NM_001961.4:c.486C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001961.4(EEF2):c.486C>T(p.Arg162Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 1,613,394 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.00074 ( 2 hom., cov: 33)

Exomes 𝑓: 0.00055 ( 7 hom. )

Consequence

EEF2
NM_001961.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.05

Publications

6 publications found

Variant links:

Genes affected

EEF2 (HGNC:3214): (eukaryotic translation elongation factor 2) This gene encodes a member of the GTP-binding translation elongation factor family. This protein is an essential factor for protein synthesis. It promotes the GTP-dependent translocation of the nascent protein chain from the A-site to the P-site of the ribosome. This protein is completely inactivated by EF-2 kinase phosporylation. [provided by RefSeq, Jul 2008]

EEF2 Gene-Disease associations (from GenCC):

spinocerebellar ataxia type 26
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
neurodevelopmental disorder
Inheritance: AD Classification: MODERATE, LIMITED Submitted by: G2P, Ambry Genetics

EEF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 19-3982933-G-A is Benign according to our data. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-3982933-G-A is described in CliVar as Benign. Clinvar id is 585834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.05 with no splicing effect.

BS2

High AC in GnomAd4 at 112 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF2	NM_001961.4 link	c.486C>T	p.Arg162Arg	synonymous_variant	Exon 4 of 15	ENST00000309311.7	NP_001952.1	P13639

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF2	ENST00000309311.7 link	c.486C>T	p.Arg162Arg	synonymous_variant	Exon 4 of 15	5	NM_001961.4	ENSP00000307940.5		P13639

Frequencies

GnomAD3 genomes

AF:

0.000742

AC:

113

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0179

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000103

Gnomad OTH

AF:

0.000956

GnomAD2 exomes

AF:

0.00119

AC:

297

AN:

249652

AF XY:

0.00131

show subpopulations

Gnomad AFR exome

AF:

0.0000619

Gnomad AMR exome

AF:

0.000145

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0148

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000444

Gnomad OTH exome

AF:

0.000327

GnomAD4 exome

AF:

0.000550

AC:

803

AN:

1461062

Hom.:

Cov.:

AF XY:

0.000563

AC XY:

409

AN XY:

726866

show subpopulations

African (AFR)

AF:

0.0000597

AC:

AN:

33476

American (AMR)

AF:

0.0000895

AC:

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.0000383

AC:

AN:

26134

East Asian (EAS)

AF:

0.0152

AC:

605

AN:

39686

South Asian (SAS)

AF:

0.000441

AC:

AN:

86214

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52770

Middle Eastern (MID)

AF:

0.000173

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0000809

AC:

AN:

1111934

Other (OTH)

AF:

0.00103

AC:

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

110

164

219

274

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000735

AC:

112

AN:

152332

Hom.:

Cov.:

AF XY:

0.000832

AC XY:

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.0000962

AC:

AN:

41580

American (AMR)

AF:

0.000131

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.0178

AC:

AN:

5172

South Asian (SAS)

AF:

0.00103

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000103

AC:

AN:

68030

Other (OTH)

AF:

0.000946

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000979

Hom.:

Bravo

AF:

0.000616

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Oct 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 22, 2018

Athena Diagnostics

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

-0.83

CADD

Benign

3.3

(source)

DANN

Benign

0.92

PhyloP100

-4.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=97/3

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over