ClinVar Miner

Submissions for variant NM_000153.4(GALC):c.1698A>T (p.Val566=) (rs421466)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000078195 SCV000110033 benign not specified 2015-10-27 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078195 SCV000302711 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000360908 SCV000389238 benign Galactosylceramide beta-galactosidase deficiency 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.
Integrated Genetics/Laboratory Corporation of America RCV000590062 SCV000695671 benign not provided 2016-05-16 criteria provided, single submitter clinical testing Variant summary: The GALC c.1698A>T (p.Val566Val) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SQp55. This variant was found in 118550/120624 control chromosomes (58347 homozygotes) at a frequency of 0.9828061, which is approximately 440 times the estimated maximal expected allele frequency of a pathogenic GALC variant (0.0022361), suggesting this variant is a benign polymorphism. The variant has been found to co-occur in Krabbe Disease patients with compound heterozygous pathogenic variants that would explain the patients phenotype. In addition, one clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as benign.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000360908 SCV000733404 benign Galactosylceramide beta-galactosidase deficiency no assertion criteria provided clinical testing
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000590062 SCV000800903 benign not provided 2015-10-19 no assertion criteria provided clinical testing

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