rs13070781

chr3-71704835-G-Achr3-71704835-G-C

Variant summary

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

The NM_001134651.2(EIF4E3):c.250-5127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,160 control chromosomes in the GnomAD database, including 39,079 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 0.71 (39079 hom., cov: 32)
• Consequence: EIF4E3 NM_001134651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

Genes affected

EIF4E3 (HGNC:31837): (eukaryotic translation initiation factor 4E family member 3) EIF4E3 belongs to the EIF4E family of translational initiation factors that interact with the 5-prime cap structure of mRNA and recruit mRNA to the ribosome (Joshi et al., 2004 [PubMed 15153109]).[supplied by OMIM, Mar 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF4E3	NM_001134651.2	c.250-5127C>T		intron_variant		ENST00000425534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF4E3	ENST00000425534.8	c.250-5127C>T		intron_variant		2	NM_001134651.2	P1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108255 AN: 152042 Hom.: 39036 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.712 AC: 108356 AN: 152160 Hom.: 39079 Cov.: 32 AF XY: 0.714 AC XY: 53121 AN XY: 74408

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.688

Alfa AF: 0.695 Hom.: 6126

Bravo AF: 0.702

Asia WGS AF: 0.691 AC: 2407 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	0.40
Dann	Benign	0.22

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: rs13070781; hg19: chr3-71753986;