9-120921704-G-T

Variant names:

• chr9-120921704-G-T
• rs7021049
• NM_005658.5:c.228+2001C>A

Variant summary

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

The NM_005658.5(TRAF1):​c.228+2001C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,864 control chromosomes in the GnomAD database, including 18,217 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 0.46 (18217 hom., cov: 30)
• Consequence: TRAF1 NM_005658.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 20 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF1	NM_005658.5	c.228+2001C>A		intron_variant	Intron 3 of 7	ENST00000373887.8	NP_005649.1
TRAF1	NM_001190945.2	c.228+2001C>A		intron_variant	Intron 4 of 8		NP_001177874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAF1	ENST00000373887.8	c.228+2001C>A		intron_variant	Intron 3 of 7	1	NM_005658.5	ENSP00000362994.3
TRAF1	ENST00000540010.1	c.228+2001C>A		intron_variant	Intron 4 of 8	1		ENSP00000443183.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69291 AN: 151748 Hom.: 18205 Cov.: 30

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.456 AC: 69321 AN: 151864 Hom.: 18217 Cov.: 30 AF XY: 0.463 AC XY: 34362 AN XY: 74198

African (AFR) AF: 0.173 AC: 7181 AN: 41436

American (AMR) AF: 0.565 AC: 8622 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2577 AN: 5156

South Asian (SAS) AF: 0.694 AC: 3334 AN: 4806

European-Finnish (FIN) AF: 0.542 AC: 5692 AN: 10506

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37924 AN: 67934

Other (OTH) AF: 0.526 AC: 1109 AN: 2108

Alfa AF: 0.541 Hom.: 27842

Bravo AF: 0.445

Asia WGS AF: 0.562 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		0.061
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: rs7021049; hg19: chr9-123683982;