Submissions for variant NM_024312.5(GNPTAB):c.1932A>G (p.Thr644=)

gnomAD frequency: 0.58708  dbSNP: rs10778148

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000082189	SCV000114135	benign	not specified	2014-05-20	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000082189	SCV000314276	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000268458	SCV000375422	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 Laboratory Services, Illumina	RCV000301696	SCV000375423	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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000585918	SCV000699450	benign	not provided	2016-10-10	criteria provided, single submitter	clinical testing	Variant summary: The GNPTAB c.1932A>G (p.Thr644Thr) 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. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 71424/121364 control chromosomes (21589 homozygotes) at a frequency of 0.5885106, indicating it is the major allele and a benign polymorphism. Multiple clinical labs have classified the variant as benign. Due to the high population frequency of this vairant, it has been classified as benign.
GeneDx	RCV000585918	SCV000969489	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	RCV001516228	SCV001724475	benign	Mucolipidosis type II; Pseudo-Hurler polydystrophy	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000301696	SCV001749156	benign	Pseudo-Hurler polydystrophy	2021-07-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000268458	SCV001749311	benign	Mucolipidosis type II	2021-07-01	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000585918	SCV000800949	benign	not provided	2017-05-16	no assertion criteria provided	clinical testing
Natera, Inc.	RCV000268458	SCV001458978	benign	Mucolipidosis type II	2020-09-16	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000082189	SCV001743633	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000082189	SCV001973663	benign	not specified		no assertion criteria provided	clinical testing