Submissions for variant NM_144599.5(NIPA1):c.312G>A (p.Pro104=)

gnomAD frequency: 0.00051  dbSNP: rs139372534

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000726331	SCV000343827	uncertain significance	not provided	2016-08-15	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001087083	SCV000390092	likely benign	Hereditary spastic paraplegia 6	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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae	RCV001087083	SCV000554107	benign	Hereditary spastic paraplegia 6	2023-12-21	criteria provided, single submitter	clinical testing
GeneDx	RCV000616724	SCV000715902	likely benign	not specified	2017-02-13	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.
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001848069	SCV002105424	likely benign	Hereditary spastic paraplegia	2018-07-01	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003940067	SCV004748729	likely benign	NIPA1-related condition	2019-03-05	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Clinical Genetics, Academic Medical Center	RCV000726331	SCV001924391	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000726331	SCV001967634	likely benign	not provided		no assertion criteria provided	clinical testing