11-36492740-T-C

Position:

• chr11-36492740-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004620.4(TRAF6):​c.679-112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 765,826 control chromosomes in the GnomAD database, including 261,797 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 0.77 (46269 hom., cov: 31)
  • Exomes 𝑓: 0.84 (215528 hom.)
• Consequence: TRAF6 NM_004620.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

TRAF6 (HGNC:12036): (TNF receptor associated factor 6) The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins are associated with, and mediate signal transduction from, members of the TNF receptor superfamily. This protein has an amino terminal RING domain which is followed by four zinc-finger motifs, a central coiled-coil region and a highly conserved carboxyl terminal domain, known as the TRAF-C domain and mediates signaling from members of the TNF receptor superfamily as well as the Toll/IL-1 family. Signals from receptors such as CD40, TNFSF11/RANCE and IL-1 have been shown to be mediated by this protein. This protein also interacts with various protein kinases including IRAK1/IRAK, SRC and PKCzeta, which provides a link between distinct signaling pathways. This protein functions as a signal transducer in the NF-kappaB pathway that activates IkappaB kinase (IKK) in response to proinflammatory cytokines. The interaction of this protein with UBE2N/UBC13, and UBE2V1/UEV1A, which are ubiquitin conjugating enzymes catalyzing the formation of polyubiquitin chains, has been found to be required for IKK activation by this protein. This protein also interacts with the transforming growth factor (TGF) beta receptor complex and is required for Smad-independent activation of the JNK and p38 kinases. The protein encoded by this gene is a key molecule in antiviral innate and antigen-specific immune responses. [provided by RefSeq, Nov 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAF6	NM_004620.4	c.679-112A>G		intron_variant		ENST00000526995.6
TRAF6	NM_145803.3	c.679-112A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAF6	ENST00000526995.6	c.679-112A>G		intron_variant		1	NM_004620.4	P1
TRAF6	ENST00000348124.5	c.679-112A>G		intron_variant		1		P1
TRAF6	ENST00000529150.1	n.224-112A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117102 AN: 151946 Hom.: 46262 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.784

GnomAD4 exome AF: 0.836 AC: 513148 AN: 613762 Hom.: 215528 AF XY: 0.836 AC XY: 273838 AN XY: 327510

Gnomad4 AFR exome AF: 0.574

Gnomad4 AMR exome AF: 0.887

Gnomad4 ASJ exome AF: 0.801

Gnomad4 EAS exome AF: 0.873

Gnomad4 SAS exome AF: 0.817

Gnomad4 FIN exome AF: 0.842

Gnomad4 NFE exome AF: 0.844

Gnomad4 OTH exome AF: 0.824

GnomAD4 genome AF: 0.770 AC: 117147 AN: 152064 Hom.: 46269 Cov.: 31 AF XY: 0.775 AC XY: 57570 AN XY: 74330

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.786

Alfa AF: 0.803 Hom.: 10430

Bravo AF: 0.765

Asia WGS AF: 0.834 AC: 2900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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

Other links and lift over

dbSNP: rs2303439; hg19: chr11-36514290; COSMIC: COSV61922498;