Submissions for variant NM_015046.7(SETX):c.59G>A (p.Arg20His)

gnomAD frequency: 0.00602  dbSNP: rs79740039

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000327408	SCV000477897	benign	Amyotrophic lateral sclerosis type 4	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.
Illumina Laboratory Services, Illumina	RCV000363505	SCV000477898	benign	Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2	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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001540050	SCV000605093	benign	not provided	2023-11-21	criteria provided, single submitter	clinical testing
Athena Diagnostics Inc	RCV000507126	SCV000615203	benign	not specified	2017-07-25	criteria provided, single submitter	clinical testing
Invitae	RCV000551163	SCV000645276	benign	Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV001540050	SCV001757886	benign	not provided	2020-01-29	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001848019	SCV002105174	benign	Hereditary spastic paraplegia	2021-11-29	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001540050	SCV002546104	benign	not provided	2024-01-01	criteria provided, single submitter	clinical testing	SETX: BP4, BS1, BS2
Fulgent Genetics, Fulgent Genetics	RCV000551163	SCV002809211	likely benign	Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2	2022-02-18	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000363505	SCV003931606	likely benign	Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2	2023-02-08	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000327408	SCV003931607	likely benign	Amyotrophic lateral sclerosis type 4	2023-02-08	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003977697	SCV004798355	benign	SETX-related condition	2019-05-10	criteria provided, single submitter	clinical testing	This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000507126	SCV001809136	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000507126	SCV001917195	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000507126	SCV001928216	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000507126	SCV001966452	benign	not specified		no assertion criteria provided	clinical testing