Submissions for variant NM_004656.4(BAP1):c.1026C>T (p.Ser342=)

gnomAD frequency: 0.00304  dbSNP: rs71651686

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000205453	SCV000261609	benign	BAP1-related tumor predisposition syndrome	2024-02-01	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000244636	SCV000310597	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000205453	SCV000445473	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	RCV000244636	SCV000518946	likely benign	not specified	2018-01-19	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.
Ambry Genetics	RCV000561863	SCV000664582	likely benign	Hereditary cancer-predisposing syndrome	2016-11-10	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	RCV000561863	SCV000682546	likely benign	Hereditary cancer-predisposing syndrome	2016-03-09	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001172150	SCV001335114	benign	not provided	2024-01-01	criteria provided, single submitter	clinical testing	BAP1: BP4, BS1, BS2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000205453	SCV001472275	benign	BAP1-related tumor predisposition syndrome	2020-02-16	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000244636	SCV002071061	benign	not specified	2019-06-19	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000561863	SCV002537240	benign	Hereditary cancer-predisposing syndrome	2020-10-22	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000244636	SCV002550824	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000244636	SCV002774068	benign	not specified	2021-07-23	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV002500656	SCV002811855	likely benign	BAP1-related tumor predisposition syndrome; Kury-Isidor syndrome	2021-07-14	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316144	SCV004016327	benign	Melanoma, uveal, susceptibility to, 2	2023-07-07	criteria provided, single submitter	clinical testing
True Health Diagnostics	RCV000561863	SCV000805224	likely benign	Hereditary cancer-predisposing syndrome	2018-06-05	no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV001172150	SCV001740454	likely benign	not provided		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV001172150	SCV001799887	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV001172150	SCV001808346	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001172150	SCV001970594	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000244636	SCV002034117	benign	not specified		no assertion criteria provided	clinical testing