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AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants
Jiale Xiang1, Jiguang Peng1, Samantha Baxter2
1BGI Genomics, BGI-Shenzhen, Shenzhen, China.
Human Mutation
|May 23, 2020
Summary
AutoPVS1 is a new tool that automates the interpretation of null variants in the human genome. It helps biocurators accurately classify pathogenicity, improving genetic variant interpretation for clinical management.
Area of Science:
- Genomics
- Clinical Genetics
- Bioinformatics
Background:
- Accurate interpretation of null variants in the human genome is crucial for clinical management.
- The Sequence Variant Interpretation (SVI) Working Group refined the PVS1 criterion for pathogenicity in 2018.
Purpose of the Study:
- To develop and assess AutoPVS1, an automated tool for streamlining the interpretation of the PVS1 criterion.
- To evaluate the accuracy and utility of AutoPVS1 in classifying genetic variants.
Main Methods:
- Developed AutoPVS1, a graphical user interface tool for automatic classification of PVS1.
- Assessed AutoPVS1 performance using 56 manually curated variants by the ClinGen SVI Working Group.
- Analyzed 28,586 putative loss-of-function variants using AutoPVS1.
Main Results:
- AutoPVS1 achieved 93% concordance with expert manual curation (52/56 variants).
- At least 27.7% of analyzed loss-of-function variants did not meet the very strong PVS1 strength level.
- Splicing variants showed a significantly higher rate (41.0%) of decreased PVS1 strength compared to frameshift (13.2%) and nonsense (10.8%) variants.
Conclusions:
- AutoPVS1 accurately and reliably assigns PVS1 strength levels, meeting an urgent need in variant interpretation.
- The tool highlights the importance of considering variant-specific issues and disease mechanisms.
- AutoPVS1 is publicly available to aid biocurators in genetic variant interpretation.
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