rs1277435377

Variant summary

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

The NM_001959.4(EEF1B2):​c.511G>A​(p.Val171Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000411 in 1,459,498 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V171L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

EEF1B2
NM_001959.4 missense

Scores

1
5
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.34
Variant links:
Genes affected
EEF1B2 (HGNC:3208): (eukaryotic translation elongation factor 1 beta 2) This gene encodes a translation elongation factor. The protein is a guanine nucleotide exchange factor involved in the transfer of aminoacylated tRNAs to the ribosome. Alternative splicing results in three transcript variants which differ only in the 5' UTR. [provided by RefSeq, Jul 2008]
SNORA41 (HGNC:32634): (small nucleolar RNA, H/ACA box 41)

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
EEF1B2NM_001959.4 linkc.511G>A p.Val171Ile missense_variant Exon 5 of 6 ENST00000392222.7 NP_001950.1 P24534A0A024R3W7
EEF1B2NM_001037663.2 linkc.511G>A p.Val171Ile missense_variant Exon 6 of 7 NP_001032752.1 P24534A0A024R3W7
EEF1B2NM_021121.4 linkc.511G>A p.Val171Ile missense_variant Exon 6 of 7 NP_066944.1 P24534A0A024R3W7
SNORA41NR_002590.1 linkn.*243G>A downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EEF1B2ENST00000392222.7 linkc.511G>A p.Val171Ile missense_variant Exon 5 of 6 1 NM_001959.4 ENSP00000376056.2 P24534

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000411
AC:
6
AN:
1459498
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
725956
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000540
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Uncertain
0.028
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.13
T;T;T
Eigen
Benign
0.074
Eigen_PC
Benign
0.16
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Benign
0.0059
T
MetaRNN
Uncertain
0.48
T;T;T
MetaSVM
Benign
-0.48
T
MutationAssessor
Benign
1.9
L;L;L
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-0.13
N;N;N
REVEL
Benign
0.15
Sift
Benign
0.046
D;D;D
Sift4G
Uncertain
0.058
T;T;T
Polyphen
0.011
B;B;B
Vest4
0.53
MutPred
0.38
Gain of catalytic residue at V171 (P = 0.0761);Gain of catalytic residue at V171 (P = 0.0761);Gain of catalytic residue at V171 (P = 0.0761);
MVP
0.56
MPC
0.28
ClinPred
0.85
D
GERP RS
4.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.089
gMVP
0.18

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: rs1277435377; hg19: chr2-207027326; API