release/115.2

Bugfix:

• Fix issues with multi-allelic variants. See #1924

release/115.1

Bugfix:

• custom annotation: fix matching logic when annotation file has SV. see #1914

release/115.0

For Ensembl VEP 115.0 we have:

• Added Ensembl VEP support for annotating structural variants with allele frequencies from gnomAD and clinical significance (CLINSIG) from ClinVar.
• Added Ensembl VEP and Ensembl Variation API support for the new ClinVar somatic classifications.
• Enabled support for GENCODE promoters, variants falling within them can now be annotated with details of the promoter
• Added a new plugin (on CLI): MechPredict

release/114.2

Bug fix:

• Fix fetching of HGVSg for multi-allelic variants. see #1867
• Fix substr outside of string error when calculating consequence with shifting. see #1885

release/114.1

Bug fix:

• HGVSg is not getting reported where alleles are altered due to shifting. ensembl-vep/1869

release/114.0

New in version 114 (May 2025)

• MAVE data has been updated from the latest version of MaveDB, representing a nearly 6.5 fold increase in variants covered (~1.2 million to ~7.7 million).
• Support for https protocol when downloading FTP files and adding GitHub Token to increase rate limit in VEP install script.
• Allele frequency from NIH AllOfUs study is now available in the web VEP.
• Plugin support added to REST for:
  • Paralogues
• Plugin data version updated:
  • dbNSFP (from 4.7c to 5.0c)
  • LOEUF (from gnomAD v2.1.1 to gnomAD v4.1)
• Plugin deprecated:
  • DisGeNET
  • Mastermind (Only from REST)

release/113.4

Bug fix:

• Modify version detection in dbNSFP.pm, adding support for 5.x+: VEP_plugins/778
• Adding all the last G2P fixes to 113: VEP_plugins/780

release/113.3

Bug fix:

• Fix method codon() in TranscriptVariationAllele: ensembl-variation/1131
• Fix transcript mismatch warning message: ensembl-vep/1788

release/113.2

Bugfix:

• CADD plugin - same score for all alt alleles: VEP_plugins/749
• HGVSc for RefSeq transcripts - represent the alleles relative to the feature: ensembl-variation/1128

release/113.1

Bugfix:

• Fix hgvsg for insertion with ref allele -: ensembl-variation/1124