Variant chr8-143580183-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001130053.5(EEF1D):c.1734C>T(p.Ala578=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 1,612,984 control chromosomes in the GnomAD database, including 275,017 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 19151 hom., cov: 32)

Exomes 𝑓: 0.58 ( 255866 hom. )

Consequence

EEF1D
NM_001130053.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.711

Variant links:

Genes affected

EEF1D (HGNC:3211): (eukaryotic translation elongation factor 1 delta) This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

EEF1D links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 8-143580183-G-A is Benign according to our data. Variant chr8-143580183-G-A is described in ClinVar as [Benign]. Clinvar id is 3060516.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.711 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEF1D	NM_001130053.5 linkuse as main transcript	c.1734C>T	p.Ala578=	synonymous_variant	9/10	ENST00000618139.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	UniProt
EEF1D	ENST00000618139.4 linkuse as main transcript	c.1734C>T	p.Ala578=	synonymous_variant	9/10	5	NM_001130053.5	P29692-2
	ENST00000623257.1 linkuse as main transcript	n.1826G>A		non_coding_transcript_exon_variant	1/1
	ENST00000529247.1 linkuse as main transcript	n.268+280G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70355

AN:

151894

Hom.:

19147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.431

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.490

GnomAD3 exomes

AF:

0.510

AC:

127296

AN:

249582

Hom.:

34738

AF XY:

0.518

AC XY:

70056

AN XY:

135152

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.432

Gnomad ASJ exome

AF:

0.492

Gnomad EAS exome

AF:

0.366

Gnomad SAS exome

AF:

0.441

Gnomad FIN exome

AF:

0.546

Gnomad NFE exome

AF:

0.621

Gnomad OTH exome

AF:

0.534

GnomAD4 exome

AF:

0.583

AC:

851458

AN:

1460972

Hom.:

255866

Cov.:

AF XY:

0.580

AC XY:

421432

AN XY:

726764

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.444

Gnomad4 ASJ exome

AF:

0.497

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.441

Gnomad4 FIN exome

AF:

0.545

Gnomad4 NFE exome

AF:

0.626

Gnomad4 OTH exome

AF:

0.547

GnomAD4 genome

AF:

0.463

AC:

70386

AN:

152012

Hom.:

19151

Cov.:

AF XY:

0.459

AC XY:

34100

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.517

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.544

Gnomad4 NFE

AF:

0.622

Gnomad4 OTH

AF:

0.494

Alfa

AF:

0.582

Hom.:

36697

Bravo

AF:

0.445

Asia WGS

AF:

0.374

AC:

1304

AN:

3478

EpiCase

AF:

0.624

EpiControl

AF:

0.627

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

EEF1D-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.86

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