chr8-143580571-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001130053.5(EEF1D):c.1645G>A(p.Ala549Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,272 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: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
EEF1D
NM_001130053.5 missense
NM_001130053.5 missense
Scores
1
6
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.78
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34771907).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EEF1D | ENST00000618139.4 | c.1645G>A | p.Ala549Thr | missense_variant | Exon 8 of 10 | 5 | NM_001130053.5 | ENSP00000484536.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250950Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135690
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461024Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726814
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74382
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T;T;.;T;T;.;.;.;T;T;.;.;.;T;.;T;T;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T;T;T;T;.;.;.;.;T;T;T;T;T;.;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;N;N;N
REVEL
Benign
Sift
Benign
T;T;D;T;D;T;D;D;T;T;T;D;.;T;D;D;D;D
Sift4G
Benign
T;T;D;T;D;T;D;T;T;T;T;T;D;.;T;T;T;.
Polyphen
P;P;D;.;D;.;D;.;P;P;.;.;.;.;.;.;.;.
Vest4
MutPred
0.45
.;.;.;.;Gain of phosphorylation at A599 (P = 0.0119);.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
MPC
0.18
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at