20-63489162-G-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001958.5(EEF1A2):c.1030-10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,609,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

EEF1A2
NM_001958.5 intron

Scores

Splicing: ADA: 0.01469

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0220

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

complex neurodevelopmental disorder
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
developmental and epileptic encephalopathy, 33
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
autosomal dominant non-syndromic intellectual disability
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
undetermined early-onset epileptic encephalopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

EEF1A2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 20-63489162-G-C is Benign according to our data. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-63489162-G-C is described in CliVar as Likely_benign. Clinvar id is 2878123.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1A2	NM_001958.5 link	c.1030-10C>G		intron_variant	Intron 6 of 7	ENST00000217182.6	NP_001949.1	Q05639

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A2	ENST00000217182.6 link	c.1030-10C>G		intron_variant	Intron 6 of 7	1	NM_001958.5	ENSP00000217182.3		Q05639

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000343

AC:

AN:

1457508

Hom.:

Cov.:

AF XY:

0.00000414

AC XY:

AN XY:

724512

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33438

American (AMR)

AF:

0.00

AC:

AN:

44644

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26090

East Asian (EAS)

AF:

0.00

AC:

AN:

39650

South Asian (SAS)

AF:

0.00

AC:

AN:

86188

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51704

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5754

European-Non Finnish (NFE)

AF:

0.00000451

AC:

AN:

1109830

Other (OTH)

AF:

0.00

AC:

AN:

60210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152248

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41462

American (AMR)

AF:

0.0000654

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5198

South Asian (SAS)

AF:

0.00

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68044

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy, 33

Benign:1

Mar 25, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely 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

-0.82

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

0.022

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.015

dbscSNV1_RF

Benign

0.11

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over