14-102799329-G-A

Variant names:

• chr14-102799329-G-A
• rs12147254
• NM_145725.3:c.-157+21654G>A

Variant summary

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

The NM_145725.3(TRAF3):​c.-157+21654G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,122 control chromosomes in the GnomAD database, including 5,198 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 0.24 (5198 hom., cov: 32)
• Consequence: TRAF3 NM_145725.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145725.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF3	NM_145725.3	MANE Select	c.-157+21654G>A		intron	N/A	NP_663777.1
	TRAF3	NM_003300.4		c.-18+21654G>A		intron	N/A	NP_003291.2
	TRAF3	NM_145726.3		c.-157+21654G>A		intron	N/A	NP_663778.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF3	ENST00000392745.8	TSL:1 MANE Select	c.-157+21654G>A		intron	N/A	ENSP00000376500.3
	TRAF3	ENST00000560371.5	TSL:1	c.-18+21654G>A		intron	N/A	ENSP00000454207.1
	TRAF3	ENST00000351691.10	TSL:1	c.-157+21654G>A		intron	N/A	ENSP00000332468.5

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35926 AN: 152004 Hom.: 5207 Cov.: 32

Gnomad AFR AF: 0.0772

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.236 AC: 35905 AN: 152122 Hom.: 5198 Cov.: 32 AF XY: 0.238 AC XY: 17676 AN XY: 74370

African (AFR) AF: 0.0771 AC: 3200 AN: 41512

American (AMR) AF: 0.187 AC: 2861 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2240 AN: 5178

South Asian (SAS) AF: 0.450 AC: 2171 AN: 4824

European-Finnish (FIN) AF: 0.268 AC: 2828 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20524 AN: 67972

Other (OTH) AF: 0.261 AC: 551 AN: 2114

Alfa AF: 0.271 Hom.: 15125

Bravo AF: 0.222

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-0.62
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: rs12147254; hg19: chr14-103265666;