12-10506741-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_001357734.3(EIF2S3B):ā€‹c.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

Scores

3
3
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.01
Variant links:
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]

Genome browser will be placed here

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
EIF2S3BNM_001357734.3 linkc.839G>C p.Gly280Ala missense_variant Exon 1 of 1 ENST00000538173.2 NP_001344663.1
EIF2S3BNM_001357731.1 linkc.839G>C p.Gly280Ala missense_variant Exon 1 of 2 NP_001344660.1
LOC105369657XR_001749003.3 linkn.443-6140C>G intron_variant Intron 3 of 4
LOC105369657XR_931355.4 linkn.443-6140C>G intron_variant Intron 3 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EIF2S3BENST00000538173.2 linkc.839G>C p.Gly280Ala missense_variant Exon 1 of 1 6 NM_001357734.3 ENSP00000445077.1 Q2VIR3-1
EIF2S3BENST00000322446.3 linkc.839G>C p.Gly280Ala missense_variant Exon 1 of 2 1 ENSP00000323063.3 Q2VIR3-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461736
Hom.:
0
Cov.:
37
AF XY:
0.00000138
AC XY:
1
AN XY:
727174
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.76
BayesDel_addAF
Benign
-0.057
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
20
DANN
Benign
0.97
DEOGEN2
Benign
0.22
.;T
Eigen
Benign
-0.27
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.64
D
LIST_S2
Uncertain
0.89
D;D
M_CAP
Benign
0.0046
T
MetaRNN
Pathogenic
0.85
D;D
MetaSVM
Benign
-0.59
T
PROVEAN
Pathogenic
-5.8
D;D
REVEL
Benign
0.22
Sift
Uncertain
0.0030
D;D
Sift4G
Uncertain
0.021
D;D
Vest4
0.58
MutPred
0.64
Loss of disorder (P = 0.1171);Loss of disorder (P = 0.1171);
MVP
0.56
MPC
0.36
ClinPred
1.0
D
GERP RS
0.37
Varity_R
0.70
gMVP
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs199779592; hg19: chr12-10659340; API