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NM_004656.4(BAP1):c.783+2T>C

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 23, 2021)
Last evaluated:
Mar 22, 2021
Accession:
VCV000422670.11
Variation ID:
422670
Description:
single nucleotide variant
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NM_004656.4(BAP1):c.783+2T>C

Allele ID
406345
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p21.1
Genomic location
3: 52406251 (GRCh38) GRCh38 UCSC
3: 52440267 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.52440267A>G
NC_000003.12:g.52406251A>G
NG_031859.1:g.8743T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:52406250:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA2437006
dbSNP: rs774730309
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Mar 22, 2021 RCV000485691.3
Likely pathogenic 1 criteria provided, single submitter Sep 24, 2020 RCV000818792.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Feb 3, 2021 RCV000579423.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BAP1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1471 1483

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Feb 03, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000682645.4
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This variant causes a T to C nucleotide substitution at the +2 position of intron 9 of the BAP1 gene. Splice site prediction tools suggest … (more)
Uncertain significance
(Mar 22, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000572190.5
Submitted: (Sep 23, 2021)
Evidence details
Comment:
Canonical splice site variant with an indeterminate effect on protein function, demonstrating no effect on splicing in one study, but the use of a cryptic … (more)
Uncertain significance
(Feb 26, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV001189319.2
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The c.783+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 9 in the BAP1 gene. This alteration has been … (more)
Likely pathogenic
(Sep 24, 2020)
criteria provided, single submitter
Method: clinical testing
Tumor susceptibility linked to germline BAP1 mutations
Allele origin: germline
Invitae
Accession: SCV000959424.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 9 of the BAP1 gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Multigene panel testing in unselected Israeli breast cancer cases: mutational spectrum and use of BRCA1/2 mutation prediction algorithms. Bernstein-Molho R Breast cancer research and treatment 2019 PMID: 30980208
Sensitivity to asbestos is increased in patients with mesothelioma and pathogenic germline variants in BAP1 or other DNA repair genes. Betti M Genes, chromosomes & cancer 2018 PMID: 30338612
Analysis of the exome aggregation consortium (ExAC) database suggests that the BAP1-tumor predisposition syndrome is underreported in cancer patients. Massengill JB Genes, chromosomes & cancer 2018 PMID: 29761599
Germline BAP1 mutations predispose to renal cell carcinomas. Popova T American journal of human genetics 2013 PMID: 23684012
Germline BAP1 mutations predispose to malignant mesothelioma. Testa JR Nature genetics 2011 PMID: 21874000
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs774730309...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 24, 2021