chr20-63488424-G-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001958.5(EEF1A2):c.1266C>A(p.Gly422Gly) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,451,404 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G422G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0038 ( 18 hom. )

Consequence

EEF1A2
NM_001958.5 splice_region, synonymous

Scores

Splicing: ADA: 0.0002270

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -0.133

Publications

2 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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 20-63488424-G-T is Benign according to our data. Variant chr20-63488424-G-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 382763.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.133 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00265 (402/151814) while in subpopulation NFE AF = 0.0043 (292/67842). AF 95% confidence interval is 0.0039. There are 1 homozygotes in GnomAd4. There are 181 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High AC in GnomAd4 at 402 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001958.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1A2	NM_001958.5	MANE Select	c.1266C>A	p.Gly422Gly	splice_region synonymous	Exon 8 of 8	NP_001949.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
EEF1A2	ENST00000217182.6	TSL:1 MANE Select	c.1266C>A	p.Gly422Gly	splice_region synonymous	Exon 8 of 8	ENSP00000217182.3
EEF1A2	ENST00000298049.13	TSL:1	c.1266C>A	p.Gly422Gly	splice_region synonymous	Exon 8 of 9	ENSP00000298049.9
EEF1A2	ENST00000706949.1		c.1266C>A	p.Gly422Gly	splice_region synonymous	Exon 8 of 9	ENSP00000516669.1

Frequencies

GnomAD3 genomes

AF:

0.00265

AC:

402

AN:

151708

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000895

Gnomad AMI

AF:

0.00442

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000473

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00430

Gnomad OTH

AF:

0.00287

GnomAD2 exomes

AF:

0.00236

AC:

184

AN:

77974

AF XY:

0.00215

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00356

Gnomad ASJ exome

AF:

0.00144

Gnomad EAS exome

AF:

0.000386

Gnomad FIN exome

AF:

0.000506

Gnomad NFE exome

AF:

0.00383

Gnomad OTH exome

AF:

0.00469

GnomAD4 exome

AF:

0.00385

AC:

5001

AN:

1299590

Hom.:

Cov.:

AF XY:

0.00372

AC XY:

2381

AN XY:

639794

show subpopulations

African (AFR)

AF:

0.000656

AC:

AN:

25902

American (AMR)

AF:

0.00345

AC:

AN:

22886

Ashkenazi Jewish (ASJ)

AF:

0.00134

AC:

AN:

22386

East Asian (EAS)

AF:

0.00

AC:

AN:

27956

South Asian (SAS)

AF:

0.0000288

AC:

AN:

69500

European-Finnish (FIN)

AF:

0.000558

AC:

AN:

37666

Middle Eastern (MID)

AF:

0.000460

AC:

AN:

4348

European-Non Finnish (NFE)

AF:

0.00450

AC:

4657

AN:

1035706

Other (OTH)

AF:

0.00363

AC:

193

AN:

53240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

235

470

706

941

1176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

184

368

552

736

920

<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:

0.00265

AC:

402

AN:

151814

Hom.:

Cov.:

AF XY:

0.00244

AC XY:

181

AN XY:

74190

show subpopulations

African (AFR)

AF:

0.000893

AC:

AN:

41444

American (AMR)

AF:

0.00321

AC:

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.00260

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5102

South Asian (SAS)

AF:

0.00

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.000473

AC:

AN:

10572

Middle Eastern (MID)

AF:

0.00

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.00430

AC:

292

AN:

67842

Other (OTH)

AF:

0.00284

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.00365

Hom.:

Bravo

AF:

0.00291

ClinVar

ClinVar submissions as Germline

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (5)

not specified (2)

Developmental and epileptic encephalopathy, 33 (1)

Developmental and epileptic encephalopathy, 33;C4225343:Intellectual disability, autosomal dominant 38 (1)

Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

-0.13

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=72/28

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00023

dbscSNV1_RF

Benign

0.0080

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over