rs202002927

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001130053.5(EEF1D):​c.1492G>T​(p.Val498Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,490 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

EEF1D
NM_001130053.5 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.03
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23515004).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EEF1DNM_001130053.5 linkc.1492G>T p.Val498Leu missense_variant Exon 8 of 10 ENST00000618139.4 NP_001123525.3 P29692-2D3DWK1B2RAR6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EEF1DENST00000618139.4 linkc.1492G>T p.Val498Leu missense_variant Exon 8 of 10 5 NM_001130053.5 ENSP00000484536.2 P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1460490
Hom.:
0
Cov.:
32
AF XY:
0.00000275
AC XY:
2
AN XY:
726594
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Uncertain
0.051
T
BayesDel_noAF
Benign
-0.16
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.011
T;T;.;T;.;.;.;T;T;.;.;.;T;.;T;T;T;T;T;.
Eigen
Benign
-0.0011
Eigen_PC
Benign
0.00012
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.78
T;.;T;T;T;.;.;.;.;T;T;T;T;T;.;T;T;T;T;T
M_CAP
Benign
0.0098
T
MetaRNN
Benign
0.24
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Uncertain
2.6
M;M;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-1.6
N;N;N;N;N;N;N;N;N;N;N;.;N;N;N;N;N;N;N;N
REVEL
Benign
0.20
Sift
Benign
0.055
T;T;D;D;T;D;D;T;T;T;D;.;T;D;D;D;D;D;D;D
Sift4G
Benign
0.41
T;T;T;D;T;T;T;T;T;T;T;T;.;T;T;T;.;.;T;.
Polyphen
0.11
B;B;D;D;.;D;.;B;B;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.38
MutPred
0.19
.;.;.;Gain of relative solvent accessibility (P = 0.0275);.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.61
MPC
0.31
ClinPred
0.83
D
GERP RS
4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.12
gMVP
0.13

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs202002927; hg19: chr8-144662894; API