rs4874159

Variant names:

• chr8-143588780-C-T
• rs4874159
• NM_001130053.5:c.1091+211G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

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

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 = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130053.5. 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
	EEF1D	NM_001130053.5	MANE Select	c.1091+211G>A		intron	N/A	NP_001123525.3
	EEF1D	NM_032378.7		c.1091+211G>A		intron	N/A	NP_115754.4
	EEF1D	NM_001130055.4		c.-4-1931G>A		intron	N/A	NP_001123527.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1D	ENST00000618139.4	TSL:5 MANE Select	c.1091+211G>A		intron	N/A	ENSP00000484536.2
	EEF1D	ENST00000532741.5	TSL:1	c.1241+211G>A		intron	N/A	ENSP00000434070.1
	EEF1D	ENST00000442189.6	TSL:1	c.1091+211G>A		intron	N/A	ENSP00000391944.2

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

African (AFR) AF: 0.518 AC: 6642 AN: 12832

American (AMR) AF: 0.742 AC: 11840 AN: 15952

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 11235 AN: 13646

East Asian (EAS) AF: 0.521 AC: 15156 AN: 29106

South Asian (SAS) AF: 0.700 AC: 32168 AN: 45950

European-Finnish (FIN) AF: 0.832 AC: 24055 AN: 28912

Middle Eastern (MID) AF: 0.807 AC: 1675 AN: 2076

European-Non Finnish (NFE) AF: 0.854 AC: 286457 AN: 335486

Other (OTH) AF: 0.795 AC: 21964 AN: 27616

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

African (AFR) AF: 0.519 AC: 21493 AN: 41452

American (AMR) AF: 0.768 AC: 11731 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2621 AN: 5158

South Asian (SAS) AF: 0.694 AC: 3347 AN: 4822

European-Finnish (FIN) AF: 0.826 AC: 8749 AN: 10598

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57847 AN: 67950

Other (OTH) AF: 0.769 AC: 1624 AN: 2112

Alfa AF: 0.822 Hom.: 99615

Bravo AF: 0.717

Asia WGS AF: 0.595 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.40
PromoterAI		0.041	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4874159; hg19: chr8-144670950;