8-143580571-C-T

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

Scores

1
6
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.78
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 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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EEF1DNM_001130053.5 linkc.1645G>A p.Ala549Thr 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.1645G>A p.Ala549Thr missense_variant Exon 8 of 10 5 NM_001130053.5 ENSP00000484536.2 P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152248
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000797
AC:
2
AN:
250950
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135690
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000123
AC:
18
AN:
1461024
Hom.:
0
Cov.:
32
AF XY:
0.0000179
AC XY:
13
AN XY:
726814
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000765
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152248
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000192
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000189
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Uncertain
0.061
T
BayesDel_noAF
Benign
-0.090
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.10
T;T;.;T;T;.;.;.;T;T;.;.;.;T;.;T;T;T
Eigen
Uncertain
0.19
Eigen_PC
Benign
0.20
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.84
T;.;T;T;T;T;.;.;.;.;T;T;T;T;T;.;T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.35
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.50
T
MutationAssessor
Uncertain
2.2
M;M;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Uncertain
-2.8
D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;N;N;N
REVEL
Benign
0.17
Sift
Benign
0.073
T;T;D;T;D;T;D;D;T;T;T;D;.;T;D;D;D;D
Sift4G
Benign
0.23
T;T;D;T;D;T;D;T;T;T;T;T;D;.;T;T;T;.
Polyphen
0.52
P;P;D;.;D;.;D;.;P;P;.;.;.;.;.;.;.;.
Vest4
0.42
MutPred
0.45
.;.;.;.;Gain of phosphorylation at A599 (P = 0.0119);.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.79
MPC
0.18
ClinPred
0.86
D
GERP RS
3.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.35
gMVP
0.34

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: rs142439099; hg19: chr8-144662741; COSMIC: COSV52787383; COSMIC: COSV52787383; API