Submissions for variant NM_004656.4(BAP1):c.294C>T (p.Ser98=)

gnomAD frequency: 0.00056  dbSNP: rs140641333

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000253448	SCV000310602	likely benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000284103	SCV000445485	benign	BAP1-related tumor predisposition 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 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	RCV000253448	SCV000530840	likely benign	not specified	2016-08-11	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	RCV000284103	SCV000563750	benign	BAP1-related tumor predisposition syndrome	2024-01-31	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000569569	SCV000664655	likely benign	Hereditary cancer-predisposing syndrome	2015-09-09	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	RCV000569569	SCV000682617	likely benign	Hereditary cancer-predisposing syndrome	2016-03-09	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000858218	SCV001153970	likely benign	not provided	2023-04-01	criteria provided, single submitter	clinical testing	BAP1: BP4, BP7
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000284103	SCV001477757	likely benign	BAP1-related tumor predisposition syndrome	2019-09-14	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000858218	SCV002046718	benign	not provided	2021-03-11	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000569569	SCV002537282	benign	Hereditary cancer-predisposing syndrome	2021-09-11	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000253448	SCV002550843	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing