rs3787116

Variant names:

• chr20-63478052-G-A
• rs3787116
• ENST00000298049.13:c.*9801C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-63478052-G-A
• chr20-63478052-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000298049.13(EEF1A2):​c.*9801C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,092 control chromosomes in the GnomAD database, including 3,327 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3327 hom., cov: 32)
• Consequence: EEF1A2 ENST00000298049.13 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 12 publications found

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

ENSG00000302022 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1A2	ENST00000298049.13	c.*9801C>T		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000298049.9
ENSG00000302022	ENST00000783502.1	n.420C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31424 AN: 151974 Hom.: 3321 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31441 AN: 152092 Hom.: 3327 Cov.: 32 AF XY: 0.201 AC XY: 14950 AN XY: 74346

African (AFR) AF: 0.188 AC: 7806 AN: 41486

American (AMR) AF: 0.184 AC: 2804 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3470

East Asian (EAS) AF: 0.161 AC: 829 AN: 5160

South Asian (SAS) AF: 0.176 AC: 847 AN: 4816

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10596

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16208 AN: 67966

Other (OTH) AF: 0.224 AC: 474 AN: 2116

Alfa AF: 0.231 Hom.: 16789

Bravo AF: 0.211

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.73
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs3787116; hg19: chr20-62109405; COSMIC: COSV60105805;