Update variant consequences from Ensembl VEP (#68):

* :issue:`68`: Refresh the variant consequences database from Ensembl VEP. The database's latest update was on May 31, 2021.
sbslee · Sep 3, 2023 · dda26c8 · dda26c8
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,6 +8,7 @@ Changelog
 * Add new submodule ``pychip``.
 * Add new method :meth:`common.reverse_complement`.
 * Fix bug in :meth:`common.extract_sequence` where a long DNA sequence output was truncated.
+* :issue:`68`: Refresh the variant consequences database from Ensembl VEP. The database's latest update was on May 31, 2021.
 
 0.36.0 (2022-08-12)
 -------------------

diff --git a/fuc/api/pymaf.py b/fuc/api/pymaf.py
@@ -97,7 +97,7 @@
 
 # Below is the list of calculated variant consequences from Ensembl VEP:
 # https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html
-# (accessed on 2021-05-31)
+# (accessed on 2023-09-03)
 #
 # Note that both frameshift_variant and protein_altering_variant require
 # additional information to find their correct Variant_Classification.
@@ -139,6 +139,11 @@
  'regulatory_region_variant': 'IGR',
  'feature_truncation': 'Targeted_Region',
  'intergenic_variant': 'IGR',
+ 'splice_donor_5th_base_variant': 'AMBIGUOUS',
+ 'splice_donor_region_variant': 'AMBIGUOUS',
+ 'splice_polypyrimidine_tract_variant': 'AMBIGUOUS',
+ 'coding_transcript_variant': 'AMBIGUOUS',
+ 'sequence_variant': 'AMBIGUOUS',
 }
 
 VARCLS_LIST = [