ClinVar Miner

Submissions for variant NM_000512.5(GALNS):c.510T>C (p.Tyr170=)

gnomAD frequency: 0.03694  dbSNP: rs3743544
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000079038 SCV000110907 benign not specified 2012-11-12 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000079038 SCV000304613 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000264801 SCV000399651 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 RCV000079038 SCV001362792 benign not specified 2019-02-15 criteria provided, single submitter clinical testing Variant summary: GALNS c.510T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.046 in 121120 control chromosomes in the ExAC database, including 159 homozygotes. The observed variant frequency is approximately 22-fold of the estimated maximal expected allele frequency for a pathogenic variant in GALNS causing Mucopolysaccharidosis Type IVA (Morquio Syndrome A) phenotype (0.002), strongly suggesting that the variant is benign. Two ClinVar submission from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV000264801 SCV001718522 benign Mucopolysaccharidosis, MPS-IV-A 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV000675549 SCV001827436 benign not provided 2018-06-25 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24035930, 9452036)
Genome-Nilou Lab RCV000264801 SCV002045070 benign Mucopolysaccharidosis, MPS-IV-A 2021-11-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000675549 SCV005252610 benign not provided criteria provided, single submitter not provided
Mayo Clinic Laboratories, Mayo Clinic RCV000675549 SCV000801240 benign not provided 2015-10-23 no assertion criteria provided clinical testing

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