ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.3135+5T>C

gnomAD frequency: 0.60955  dbSNP: rs759935
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000082191 SCV000114137 benign not specified 2014-05-20 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000082191 SCV000314278 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000362355 SCV000375404 benign Pseudo-Hurler polydystrophy 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.
Illumina Laboratory Services, Illumina RCV000270011 SCV000375405 benign Mucolipidosis type II 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 RCV000586973 SCV000699479 benign not provided 2016-10-10 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.3135+5T>C variant involves the alteration of a non-conserved intronic nucleotide with 5/5 splice prediction tools predict no significant impact on normal splicing. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 72377/120336 (22256 homozygotes) at a frequency of 0.6014576, with indicates the C allele is the major allele (the allele most commonly observed in the general population). In addition, multiple clinical diagnostic laboratories/databases cite the variant as "benign." Therefore, the variant of interest has been classified as Benign.
GeneDx RCV000586973 SCV000972958 benign not provided 2018-06-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001516227 SCV001724474 benign Mucolipidosis type II; Pseudo-Hurler polydystrophy 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000270011 SCV001749309 benign Mucolipidosis type II 2021-07-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000362355 SCV001749310 benign Pseudo-Hurler polydystrophy 2021-07-01 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000586973 SCV000800947 benign not provided 2015-10-20 no assertion criteria provided clinical testing
Natera, Inc. RCV000270011 SCV001457940 benign Mucolipidosis type II 2020-09-16 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000082191 SCV001741817 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000082191 SCV001973010 benign not specified no assertion criteria provided clinical testing

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