12-57780523-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015433.3(EEF1AKMT3):c.558T>A(p.His186Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
Consequence
EEF1AKMT3
NM_015433.3 missense
NM_015433.3 missense
Scores
4
1
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.46
Genes affected
EEF1AKMT3 (HGNC:24936): (EEF1A lysine methyltransferase 3) Enables heat shock protein binding activity and protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Located in several cellular components, including centrosome; chromosome; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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=0.36630616).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EEF1AKMT3 | NM_015433.3 | c.558T>A | p.His186Gln | missense_variant | 3/3 | ENST00000300209.13 | |
EEF1AKMT3 | NM_206914.2 | c.*247T>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EEF1AKMT3 | ENST00000300209.13 | c.558T>A | p.His186Gln | missense_variant | 3/3 | 1 | NM_015433.3 | P1 | |
EEF1AKMT3 | ENST00000333012.5 | c.*247T>A | 3_prime_UTR_variant | 4/4 | 1 | ||||
EEF1AKMT3 | ENST00000551420.1 | c.15T>A | p.His5Gln | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 62
GnomAD4 exome
Cov.:
62
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;N
REVEL
Benign
Sift
Pathogenic
D;T
Sift4G
Pathogenic
D;T
Polyphen
1.0
.;D
Vest4
MutPred
0.40
.;Gain of methylation at K181 (P = 0.0859);
MVP
MPC
1.6
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at