:
4
Gnomad4 FIN exome
AF:
AC:
27
AN:
54
Gnomad4 NFE exome
AF:
AC:
68
AN:
90
Gnomad4 Remaining exome
AF:
AC:
21
AN:
32
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.529 AC: 80233AN: 151812Hom.: 21716 Cov.: 31 AF XY: 0.534 AC XY: 39598AN XY: 74180 show subpopulations
GnomAD4 genome
AF:
AC:
80233
AN:
151812
Hom.:
Cov.:
31
AF XY:
AC XY:
39598
AN XY:
74180
Gnomad4 AFR
AF:
AC:
0.404718
AN:
0.404718
Gnomad4 AMR
AF:
AC:
0.59983
AN:
0.59983
Gnomad4 ASJ
AF:
AC:
0.663306
AN:
0.663306
Gnomad4 EAS
AF:
AC:
0.524031
AN:
0.524031
Gnomad4 SAS
AF:
AC:
0.702381
AN:
0.702381
Gnomad4 FIN
AF:
AC:
0.542686
AN:
0.542686
Gnomad4 NFE
AF:
AC:
0.565685
AN:
0.565685
Gnomad4 OTH
AF:
AC:
0.574478
AN:
0.574478
Heterozygous variant carriers
0
1911
3822
5733
7644
9555
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
716
1432
2148
2864
3580
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2134
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=300/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at