rs4874159

Positions:

• chr8-143588780-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001130053.5(EEF1D):​c.1091+211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 663,628 control chromosomes in the GnomAD database, including 210,534 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 0.73 (42460 hom., cov: 31)
  • Exomes 𝑓: 0.80 (168074 hom.)
• Consequence: EEF1D NM_001130053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

EEF1D (HGNC:3211): (eukaryotic translation elongation factor 1 delta) This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -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 = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEF1D	NM_001130053.5	c.1091+211G>A		intron_variant		ENST00000618139.4	NP_001123525.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1D	ENST00000618139.4	c.1091+211G>A		intron_variant		5	NM_001130053.5	ENSP00000484536

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111236 AN: 151934 Hom.: 42450 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.768

GnomAD4 exome AF: 0.804 AC: 411192 AN: 511576 Hom.: 168074 Cov.: 6 AF XY: 0.800 AC XY: 212655 AN XY: 265930

Gnomad4 AFR exome AF: 0.518

Gnomad4 AMR exome AF: 0.742

Gnomad4 ASJ exome AF: 0.823

Gnomad4 EAS exome AF: 0.521

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.832

Gnomad4 NFE exome AF: 0.854

Gnomad4 OTH exome AF: 0.795

GnomAD4 genome AF: 0.732 AC: 111280 AN: 152052 Hom.: 42460 Cov.: 31 AF XY: 0.729 AC XY: 54192 AN XY: 74350

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.769

Alfa AF: 0.829 Hom.: 74262

Bravo AF: 0.717

Asia WGS AF: 0.595 AC: 2072 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	1.4
DANN	Benign	0.33

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

Other links and lift over

dbSNP: rs4874159; hg19: chr8-144670950;