rs310617

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001958.5(EEF1A2):c.594T>C(p.Gly198Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,611,412 control chromosomes in the GnomAD database, including 268,138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 25576 hom., cov: 34)

Exomes 𝑓: 0.57 ( 242562 hom. )

Consequence

EEF1A2
NM_001958.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -5.77

Variant links:

Genes affected

EEF1A2 (HGNC:3192): (eukaryotic translation elongation factor 1 alpha 2) This gene encodes an isoform of the alpha subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This isoform (alpha 2) is expressed in brain, heart and skeletal muscle, and the other isoform (alpha 1) is expressed in brain, placenta, lung, liver, kidney, and pancreas. This gene may be critical in the development of ovarian cancer. [provided by RefSeq, Mar 2014]

EEF1A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 20-63494832-A-G is Benign according to our data. Variant chr20-63494832-A-G is described in ClinVar as [Benign]. Clinvar id is 379689.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-63494832-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-5.77 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1A2	NM_001958.5 link	c.594T>C	p.Gly198Gly	synonymous_variant	Exon 4 of 8	ENST00000217182.6	NP_001949.1	Q05639

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A2	ENST00000217182.6 link	c.594T>C	p.Gly198Gly	synonymous_variant	Exon 4 of 8	1	NM_001958.5	ENSP00000217182.3		Q05639

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87924

AN:

152002

Hom.:

25563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.596

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.561

Gnomad EAS

AF:

0.635

Gnomad SAS

AF:

0.614

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.576

GnomAD3 exomes

AF:

0.562

AC:

139295

AN:

247972

Hom.:

40002

AF XY:

0.569

AC XY:

76748

AN XY:

134896

show subpopulations

Gnomad AFR exome

AF:

0.595

Gnomad AMR exome

AF:

0.395

Gnomad ASJ exome

AF:

0.567

Gnomad EAS exome

AF:

0.619

Gnomad SAS exome

AF:

0.621

Gnomad FIN exome

AF:

0.635

Gnomad NFE exome

AF:

0.568

Gnomad OTH exome

AF:

0.571

GnomAD4 exome

AF:

0.575

AC:

838538

AN:

1459292

Hom.:

242562

Cov.:

AF XY:

0.576

AC XY:

418045

AN XY:

725820

show subpopulations

Gnomad4 AFR exome

AF:

0.593

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.562

Gnomad4 EAS exome

AF:

0.658

Gnomad4 SAS exome

AF:

0.611

Gnomad4 FIN exome

AF:

0.634

Gnomad4 NFE exome

AF:

0.572

Gnomad4 OTH exome

AF:

0.576

GnomAD4 genome

AF:

0.578

AC:

87973

AN:

152120

Hom.:

25576

Cov.:

AF XY:

0.584

AC XY:

43460

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.596

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.561

Gnomad4 EAS

AF:

0.636

Gnomad4 SAS

AF:

0.612

Gnomad4 FIN

AF:

0.632

Gnomad4 NFE

AF:

0.570

Gnomad4 OTH

AF:

0.578

Alfa

AF:

0.581

Hom.:

8594

Bravo

AF:

0.563

Asia WGS

AF:

0.620

AC:

2154

AN:

3478

EpiCase

AF:

0.562

EpiControl

AF:

0.564

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Jan 07, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Developmental and epileptic encephalopathy, 33

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 20, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn genetic diseases

Benign:1

Dec 31, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Intellectual disability, autosomal dominant 38

Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.027

DANN

Benign

0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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