Submissions for variant NM_000081.4(LYST):c.2769A>C (p.Ser923=)

gnomAD frequency: 0.00086  dbSNP: rs112739986

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000274201	SCV000355780	uncertain significance	Chédiak-Higashi syndrome	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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Genetic Services Laboratory, University of Chicago	RCV000500677	SCV000595665	likely benign	not specified	2017-03-27	criteria provided, single submitter	clinical testing
Invitae	RCV000274201	SCV001720547	benign	Chédiak-Higashi syndrome	2024-01-25	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV002262935	SCV002543617	likely benign	Autoinflammatory syndrome	2020-09-08	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003957550	SCV004776044	likely benign	LYST-related disorder	2020-01-29	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).
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV001573880	SCV001800373	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001573880	SCV001975704	likely benign	not provided		no assertion criteria provided	clinical testing