Submissions for variant NM_004656.4(BAP1):c.1268C>A (p.Thr423Lys)

gnomAD frequency: 0.00166  dbSNP: rs115109161

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000228893	SCV000288737	benign	BAP1-related tumor predisposition syndrome	2024-01-30	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000228893	SCV000445471	benign	BAP1-related tumor predisposition syndrome	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.
Ambry Genetics	RCV000563367	SCV000664594	likely benign	Hereditary cancer-predisposing syndrome	2018-08-16	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Color Diagnostics, LLC DBA Color Health	RCV000563367	SCV000682561	likely benign	Hereditary cancer-predisposing syndrome	2015-03-23	criteria provided, single submitter	clinical testing
GeneDx	RCV000844571	SCV000986622	likely benign	not provided	2020-10-13	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 28873162)
Genetic Services Laboratory, University of Chicago	RCV001818616	SCV002064677	benign	not specified	2019-07-12	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000563367	SCV002537251	benign	Hereditary cancer-predisposing syndrome	2021-11-23	criteria provided, single submitter	curation
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316284	SCV004016346	benign	Melanoma, uveal, susceptibility to, 2	2023-07-07	criteria provided, single submitter	clinical testing