fix: do not include n/a clinvar ids in mappings

civicpy/exports/civic_gks_record.py

@@ -343,6 +343,7 @@ def _get_variant_concept_mapping(variant: GeneVariant) -> ConceptMapping:
                     relation=Relation.RELATED_MATCH,
                 )
                 for clinvar_id in clinvar_ids
+                if clinvar_id and clinvar_id != "N/A"
             )
 
         for a in molecular_profile.aliases:

civicpy/tests/test_exports.py

@@ -687,6 +687,19 @@ def test_get_extensions(self, v600e_mp):
             )
             assert expressions is None
 
+    def test_na_clinvar_mapping(self, v600e_mp):
+        """Test that get_aliases_and_mappings method works as expected when no clinvar entry found"""
+        variant = v600e_mp.variants[0]
+
+        with patch.object(variant, "clinvar_entries", new=["N/A"]):
+            gks_mp = CivicGksMolecularProfile(v600e_mp)
+            _, mappings = gks_mp.get_aliases_and_mappings(v600e_mp)
+            assert mappings
+            assert not any(
+                m.coding.system == "https://www.ncbi.nlm.nih.gov/clinvar/variation/"
+                for m in mappings
+            )
+
 
 class TestCivicGksTherapyGroup(object):
     """Test that CivicGksTherapyGroup works as expected"""