chr4-102632120-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005908.4(MANBA):c.2577G>A(p.Glu859=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
MANBA
NM_005908.4 synonymous
NM_005908.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.60
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 4-102632120-C-T is Benign according to our data. Variant chr4-102632120-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1927056.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.6 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MANBA | NM_005908.4 | c.2577G>A | p.Glu859= | synonymous_variant | 17/17 | ENST00000647097.2 | |
MANBA | XM_047415692.1 | c.2502G>A | p.Glu834= | synonymous_variant | 18/18 | ||
MANBA | XM_047415693.1 | c.2502G>A | p.Glu834= | synonymous_variant | 18/18 | ||
MANBA | XM_047415694.1 | c.1929G>A | p.Glu643= | synonymous_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MANBA | ENST00000647097.2 | c.2577G>A | p.Glu859= | synonymous_variant | 17/17 | NM_005908.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251448Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135894
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460788Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726750
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Beta-D-mannosidosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 28, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at