rs13070781

Variant names:

• chr3-71704835-G-A
• rs13070781
• NM_001134651.2:c.250-5127C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-71704835-G-A
• chr3-71704835-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000285708 (HGNC:):

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 = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF4E3	NM_001134651.2	c.250-5127C>T		intron_variant	Intron 2 of 6	ENST00000425534.8	NP_001128123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF4E3	ENST00000425534.8	c.250-5127C>T		intron_variant	Intron 2 of 6	2	NM_001134651.2	ENSP00000393324.2
ENSG00000285708	ENST00000647725.1	c.-737-5127C>T		intron_variant	Intron 3 of 25			ENSP00000497585.1

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

African (AFR) AF: 0.825 AC: 34291 AN: 41540

American (AMR) AF: 0.589 AC: 9001 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3494 AN: 5156

South Asian (SAS) AF: 0.707 AC: 3410 AN: 4824

European-Finnish (FIN) AF: 0.761 AC: 8058 AN: 10592

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45572 AN: 67992

Other (OTH) AF: 0.688 AC: 1451 AN: 2108

Alfa AF: 0.689 Hom.: 11270

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
PhyloP100		-0.25
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: rs13070781; hg19: chr3-71753986;