Submissions for variant NM_000203.5(IDUA):c.590-8C>T

dbSNP: rs6848974

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000404425	SCV005619883	benign	Mucopolysaccharidosis type 1	2024-12-06	reviewed by expert panel	curation	The NM_000203.5:c.590-8C>T variant is a nucleotide substitution in the acceptor splice site region of intron 5 of IDUA. The highest population minor allele frequency in gnomAD v4.1.0 is 0.2984 (27112/90864 alleles; 4285 homozygotes; Grpmax Filtering AF 95% confidence = 0.2954) in the South Asian population, which is higher than the ClinGen Lysosomal Diseases VCEP’s threshold for BA1 (>0.005), and therefore meets this criterion (BA1). There is a ClinVar entry for this variant (Variation ID: 92646). In summary, this variant meets the criteria to be classified as benign for mucopolysaccharidosis type 1. IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel (Specifications Version 1.0.0): BA1. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on December 6, 2024)
Eurofins Ntd Llc (ga)	RCV000078396	SCV000110242	benign	not specified	2017-11-02	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000078396	SCV000302981	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000404425	SCV000451773	benign	Mucopolysaccharidosis type 1	2018-01-12	criteria provided, single submitter	clinical testing	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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000589331	SCV000695974	benign	not provided	2016-01-15	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000404425	SCV001730205	benign	Mucopolysaccharidosis type 1	2025-02-04	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543820	SCV001762690	benign	Hurler syndrome	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543821	SCV001762691	benign	Mucopolysaccharidosis, MPS-I-H/S	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543822	SCV001762692	benign	Mucopolysaccharidosis, MPS-I-S	2021-07-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000589331	SCV001851983	benign	not provided	2018-07-05	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV000589331	SCV005306385	benign	not provided		criteria provided, single submitter	not provided
Mayo Clinic Laboratories, Mayo Clinic	RCV000589331	SCV000801299	benign	not provided	2016-02-02	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000078396	SCV001742134	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000078396	SCV001919603	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000078396	SCV001976122	benign	not specified		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000404425	SCV002075297	benign	Mucopolysaccharidosis type 1	2017-08-08	no assertion criteria provided	clinical testing