rs6749955

Positions:

• chr2-232573207-G-A
• chr2-232573207-G-C
• chr2-232573207-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000409098.5(EIF4E2):​c.665+5993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: EIF4E2 ENST00000409098.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

Genes affected

EIF4E2 (HGNC:3293): (eukaryotic translation initiation factor 4E family member 2) Enables ubiquitin protein ligase binding activity. Involved in positive regulation of miRNA mediated inhibition of translation. Acts upstream of or within negative regulation of translation. Located in P-body. Part of mRNA cap binding activity complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF4E2	NM_001276336.2	c.665+5993G>A		intron_variant			NP_001263265.1
EIF4E2	NM_001276337.2	c.530+5993G>A		intron_variant			NP_001263266.1
EIF4E2	NM_001282958.2	c.666-1056G>A		intron_variant			NP_001269887.1
EIF4E2	NM_001330203.2	c.531-1056G>A		intron_variant			NP_001317132.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF4E2	ENST00000409098.5	c.665+5993G>A		intron_variant		1		ENSP00000386996	P4
EIF4E2	ENST00000409394.5	c.530+5993G>A		intron_variant		3		ENSP00000386983
EIF4E2	ENST00000409514.5	c.666-1056G>A		intron_variant		5		ENSP00000387336	A1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6749955; hg19: chr2-233437917;