rs11119344

Positions:

• chr1-209770144-G-A

Variant summary

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

The NM_025228.4(TRAF3IP3):​c.703-2804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,168 control chromosomes in the GnomAD database, including 2,830 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 0.18 (2830 hom., cov: 33)
• Consequence: TRAF3IP3 NM_025228.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

Genes affected

TRAF3IP3 (HGNC:30766): (TRAF3 interacting protein 3) The gene encodes a protein that mediates cell growth by modulating the c-Jun N-terminal kinase signal transduction pathway. The encoded protein may also interact with a large multi-protein assembly containing the phosphatase 2A catalytic subunit. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAF3IP3	NM_025228.4	c.703-2804G>A		intron_variant		ENST00000367025.8	NP_079504.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAF3IP3	ENST00000367025.8	c.703-2804G>A		intron_variant		1	NM_025228.4	ENSP00000355992	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27210 AN: 152050 Hom.: 2832 Cov.: 33

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.179 AC: 27209 AN: 152168 Hom.: 2830 Cov.: 33 AF XY: 0.179 AC XY: 13305 AN XY: 74366

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.191

Alfa AF: 0.223 Hom.: 5056

Bravo AF: 0.167

Asia WGS AF: 0.116 AC: 405 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	9.5
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs11119344; hg19: chr1-209943489;