3-71694655-A-G

Position:

• chr3-71694655-A-G

Variant summary

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

The NM_001134651.2(EIF4E3):​c.406-714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,032 control chromosomes in the GnomAD database, including 7,266 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 0.31 (7266 hom., cov: 32)
• Consequence: EIF4E3 NM_001134651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF4E3	NM_001134651.2	c.406-714T>C		intron_variant		ENST00000425534.8	NP_001128123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF4E3	ENST00000425534.8	c.406-714T>C		intron_variant		2	NM_001134651.2	ENSP00000393324.2
ENSG00000285708	ENST00000647725.1	c.-642-714T>C		intron_variant				ENSP00000497585.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46524 AN: 151914 Hom.: 7251 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.306 AC: 46569 AN: 152032 Hom.: 7266 Cov.: 32 AF XY: 0.313 AC XY: 23240 AN XY: 74306

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.296

Alfa AF: 0.309 Hom.: 5236

Bravo AF: 0.292

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.4
DANN	Benign	0.84

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: rs7620998; hg19: chr3-71743806;