rs5860729
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_005908.4(MANBA):c.2416-11_2416-10delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 1,389,222 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00075 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
MANBA
NM_005908.4 intron
NM_005908.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.248
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 -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 4-102632290-GAA-G is Benign according to our data. Variant chr4-102632290-GAA-G is described in ClinVar as [Benign]. Clinvar id is 1639188.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000748 (111/148450) while in subpopulation AFR AF= 0.00251 (102/40718). AF 95% confidence interval is 0.00211. There are 0 homozygotes in gnomad4. There are 56 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MANBA | NM_005908.4 | c.2416-11_2416-10delTT | intron_variant | Intron 16 of 16 | ENST00000647097.2 | NP_005899.3 | ||
| MANBA | XM_047415692.1 | c.2341-11_2341-10delTT | intron_variant | Intron 17 of 17 | XP_047271648.1 | |||
| MANBA | XM_047415693.1 | c.2341-11_2341-10delTT | intron_variant | Intron 17 of 17 | XP_047271649.1 | |||
| MANBA | XM_047415694.1 | c.1768-11_1768-10delTT | intron_variant | Intron 12 of 12 | XP_047271650.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.000742 AC: 110AN: 148344Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000328 AC: 407AN: 1240772Hom.: 0 AF XY: 0.000305 AC XY: 190AN XY: 622834
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GnomAD4 genome 0.000748 AC: 111AN: 148450Hom.: 0 Cov.: 0 AF XY: 0.000775 AC XY: 56AN XY: 72282
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Beta-D-mannosidosis Benign:1
Nov 11, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at