Submissions for variant NM_004656.4(BAP1):c.501G>A (p.Ala167=)

gnomAD frequency: 0.00050  dbSNP: rs148631953

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000227823	SCV000288754	benign	BAP1-related tumor predisposition syndrome	2024-02-01	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000227823	SCV000445483	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	RCV000442771	SCV000529879	likely benign	not specified	2018-02-09	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	RCV000566910	SCV000664649	likely benign	Hereditary cancer-predisposing syndrome	2015-09-16	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	RCV000566910	SCV000682626	likely benign	Hereditary cancer-predisposing syndrome	2016-03-18	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000442771	SCV002071064	benign	not specified	2020-08-12	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000566910	SCV002537285	benign	Hereditary cancer-predisposing syndrome	2021-01-28	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000442771	SCV002550837	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV002512066	SCV002821193	likely benign	not provided	2024-01-01	criteria provided, single submitter	clinical testing	BAP1: BP4, BP7, BS1
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316288	SCV004016337	benign	Melanoma, uveal, susceptibility to, 2	2023-07-07	criteria provided, single submitter	clinical testing