ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.1413C>T (p.Val471=) (rs73251084)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000079025 SCV000110894 benign not specified 2013-11-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001078610 SCV000399626 benign Mucopolysaccharidosis, MPS-IV-A 2018-01-13 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 RCV000079025 SCV000917405 benign not specified 2017-10-30 criteria provided, single submitter clinical testing Variant summary: The GALNS c.1413C>T (p.Val471Val) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect the binding sites for splicing enhancers. However, these predictions have yet to be confirmed by functional studies. This variant was found in 884/216186 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.041844 (827/19764). This frequency is about 20 times the estimated maximal expected allele frequency of a pathogenic GALNS variant (0.0020412), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV001078610 SCV001116896 benign Mucopolysaccharidosis, MPS-IV-A 2020-12-02 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675528 SCV000801219 likely benign not provided 2017-05-01 no assertion criteria provided clinical testing

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