Submissions for variant NM_014946.4(SPAST):c.879G>A (p.Pro293=)

gnomAD frequency: 0.00943  dbSNP: rs145264166

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV001086304	SCV000259937	benign	Hereditary spastic paraplegia 4	2024-02-01	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001086304	SCV000430106	benign	Hereditary spastic paraplegia 4	2018-03-06	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.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000435691	SCV000510568	likely benign	not provided	2017-01-26	criteria provided, single submitter	clinical testing	Converted during submission to Likely benign.
GeneDx	RCV000434697	SCV000518783	benign	not specified	2016-07-28	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000434697	SCV000540414	benign	not specified	2016-03-29	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Not present in FAST (due to DM? classification). ExAC: 1.4% (898/66366) European. Silent and not in splice consensus.
Athena Diagnostics Inc	RCV000434697	SCV001476158	benign	not specified	2020-06-10	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001847928	SCV002105651	benign	Hereditary spastic paraplegia	2020-12-08	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000435691	SCV002498545	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	SPAST: BP4, BP7, BS1, BS2
Clinical Genetics, Academic Medical Center	RCV000434697	SCV001922282	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000434697	SCV001930611	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000435691	SCV001952053	likely benign	not provided		no assertion criteria provided	clinical testing