Submissions for variant NM_000153.4(GALC):c.1685T>C (p.Ile562Thr)

gnomAD frequency: 0.49946  dbSNP: rs398607

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000078194	SCV000110032	benign	not specified	2015-10-27	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000078194	SCV000302710	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000399633	SCV000389239	benign	Galactosylceramide beta-galactosidase deficiency	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.
Invitae	RCV000399633	SCV000837663	other	Galactosylceramide beta-galactosidase deficiency	2019-01-08	criteria provided, single submitter	clinical testing
Mendelics	RCV000399633	SCV001139494	benign	Galactosylceramide beta-galactosidase deficiency	2019-05-28	criteria provided, single submitter	clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000399633	SCV001435246	benign	Galactosylceramide beta-galactosidase deficiency		criteria provided, single submitter	research	The p.Ile562Thr variant in GALC has been identified in 1 Japanese individual with Krabbe disease (PMID: 24252386). This variant is classified as benign for autosomal recessive Krabbe disease because it has been identified in >60% of African chromosomes by ExAC (http://gnomad.broadinstitute.org/).
Genome-Nilou Lab	RCV000399633	SCV001750166	benign	Galactosylceramide beta-galactosidase deficiency	2021-07-01	criteria provided, single submitter	clinical testing
GeneDx	RCV001249259	SCV001837983	benign	not provided	2018-01-04	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 32661301, 27126738, 26865610, 27535533, 24078576, 26795590, 24252386)
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000399633	SCV000733405	benign	Galactosylceramide beta-galactosidase deficiency		no assertion criteria provided	clinical testing
GenomeConnect, ClinGen	RCV001249259	SCV001423201	not provided	not provided		no assertion provided	phenotyping only	Variant identified in multiple GenomeConnect participants. Variant classified as Benign (pseudodeficiency allele) and reported, most recently, on 06-18-2021 by Lab or GTR ID 500031. Variant also classified as Benign and reported on 09-16-2019 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
GenomeConnect - Invitae Patient Insights Network	RCV000399633	SCV001749725	not provided	Galactosylceramide beta-galactosidase deficiency		no assertion provided	phenotyping only	Variant interpreted as Benign and reported on 11-13-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
Clinical Genetics, Academic Medical Center	RCV000078194	SCV001924286	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000078194	SCV001970854	benign	not specified		no assertion criteria provided	clinical testing
GenomeConnect - Brain Gene Registry	RCV001249259	SCV003804784	not provided	not provided		no assertion provided	phenotyping only	Variant reported in multiple GenomeConnect participants by mulitple clinical testing laboratories. Variant classified as other/Benign by all laboratories and reported most recently on 05-11-2022 by Variantxy and on 01-25-2022 by Invitae. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.
GeneReviews	RCV000399633	SCV004035012	not provided	Galactosylceramide beta-galactosidase deficiency		no assertion provided	literature only