Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs
Open accessAbstract
A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T>A and c.4986+5G>T; BRCA2, c.7617+2T>G and c.8754+5G>A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T>A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No false-negative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.
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Splice site prediction tools have increased sensitivity (~90-100%) relative to specificity (~60-80%) in predicting splice site abnormalities.
“In general, splice site prediction tools have increased sensitivity (~90-100%) relative to specificity (~60-80%) in predicting splice site abnormalities. 23,24”
From Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (2015) · cites this paper as [24]
The Splice-Site Prediction of Intronic Variants in BRCA1 and BRCA2 section (page unavailable) reports no false-negative predictions among 161 informative predictions, supporting high sensitivity in the variants studied. It reports four false positives but does not give a specificity of approximately 60–80% or establish the claimed ranges for splice-site prediction tools in general. (LLM, conf=0.86)
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- Authors
- Vreeswijk, M. P. G., Kraan, J. N., van der Klift, H. M., Vink, G. R., Cornelisse, C. J., Wijnen, J. T., Bakker, E., van Asperen, C. J., & Devilee, P.
- Affiliations
- Leiden University Medical Center (NL)
- Corresponding author
- Vreeswijk, Maaike P.G.
- Venue
- Human Mutation
- Publisher
- Hindawi Limited
- Published
- 2009-01
- Volume
- 30
- Issue
- 1
- Pages
- 107-114
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- OpenAlex
- W2013639985
- Cited by
- 98
- References
- 47
- Citations by year
- 2025: 1 · 2023: 2 · 2022: 4 · 2021: 5 · 2020: 3 · 2019: 9 · 2018: 9 · 2017: 7 · 2016: 10 · 2015: 5 · 2014: 5 · 2013: 7 · 2012: 6
- FWCI
- 4.75
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- BRCA1, BRCA2, intronic variants, splice site prediction, RNA splicing, unclassified variants, variant interpretation, false positive prediction
- MeSH terms
- Adult, Base Sequence, Breast Neoplasms, Female, Humans, Introns, Molecular Sequence Data, RNA Splicing, Software, Genetic Variation, Sequence Analysis, RNA, BRCA1 Protein, RNA Splice Sites, BRCA2 Protein
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