Submissions for variant NM_015346.4(ZFYVE26):c.1224G>T (p.Gly408=)

gnomAD frequency: 0.03409  dbSNP: rs17104689

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000372381	SCV000388062	benign	Hereditary spastic paraplegia 15	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.
GeneDx	RCV000118894	SCV000519738	benign	not specified	2016-05-25	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	RCV001083221	SCV000556825	benign	Spastic paraplegia	2024-02-01	criteria provided, single submitter	clinical testing
Athena Diagnostics Inc	RCV000713423	SCV000844030	benign	not provided	2017-09-30	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001847731	SCV002106001	benign	Hereditary spastic paraplegia	2021-11-11	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000372381	SCV002514143	benign	Hereditary spastic paraplegia 15	2021-12-05	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000118894	SCV000153563	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.