chr2-25131455-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_014971.2(EFR3B):c.937G>A(p.Val313Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,318 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
EFR3B
NM_014971.2 missense
NM_014971.2 missense
Scores
2
10
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 9.77
Genes affected
EFR3B (HGNC:29155): (EFR3 homolog B) Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in actin cytoskeleton; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant where missense usually causes diseases, EFR3B
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3B | NM_014971.2 | c.937G>A | p.Val313Met | missense_variant | 9/23 | ENST00000403714.8 | |
EFR3B | NM_001319099.2 | c.832G>A | p.Val278Met | missense_variant | 9/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3B | ENST00000403714.8 | c.937G>A | p.Val313Met | missense_variant | 9/23 | 5 | NM_014971.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000662 AC: 1AN: 151074Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80622
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GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1398318Hom.: 0 Cov.: 33 AF XY: 0.00000145 AC XY: 1AN XY: 689732
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GnomAD4 genome Cov.: 32
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32
Bravo
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Uncertain
Sift
Benign
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
D;P;.;.;.
Vest4
MutPred
Loss of methylation at R309 (P = 0.2165);Loss of methylation at R309 (P = 0.2165);.;.;.;
MVP
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at