Is your feature request related to a problem? Please describe.
After #81 we have initial AutoBP7 class. Now we need to properly implement the criteria, test it and document.
Describe the solution you'd like
Implement _check_proximity_to_splice_site and _predict_spliceai methods.
Add unit tests to tests/criteria/test_bp7.py
Add integration tests to tests/assets/e2e_variants/other_criteria.csv
Add docstrings for each method of the AutoBP7 class
Describe alternatives you've considered
N/A
Additional context
Here is the info about BP7:
BP7 (synonymous)
Original Definition
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
-- Richards et al. (2015); Table 4
Preconditions / Precomputations
If the variant is on chrMT then this criterion is skipped according to McCormick et al. (2020).
Implemented Criterion
If there is a pathogenic variant +/- 2bp of the position in ClinVar then the criterion is skipped.
If the variant is closer than 2bp to a splice site then the criterion is skipped.
If the variant is not predicted to alter the splice site using SpliceAI then the criterion is triggered.
User Report
The variant position and the reason for triggering or skipping.
Literature
McCormick et al. (2020) describe the ACMG criteria for chrMT variants.
Caveats
N/A
Notes
We use the thresholds from PMID:30376034 <https://pubmed.ncbi.nlm.nih.gov/30376034/>__.
Intervar
BP7 by Automated Scoring
If a synonymous (silent) variant has no effect on splicing and if the nucleotide position is not highly conserved, then we can classify this variant as likely benign and assign BP7 as 1. The prediction on the effect on splicing can be extracted by ANNOVAR with the “dbscSNV” database. Both scores dbscSNV_RF_SCORE and dbscSNV_ADA_SCORE should be <0.6 when the variant is predicted to have no impact on splicing. The conservation information is retrieved from the “dbnsfp30a” database, where a GERP++ score > 2 indicates that the nucleotide is highly conserved.
Is your feature request related to a problem? Please describe. After #81 we have initial AutoBP7 class. Now we need to properly implement the criteria, test it and document.
Describe the solution you'd like
_check_proximity_to_splice_siteand_predict_spliceaimethods.tests/criteria/test_bp7.pytests/assets/e2e_variants/other_criteria.csvDescribe alternatives you've considered N/A
Additional context Here is the info about BP7: BP7 (synonymous)
Original Definition
Preconditions / Precomputations
Implemented Criterion
User Report
Literature
Caveats
N/A
Notes
PMID:30376034 <https://pubmed.ncbi.nlm.nih.gov/30376034/>__.Intervar
BP7 by Automated Scoring If a synonymous (silent) variant has no effect on splicing and if the nucleotide position is not highly conserved, then we can classify this variant as likely benign and assign BP7 as 1. The prediction on the effect on splicing can be extracted by ANNOVAR with the “dbscSNV” database. Both scores dbscSNV_RF_SCORE and dbscSNV_ADA_SCORE should be <0.6 when the variant is predicted to have no impact on splicing. The conservation information is retrieved from the “dbnsfp30a” database, where a GERP++ score > 2 indicates that the nucleotide is highly conserved.