12-10506741-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001357734.3(EIF2S3B):āc.839G>Cā(p.Gly280Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
EIF2S3B
NM_001357734.3 missense
NM_001357734.3 missense
Scores
3
3
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.01
Genes affected
EIF2S3B (HGNC:43863): (eukaryotic translation initiation factor 2 subunit gamma B) Predicted to enable translation initiation factor activity. Predicted to contribute to tRNA binding activity. Predicted to be involved in formation of translation preinitiation complex and positive regulation of translational fidelity. Predicted to be part of eukaryotic translation initiation factor 2 complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.852
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EIF2S3B | NM_001357734.3 | c.839G>C | p.Gly280Ala | missense_variant | Exon 1 of 1 | ENST00000538173.2 | NP_001344663.1 | |
EIF2S3B | NM_001357731.1 | c.839G>C | p.Gly280Ala | missense_variant | Exon 1 of 2 | NP_001344660.1 | ||
LOC105369657 | XR_001749003.3 | n.443-6140C>G | intron_variant | Intron 3 of 4 | ||||
LOC105369657 | XR_931355.4 | n.443-6140C>G | intron_variant | Intron 3 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF2S3B | ENST00000538173.2 | c.839G>C | p.Gly280Ala | missense_variant | Exon 1 of 1 | 6 | NM_001357734.3 | ENSP00000445077.1 | ||
EIF2S3B | ENST00000322446.3 | c.839G>C | p.Gly280Ala | missense_variant | Exon 1 of 2 | 1 | ENSP00000323063.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461736Hom.: 0 Cov.: 37 AF XY: 0.00000138 AC XY: 1AN XY: 727174
GnomAD4 exome
AF:
AC:
1
AN:
1461736
Hom.:
Cov.:
37
AF XY:
AC XY:
1
AN XY:
727174
Gnomad4 AFR exome
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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
DEOGEN2
Benign
.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Vest4
MutPred
Loss of disorder (P = 0.1171);Loss of disorder (P = 0.1171);
MVP
MPC
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