ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.3602+8C>A (rs79493678)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082194 SCV000114140 benign not specified 2015-12-08 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082194 SCV000314281 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000273773 SCV000375385 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.
Illumina Clinical Services Laboratory,Illumina RCV000328761 SCV000375386 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000082194 SCV000603853 benign not specified 2018-07-22 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000082194 SCV001362261 benign not specified 2019-12-09 criteria provided, single submitter clinical testing Variant summary: GNPTAB c.3602+8C>A alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 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 0.032 in 251282 control chromosomes in the gnomAD database, including 202 homozygotes. The observed variant frequency is approximately 14.52 fold of the estimated maximal expected allele frequency for a pathogenic variant in GNPTAB causing Mucolipidosis phenotype (0.0022), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.3602+8C>A in individuals affected with Mucolipidosis and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions (evaluation after 2014) cite the variant three times as benign and once as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000675284 SCV000800943 benign not provided 2017-05-01 no assertion criteria provided clinical testing

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