Genetic Variant NM_001130053.5:c.1488+149C>T (chr8-143580905-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740

Publications

46 publications found

Variant links:

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 links:

ENSG00000279605 (HGNC:):

ENSG00000279605 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1D	NM_001130053.5 link	c.1488+149C>T		intron_variant	Intron 7 of 9	ENST00000618139.4	NP_001123525.3	P29692-2D3DWK1B2RAR6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1D	ENST00000618139.4 link	c.1488+149C>T		intron_variant	Intron 7 of 9	5	NM_001130053.5	ENSP00000484536.2		P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30047

AN:

152124

Hom.:

3416

Cov.:

show subpopulations

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.:

AF XY:

0.153

AC XY:

76044

AN XY:

497732

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

7180

14359

21539

28718

35898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.198

AC:

30079

AN:

152242

Hom.:

3417

Cov.:

AF XY:

0.201

AC XY:

14966

AN XY:

74434

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.137

AC:

9333

AN:

67992

Other (OTH)

AF:

0.184

AC:

388

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1238

2476

3714

4952

6190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.3

(source)

DANN

Benign

0.61

PhyloP100

0.074

PromoterAI

0.0086

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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NM_001130053.5:c.1488+149C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over