fix: improve consequence predictions (#690)

Cargo.toml

@@ -45,7 +45,7 @@ enumflags2 = { version = "0.7.11", features = ["serde"] }
 env_logger = "0.11"
 flate2 = "1.1"
 futures = "0.3"
-hgvs = "0.18.0"
+hgvs = "0.18.1"
 indexmap = { version = "2.7", features = ["serde"] }
 itertools = "0.14"
 jsonl = "4.0"

openapi.schema.yaml

@@ -8,7 +8,7 @@ info:
   license:
     name: MIT
     identifier: MIT
-  version: 0.30.1
+  version: 0.31.0
 paths:
   /api/v1/genes/transcripts:
     get:
@@ -412,6 +412,8 @@ components:
       - splice_donor_variant
       - stop_gained
       - frameshift_variant
+      - frameshift_elongation
+      - frameshift_truncation
       - stop_lost
       - start_lost
       - transcript_amplification
@@ -423,6 +425,7 @@ components:
       - conservative_inframe_deletion
       - missense_variant
       - rare_amino_acid_variant
+      - protein_altering_variant
       - splice_donor_5th_base_variant
       - splice_region_variant
       - splice_donor_region_variant

src/annotate/seqvars/ann.rs

@@ -85,6 +85,14 @@ pub enum Consequence {
     /// SO:frameshift_variant, VEP:frameshift_variant
     FrameshiftVariant,
 
+    /// "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature."
+    /// SO:frameshift_elongation
+    FrameshiftElongation,
+
+    /// "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature."
+    /// SO:frameshift_truncation
+    FrameshiftTruncation,
+
     /// "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript."
     /// SO:stop_lost, VEP:stop_lost
     StopLost,
@@ -131,10 +139,9 @@ pub enum Consequence {
     /// SO:rare_amino_acid_variant
     RareAminoAcidVariant,
 
-    // Not used by mehari, but by VEP (we're usually more specific)
-    // /// "A sequence_variant which is predicted to change the protein encoded in the coding sequence."
-    // /// SO:protein_altering_variant, VEP:missense_variant
-    // ProteinAlteringVariant,
+    /// "A sequence_variant which is predicted to change the protein encoded in the coding sequence."
+    /// SO:protein_altering_variant, VEP:missense_variant
+    ProteinAlteringVariant,
 
     // low impact
     /// "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript."
@@ -284,6 +291,8 @@ impl From<Consequence> for PutativeImpact {
             | SpliceDonorVariant
             | StopGained
             | FrameshiftVariant
+            | FrameshiftElongation
+            | FrameshiftTruncation
             | StopLost
             | StartLost
             | TranscriptAmplification
@@ -293,6 +302,7 @@ impl From<Consequence> for PutativeImpact {
             | DisruptiveInframeDeletion
             | ConservativeInframeInsertion
             | ConservativeInframeDeletion
+            | ProteinAlteringVariant
             | MissenseVariant
             | RareAminoAcidVariant => PutativeImpact::Moderate,
             SpliceDonorFifthBaseVariant