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NM_000262.3(NAGA):c.*1930G>A AND Alpha-N-acetylgalactosaminidase deficiency type 2

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 12, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001148197.4

Allele description [Variation Report for NM_000262.3(NAGA):c.*1930G>A]

NM_000262.3(NAGA):c.*1930G>A

Genes:
WBP2NL:WBP2 N-terminal like [Gene - OMIM - HGNC]
NAGA:alpha-N-acetylgalactosaminidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.2
Genomic location:
Preferred name:
NM_000262.3(NAGA):c.*1930G>A
HGVS:
  • NC_000022.11:g.42058349C>T
  • NG_009247.1:g.17494G>A
  • NM_000262.3:c.*1930G>AMANE SELECT
  • NM_001362848.1:c.*1930G>A
  • NM_001362850.1:c.*1930G>A
  • NC_000022.10:g.42454353C>T
  • NM_000262.2:c.*1930G>A
Links:
dbSNP: rs144373253
NCBI 1000 Genomes Browser:
rs144373253
Molecular consequence:
  • NM_000262.3:c.*1930G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001362848.1:c.*1930G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001362850.1:c.*1930G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Name:
Alpha-N-acetylgalactosaminidase deficiency type 2
Synonyms:
ALPHA-N-ACETYLGALACTOSAMINIDASE DEFICIENCY, TYPE II; NAGA DEFICIENCY, TYPE II; SCHINDLER DISEASE, TYPE II; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012222; MedGen: C1836522; Orphanet: 3137; Orphanet: 79280; OMIM: 609242

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001309079Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Jan 12, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001309079.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 13, 2025