chr4-102634835-A-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005908.4(MANBA):c.2368T>A(p.Leu790Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L790L) has been classified as Benign.
Frequency
Genomes: not found (cov: 32)
Consequence
MANBA
NM_005908.4 missense
NM_005908.4 missense
Scores
7
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.00
Genes affected
MANBA (HGNC:6831): (mannosidase beta) This gene encodes a member of the glycosyl hydrolase 2 family. The encoded protein localizes to the lysosome where it is the final exoglycosidase in the pathway for N-linked glycoprotein oligosaccharide catabolism. Mutations in this gene are associated with beta-mannosidosis, a lysosomal storage disease that has a wide spectrum of neurological involvement. [provided by RefSeq, Jul 2008]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MANBA | NM_005908.4 | c.2368T>A | p.Leu790Met | missense_variant | 16/17 | ENST00000647097.2 | |
MANBA | XM_047415692.1 | c.2293T>A | p.Leu765Met | missense_variant | 17/18 | ||
MANBA | XM_047415693.1 | c.2293T>A | p.Leu765Met | missense_variant | 17/18 | ||
MANBA | XM_047415694.1 | c.1720T>A | p.Leu574Met | missense_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MANBA | ENST00000647097.2 | c.2368T>A | p.Leu790Met | missense_variant | 16/17 | NM_005908.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 60
GnomAD4 exome
Cov.:
60
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
P;P
PrimateAI
Benign
T
Polyphen
1.0, 1.0
.;D;D;.;D
Vest4
0.60, 0.63
MutPred
Gain of disorder (P = 0.0745);Gain of disorder (P = 0.0745);Gain of disorder (P = 0.0745);.;.;
MVP
0.31
MPC
0.43
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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