8-143580905-G-A

Position:

• chr8-143580905-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.1488+149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,134,988 control chromosomes in the GnomAD database, including 16,831 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 0.20 (3417 hom., cov: 34)
  • Exomes 𝑓: 0.15 (13414 hom.)
• Consequence: EEF1D NM_001130053.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEF1D	NM_001130053.5	c.1488+149C>T		intron_variant		ENST00000618139.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEF1D	ENST00000618139.4	c.1488+149C>T		intron_variant		5	NM_001130053.5
	ENST00000623257.1	n.2548G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30047 AN: 152124 Hom.: 3416 Cov.: 34

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.153 AC: 150273 AN: 982746 Hom.: 13414 Cov.: 13 AF XY: 0.153 AC XY: 76044 AN XY: 497732

Gnomad4 AFR exome AF: 0.291

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.347

Gnomad4 SAS exome AF: 0.183

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.162

GnomAD4 genome AF: 0.198 AC: 30079 AN: 152242 Hom.: 3417 Cov.: 34 AF XY: 0.201 AC XY: 14966 AN XY: 74434

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.184

Alfa AF: 0.148 Hom.: 2422

Bravo AF: 0.207

Asia WGS AF: 0.254 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.61

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: rs1809148; hg19: chr8-144663075; COSMIC: COSV52785016; COSMIC: COSV52785016;