Submissions for variant NM_015915.5(ATL1):c.351G>A (p.Glu117=)

gnomAD frequency: 0.79691  dbSNP: rs1060197

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000020720	SCV000386880	benign	Hereditary spastic paraplegia 3A	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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000020720	SCV001000156	benign	Hereditary spastic paraplegia 3A	2024-02-01	criteria provided, single submitter	clinical testing
Athena Diagnostics	RCV000860187	SCV001145767	benign	not provided	2019-07-18	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001553934	SCV001775041	benign	Neuropathy, hereditary sensory, type 1D	2021-07-14	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000020720	SCV001775042	benign	Hereditary spastic paraplegia 3A	2021-07-14	criteria provided, single submitter	clinical testing
GeneDx	RCV000860187	SCV001945458	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001847616	SCV002106232	benign	Hereditary spastic paraplegia	2016-12-12	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV002496429	SCV002810593	benign	Hereditary spastic paraplegia 3A; Neuropathy, hereditary sensory, type 1D	2021-08-11	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV000860187	SCV005292422	benign	not provided		criteria provided, single submitter	not provided
GeneReviews	RCV000020720	SCV000041290	not provided	Hereditary spastic paraplegia 3A		no assertion provided	literature only
Genetic Services Laboratory, University of Chicago	RCV000116420	SCV000150345	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000116420	SCV001741361	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000116420	SCV001923753	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000116420	SCV001951417	benign	not specified		no assertion criteria provided	clinical testing