14.1.0 Nice and Splicy

[julesjacobsen]

The main changes in this release focus on further updates to ACMG assignment categories, including addition of PS1, PM1, PM5, BS1, BS2 categories to ACMG assignments. This release also includes implementation of the assignment of the ClinGen recommendations for splicing variants.

• New AcmgMissenseInFrameIndelEvidenceAssigner class to assign PS1, PM1, PM5, PP2, BP1, PP3, BP4 to missense and inframe
  indels.
• New AcmgSpliceEvidenceAssigner class which applies PS1, PP3, BP4, BP7 to splice region variants according to ClinGen
  recommendations for splicing variants published in
  Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations
  from the ClinGen SVI Splicing Subgroup.
• New AcmgPVS1EvidenceAssigner handles assignment of PVS1 to loss of function variants according
  to Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion
• Downgraded BP4 to have a maximum of Supporting evidence for REVEL scores under 0.290
• Updated gene constraints to use gnomad v4.1 data

Under the hood changes

• Deprecate out of date Acmg2015Classifier and Acgs2020Classifier
• Update JannovarSmallVariantAnnotator to remove MNV annotations from effects as these were overriding more damaging
  functional effects such as STOP_LOSS, STOP_GAIN, SPLICE_DONOR, SPLICE_ACCEPTOR which prevented potential assignment of
  PVS1.
• Update Acmg2015EvidenceAssigner to include BS1, BS2 assignments.
• Refactor Acmg2015EvidenceAssigner missense assignment methods into new AcmgMissenseInFrameIndelEvidenceAssigner class.
• Add PP2/BP1 assignments to AcmgMissenseInFrameIndelEvidenceAssigner using GeneStatistics
• Update ClinVarDao with new getGeneStatistics() method.
• Add new GeneStatistics class for handling aggregated ClinVar gene-level variant effect counts.
• Add new AcmgEvidence.parseAcmgEvidence() method.
• Changes to enable SpliceAI PP3 and other splicing-related ACMG assignments.
• Add new AcmgPVS1EvidenceAssigner class to assign PVS1 to loss of function variants
• Add new AcmgMissenseInFrameIndelEvidenceAssigner class to assign PS1, PM1, PM5, PP2, BP1, PP3, BP4 to missense and
  inframe indels
• Add new AcmgSpliceEvidenceAssigner class to assign PS1, PP3, BP4, BP7 to splice region variants
• Add new AcmgEvidence.Builder.containsWithEvidence method
• Add @nullable to PathogenicityData.pathogenicityScore method

This update also includes a new 2410 data release. See the data-release discussions for links.

Full Changelog: 14.0.2...14.1.0

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This discussion was created from the release 14.1.0 Nice and Splicy.