8-143580606-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001130053.5(EEF1D):​c.1610C>T​(p.Ala537Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

EEF1D
NM_001130053.5 missense

Scores

4
9
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.82
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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EEF1DNM_001130053.5 linkc.1610C>T p.Ala537Val 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.1610C>T p.Ala537Val missense_variant Exon 8 of 10 5 NM_001130053.5 ENSP00000484536.2 P29692-2A0A087X1X7

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152180
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000756
AC:
19
AN:
251216
Hom.:
0
AF XY:
0.0000663
AC XY:
9
AN XY:
135808
show subpopulations
Gnomad AFR exome
AF:
0.0000616
Gnomad AMR exome
AF:
0.000376
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000653
GnomAD4 exome
AF:
0.0000253
AC:
37
AN:
1461430
Hom.:
0
Cov.:
32
AF XY:
0.0000261
AC XY:
19
AN XY:
727050
show subpopulations
Gnomad4 AFR exome
AF:
0.0000598
Gnomad4 AMR exome
AF:
0.000313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000144
Gnomad4 OTH exome
AF:
0.0000331
GnomAD4 genome
AF:
0.0000525
AC:
8
AN:
152298
Hom.:
0
Cov.:
33
AF XY:
0.0000537
AC XY:
4
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000277
Hom.:
0
Bravo
AF:
0.0000416
ExAC
AF:
0.0000824
AC:
10

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
May 15, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1610C>T (p.A537V) alteration is located in exon 8 (coding exon 6) of the EEF1D gene. This alteration results from a C to T substitution at nucleotide position 1610, causing the alanine (A) at amino acid position 537 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.058
T
BayesDel_noAF
Uncertain
-0.010
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.12
T;T;.;T;T;.;.;.;T;T;.;.;.;T;.;T;T;T
Eigen
Pathogenic
0.71
Eigen_PC
Pathogenic
0.66
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.98
D;.;D;D;D;D;.;.;.;.;D;D;D;D;D;.;D;D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.59
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.12
T
MutationAssessor
Uncertain
2.8
M;M;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.
PrimateAI
Benign
0.43
T
PROVEAN
Uncertain
-3.5
D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;D;D;D
REVEL
Uncertain
0.63
Sift
Uncertain
0.0020
D;D;D;T;D;D;D;D;D;D;D;D;.;D;D;D;D;D
Sift4G
Uncertain
0.011
D;D;D;T;D;D;D;D;D;D;D;D;D;.;D;D;D;.
Polyphen
0.99
D;D;D;.;D;.;D;.;D;D;.;.;.;.;.;.;.;.
Vest4
0.55
MutPred
0.52
.;.;.;.;Loss of glycosylation at K585 (P = 0.2339);.;.;.;.;.;.;.;.;.;.;.;.;.;
MVP
0.80
MPC
0.38
ClinPred
0.84
D
GERP RS
4.6
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.79
gMVP
0.37

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: rs562488930; hg19: chr8-144662776; COSMIC: COSV52784809; COSMIC: COSV52784809; API