chr9-120925556-G-A

Variant names:

• chr9-120925556-G-A
• rs1930781
• NM_005658.5:c.140+380C>T

Variant summary

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

The NM_005658.5(TRAF1):​c.140+380C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,158 control chromosomes in the GnomAD database, including 33,579 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 0.66 (33579 hom., cov: 33)
• Consequence: TRAF1 NM_005658.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• Publications: 14 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF1	NM_005658.5	c.140+380C>T		intron_variant	Intron 2 of 7	ENST00000373887.8	NP_005649.1
TRAF1	NM_001190945.2	c.140+380C>T		intron_variant	Intron 3 of 8		NP_001177874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAF1	ENST00000373887.8	c.140+380C>T		intron_variant	Intron 2 of 7	1	NM_005658.5	ENSP00000362994.3
TRAF1	ENST00000540010.1	c.140+380C>T		intron_variant	Intron 3 of 8	1		ENSP00000443183.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100768 AN: 152040 Hom.: 33536 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.663 AC: 100861 AN: 152158 Hom.: 33579 Cov.: 33 AF XY: 0.664 AC XY: 49388 AN XY: 74386

African (AFR) AF: 0.673 AC: 27948 AN: 41520

American (AMR) AF: 0.694 AC: 10607 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2579 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3736 AN: 5186

South Asian (SAS) AF: 0.818 AC: 3945 AN: 4822

European-Finnish (FIN) AF: 0.578 AC: 6106 AN: 10570

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43802 AN: 67988

Other (OTH) AF: 0.690 AC: 1459 AN: 2114

Alfa AF: 0.667 Hom.: 7019

Bravo AF: 0.670

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.56
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1930781; hg19: chr9-123687834; COSMIC: COSV65868757;