8-143592602-G-A

Variant names:

• chr8-143592602-G-A
• rs4874163
• NM_001130053.5:c.-1+45C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.82).
• 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.-1+45C>T		intron	N/A	NP_001123525.3
	EEF1D	NM_032378.7		c.-131-1864C>T		intron	N/A	NP_115754.4
	EEF1D	NM_001130055.4		c.-5+1291C>T		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.-1+45C>T		intron	N/A	ENSP00000484536.2
	EEF1D	ENST00000442189.6	TSL:1	c.-131-1864C>T		intron	N/A	ENSP00000391944.2
	EEF1D	ENST00000395119.7	TSL:1	c.-8+4746C>T		intron	N/A	ENSP00000378551.3

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

African (AFR) AF: 0.492 AC: 7770 AN: 15778

American (AMR) AF: 0.761 AC: 752 AN: 988

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 4237 AN: 5152

East Asian (EAS) AF: 0.518 AC: 1880 AN: 3632

South Asian (SAS) AF: 0.706 AC: 11624 AN: 16456

European-Finnish (FIN) AF: 0.802 AC: 231 AN: 288

Middle Eastern (MID) AF: 0.801 AC: 1299 AN: 1622

European-Non Finnish (NFE) AF: 0.858 AC: 653631 AN: 761696

Other (OTH) AF: 0.811 AC: 22159 AN: 27308

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

African (AFR) AF: 0.500 AC: 20755 AN: 41472

American (AMR) AF: 0.765 AC: 11702 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5176

South Asian (SAS) AF: 0.694 AC: 3348 AN: 4824

European-Finnish (FIN) AF: 0.827 AC: 8765 AN: 10600

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57901 AN: 68006

Other (OTH) AF: 0.765 AC: 1618 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.60
PhyloP100		0.58
PromoterAI		-0.0017	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs4874163; hg19: chr8-144674772;