chr8-143580905-G-A

Variant names:

• chr8-143580905-G-A
• rs1809148
• NM_001130053.5:c.1488+149C>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.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
• Publications: 46 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]

ENSG00000279605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1D	NM_001130053.5	MANE Select	c.1488+149C>T		intron	N/A	NP_001123525.3	P29692-2
	EEF1D	NM_032378.7		c.1488+149C>T		intron	N/A	NP_115754.4
	EEF1D	NM_001130055.4		c.390+149C>T		intron	N/A	NP_001123527.1	P29692-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1D	ENST00000618139.4	TSL:5 MANE Select	c.1488+149C>T		intron	N/A	ENSP00000484536.2	P29692-2
	EEF1D	ENST00000532741.5	TSL:1	c.1638+149C>T		intron	N/A	ENSP00000434070.1	E9PRY8
	EEF1D	ENST00000442189.6	TSL:1	c.1488+149C>T		intron	N/A	ENSP00000391944.2	P29692-2

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

African (AFR) AF: 0.291 AC: 6899 AN: 23692

American (AMR) AF: 0.271 AC: 9352 AN: 34456

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 3078 AN: 19088

East Asian (EAS) AF: 0.347 AC: 12492 AN: 36006

South Asian (SAS) AF: 0.183 AC: 12257 AN: 66812

European-Finnish (FIN) AF: 0.157 AC: 5745 AN: 36662

Middle Eastern (MID) AF: 0.180 AC: 568 AN: 3154

European-Non Finnish (NFE) AF: 0.129 AC: 92731 AN: 718718

Other (OTH) AF: 0.162 AC: 7151 AN: 44158

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

African (AFR) AF: 0.292 AC: 12120 AN: 41544

American (AMR) AF: 0.197 AC: 3021 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1854 AN: 5174

South Asian (SAS) AF: 0.181 AC: 874 AN: 4828

European-Finnish (FIN) AF: 0.163 AC: 1727 AN: 10610

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9333 AN: 67992

Other (OTH) AF: 0.184 AC: 388 AN: 2114

Alfa AF: 0.156 Hom.: 6270

Bravo AF: 0.207

Asia WGS AF: 0.254 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		0.074
PromoterAI		0.0086	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: rs1809148; hg19: chr8-144663075; COSMIC: COSV52785016; COSMIC: COSV52785016;