Variant chr3-128153651-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_021937.5(EEFSEC):c.144G>T(p.Thr48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00369 in 1,598,438 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 1 hom., cov: 29)

Exomes 𝑓: 0.0038 ( 20 hom. )

Consequence

EEFSEC
NM_021937.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.845

Variant links:

Genes affected

EEFSEC (HGNC:24614): (eukaryotic elongation factor, selenocysteine-tRNA specific) Predicted to enable translation elongation factor activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

EEFSEC links:

RUVBL1 (HGNC:10474): (RuvB like AAA ATPase 1) This gene encodes a protein that has both DNA-dependent ATPase and DNA helicase activities and belongs to the ATPases associated with diverse cellular activities (AAA+) protein family. The encoded protein associates with several multisubunit transcriptional complexes and with protein complexes involved in both ATP-dependent remodeling and histone modification. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

RUVBL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant 3-128153651-G-T is Benign according to our data. Variant chr3-128153651-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2654109.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.845 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEFSEC	NM_021937.5 linkuse as main transcript	c.144G>T	p.Thr48=	synonymous_variant	1/7	ENST00000254730.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEFSEC	ENST00000254730.11 linkuse as main transcript	c.144G>T	p.Thr48=	synonymous_variant	1/7	1	NM_021937.5	P1	P57772-1
EEFSEC	ENST00000483457.1 linkuse as main transcript	c.144G>T	p.Thr48=	synonymous_variant	1/5	5
RUVBL1	ENST00000464873.5 linkuse as main transcript	c.-488C>A		5_prime_UTR_variant	1/10	2
EEFSEC	ENST00000484438.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00239

AC:

364

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000916

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00401

Gnomad OTH

AF:

0.000955

GnomAD3 exomes

AF:

0.00253

AC:

561

AN:

221714

Hom.:

AF XY:

0.00265

AC XY:

327

AN XY:

123320

show subpopulations

Gnomad AFR exome

AF:

0.000792

Gnomad AMR exome

AF:

0.00121

Gnomad ASJ exome

AF:

0.00622

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00382

Gnomad FIN exome

AF:

0.000556

Gnomad NFE exome

AF:

0.00318

Gnomad OTH exome

AF:

0.00270

GnomAD4 exome

AF:

0.00382

AC:

5527

AN:

1446188

Hom.:

Cov.:

AF XY:

0.00384

AC XY:

2766

AN XY:

719776

show subpopulations

Gnomad4 AFR exome

AF:

0.000896

Gnomad4 AMR exome

AF:

0.00110

Gnomad4 ASJ exome

AF:

0.00762

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00373

Gnomad4 FIN exome

AF:

0.000468

Gnomad4 NFE exome

AF:

0.00428

Gnomad4 OTH exome

AF:

0.00245

GnomAD4 genome

AF:

0.00239

AC:

364

AN:

152250

Hom.:

Cov.:

AF XY:

0.00230

AC XY:

171

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.000915

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000753

Gnomad4 NFE

AF:

0.00402

Gnomad4 OTH

AF:

0.000945

Alfa

AF:

0.00296

Hom.:

Bravo

AF:

0.00228

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

EEFSEC: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.92

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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