rs4874163

Positions:

• chr8-143592602-G-A

Variant summary

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

The NM_001130053.5(EEF1D):​c.-1+45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 985,088 control chromosomes in the GnomAD database, including 340,890 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 (42087 hom., cov: 34)
  • Exomes 𝑓: 0.84 (298803 hom.)
• Consequence: EEF1D NM_001130053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584

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]

EEF1D (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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.-1+45C>T		intron_variant		ENST00000618139.4	NP_001123525.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1D	ENST00000618139.4	c.-1+45C>T		intron_variant		5	NM_001130053.5	ENSP00000484536.2

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110544 AN: 152050 Hom.: 42080 Cov.: 34

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.764

GnomAD4 exome AF: 0.845 AC: 703583 AN: 832920 Hom.: 298803 Cov.: 31 AF XY: 0.845 AC XY: 325226 AN XY: 384666

Gnomad4 AFR exome AF: 0.492

Gnomad4 AMR exome AF: 0.761

Gnomad4 ASJ exome AF: 0.822

Gnomad4 EAS exome AF: 0.518

Gnomad4 SAS exome AF: 0.706

Gnomad4 FIN exome AF: 0.802

Gnomad4 NFE exome AF: 0.858

Gnomad4 OTH exome AF: 0.811

GnomAD4 genome AF: 0.727 AC: 110585 AN: 152168 Hom.: 42087 Cov.: 34 AF XY: 0.724 AC XY: 53865 AN XY: 74402

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.765

Alfa AF: 0.779 Hom.: 5875

Bravo AF: 0.712

Asia WGS AF: 0.593 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4874163; hg19: chr8-144674772;