rs17008958

Variant names:

• chr3-71706337-G-A
• rs17008958
• NM_001134651.2:c.249+4075C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-71706337-G-A
• chr3-71706337-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.249+4075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,110 control chromosomes in the GnomAD database, including 1,732 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 0.14 (1732 hom., cov: 32)
• Consequence: EIF4E3 NM_001134651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF4E3	NM_001134651.2	c.249+4075C>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.249+4075C>T		intron_variant	Intron 2 of 6	2	NM_001134651.2	ENSP00000393324.2
ENSG00000285708	ENST00000647725.1	c.-738+4075C>T		intron_variant	Intron 3 of 25			ENSP00000497585.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21976 AN: 151992 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.145 AC: 22013 AN: 152110 Hom.: 1732 Cov.: 32 AF XY: 0.147 AC XY: 10902 AN XY: 74356

African (AFR) AF: 0.130 AC: 5411 AN: 41482

American (AMR) AF: 0.112 AC: 1704 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1891 AN: 5168

South Asian (SAS) AF: 0.185 AC: 890 AN: 4818

European-Finnish (FIN) AF: 0.178 AC: 1882 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9159 AN: 67998

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.137 Hom.: 5138

Bravo AF: 0.140

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.083
DANN	Benign	0.59
PhyloP100		-0.60
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: rs17008958; hg19: chr3-71755488;