Variant 8-38057220-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_004095.4(EIF4EBP1):c.285G>A(p.Gln95Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,614,060 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0093 ( 10 hom., cov: 34)

Exomes 𝑓: 0.013 ( 147 hom. )

Consequence

EIF4EBP1
NM_004095.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.212

Variant links:

Genes affected

EIF4EBP1 (HGNC:3288): (eukaryotic translation initiation factor 4E binding protein 1) This gene encodes one member of a family of translation repressor proteins. The protein directly interacts with eukaryotic translation initiation factor 4E (eIF4E), which is a limiting component of the multisubunit complex that recruits 40S ribosomal subunits to the 5' end of mRNAs. Interaction of this protein with eIF4E inhibits complex assembly and represses translation. This protein is phosphorylated in response to various signals including UV irradiation and insulin signaling, resulting in its dissociation from eIF4E and activation of mRNA translation. [provided by RefSeq, Jul 2008]

EIF4EBP1 links:

EIF4EBP1 (HGNC:):

EIF4EBP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 8-38057220-G-A is Benign according to our data. Variant chr8-38057220-G-A is described in ClinVar as [Benign]. Clinvar id is 774460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.212 with no splicing effect.

BS2

High AC in GnomAd4 at 1417 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF4EBP1	NM_004095.4 linkuse as main transcript	c.285G>A	p.Gln95Gln	synonymous_variant	2/3	ENST00000338825.5	NP_004086.1	Q13541

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF4EBP1	ENST00000338825.5 linkuse as main transcript	c.285G>A	p.Gln95Gln	synonymous_variant	2/3	1	NM_004095.4	ENSP00000340691.4		Q13541
EIF4EBP1	ENST00000520657.1 linkuse as main transcript	n.193G>A		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.00931

AC:

1417

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00289

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.00811

Gnomad ASJ

AF:

0.0329

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00662

Gnomad FIN

AF:

0.00442

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0137

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00940

AC:

2359

AN:

250876

Hom.:

AF XY:

0.00931

AC XY:

1262

AN XY:

135600

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00616

Gnomad ASJ exome

AF:

0.0308

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00454

Gnomad FIN exome

AF:

0.00231

Gnomad NFE exome

AF:

0.0136

Gnomad OTH exome

AF:

0.0132

GnomAD4 exome

AF:

0.0129

AC:

18802

AN:

1461730

Hom.:

147

Cov.:

AF XY:

0.0124

AC XY:

9045

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.00164

Gnomad4 AMR exome

AF:

0.00637

Gnomad4 ASJ exome

AF:

0.0317

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00479

Gnomad4 FIN exome

AF:

0.00286

Gnomad4 NFE exome

AF:

0.0145

Gnomad4 OTH exome

AF:

0.0149

GnomAD4 genome

AF:

0.00930

AC:

1417

AN:

152330

Hom.:

Cov.:

AF XY:

0.00913

AC XY:

680

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00289

Gnomad4 AMR

AF:

0.00810

Gnomad4 ASJ

AF:

0.0329

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00662

Gnomad4 FIN

AF:

0.00442

Gnomad4 NFE

AF:

0.0137

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.0132

Hom.:

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0158

EpiControl

AF:

0.0141

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.7

DANN

Benign

0.52

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over