rs11160706

Variant names:

• chr14-102895399-G-A
• rs11160706
• NM_145725.3:c.820-1862G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-102895399-G-A
• chr14-102895399-G-C
• chr14-102895399-G-T

Variant summary

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

The NM_145725.3(TRAF3):​c.820-1862G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,176 control chromosomes in the GnomAD database, including 16,087 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 0.40 (16087 hom., cov: 33)
• Consequence: TRAF3 NM_145725.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 8 publications found

Genes affected

TRAF3 (HGNC:12033): (TNF receptor associated factor 3) The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from, members of the TNF receptor (TNFR) superfamily. This protein participates in the signal transduction of CD40, a TNFR family member important for the activation of the immune response. This protein is found to be a critical component of the lymphotoxin-beta receptor (LTbetaR) signaling complex, which induces NF-kappaB activation and cell death initiated by LTbeta ligation. Epstein-Barr virus encoded latent infection membrane protein-1 (LMP1) can interact with this and several other members of the TRAF family, which may be essential for the oncogenic effects of LMP1. The protein also plays a role in the regulation of antiviral response. Mutations in this are associated with Encephalopathy, acute, infection-induced, herpes-specific 5. [provided by RefSeq, Jul 2020]

TRAF3 Gene-Disease associations (from GenCC):

• TRAF3 haploinsufficiency

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF3	NM_145725.3	c.820-1862G>A		intron_variant	Intron 9 of 11	ENST00000392745.8	NP_663777.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAF3	ENST00000392745.8	c.820-1862G>A		intron_variant	Intron 9 of 11	1	NM_145725.3	ENSP00000376500.3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60293 AN: 152058 Hom.: 16016 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.397 AC: 60435 AN: 152176 Hom.: 16087 Cov.: 33 AF XY: 0.395 AC XY: 29352 AN XY: 74396

African (AFR) AF: 0.755 AC: 31337 AN: 41528

American (AMR) AF: 0.392 AC: 5989 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3468

East Asian (EAS) AF: 0.388 AC: 2010 AN: 5176

South Asian (SAS) AF: 0.173 AC: 838 AN: 4832

European-Finnish (FIN) AF: 0.260 AC: 2742 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15286 AN: 68004

Other (OTH) AF: 0.367 AC: 775 AN: 2112

Alfa AF: 0.343 Hom.: 2051

Bravo AF: 0.428

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.68
PhyloP100		-0.30
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: rs11160706; hg19: chr14-103361736;