22-42058489-GA-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000262.3(NAGA):c.*1789del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.89 ( 60221 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
NAGA
NM_000262.3 3_prime_UTR
NM_000262.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.27
Genes affected
NAGA (HGNC:7631): (alpha-N-acetylgalactosaminidase) NAGA encodes the lysosomal enzyme alpha-N-acetylgalactosaminidase, which cleaves alpha-N-acetylgalactosaminyl moieties from glycoconjugates. Mutations in NAGA have been identified as the cause of Schindler disease types I and II (type II also known as Kanzaki disease). [provided by RefSeq, Jul 2008]
WBP2NL (HGNC:28389): (WBP2 N-terminal like) WBP2NL is a sperm-specific WW domain-binding protein that promotes meiotic resumption and pronuclear development during oocyte fertilization (Wu et al., 2007 [PubMed 17289678]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAGA | NM_000262.3 | c.*1789del | 3_prime_UTR_variant | 9/9 | ENST00000396398.8 | NP_000253.1 | ||
NAGA | NM_001362848.1 | c.*1789del | 3_prime_UTR_variant | 10/10 | NP_001349777.1 | |||
NAGA | NM_001362850.1 | c.*1789del | 3_prime_UTR_variant | 10/10 | NP_001349779.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAGA | ENST00000396398.8 | c.*1789del | 3_prime_UTR_variant | 9/9 | 1 | NM_000262.3 | ENSP00000379680 | P1 | ||
WBP2NL | ENST00000436265.5 | downstream_gene_variant | 2 | ENSP00000401002 |
Frequencies
GnomAD3 genomes AF: 0.887 AC: 134083AN: 151110Hom.: 60206 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome AF: 0.887 AC: 134144AN: 151224Hom.: 60221 Cov.: 0 AF XY: 0.890 AC XY: 65761AN XY: 73858
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Alpha-N-acetylgalactosaminidase deficiency type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Alpha-N-acetylgalactosaminidase deficiency type 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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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