Also handle insertions

biocommons · May 24, 2024 · 59966a9 · 59966a9
1 parent 509c543
commit 59966a9
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Showing 3 changed files with 13 additions and 2 deletions.
diff --git a/src/hgvs/utils/altseqbuilder.py b/src/hgvs/utils/altseqbuilder.py
@@ -184,7 +184,7 @@ def _get_variant_region(self):
         ):
             result = self.T_UTR
         elif (
-            self._var_c.posedit.edit.type == "dup"
+            self._var_c.posedit.edit.type in ["dup", "ins"]
             and self._var_c.posedit.pos.end.datum == Datum.CDS_END
         ):
             result = self.T_UTR

diff --git a/tests/test_hgvs_variantmapper.py b/tests/test_hgvs_variantmapper.py
@@ -116,6 +116,12 @@ def test_map_of_c_out_of_reference_bound(self):
         with pytest.raises(HGVSError, match="coordinate is out of bounds"):
             self.vm.c_to_p(var_c)
 
+    def test_map_of_ins_three_prime_utr(self):
+        hgvs_c = "NM_004985.4:c.567_*1insCCC"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_004976.2:p.?")
+
     def test_map_of_dup_three_prime_utr(self):
         hgvs_c = "NM_153223.3:c.2959_*1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)

diff --git a/tests/test_hgvs_variantmapper_cp_sanity.py b/tests/test_hgvs_variantmapper_cp_sanity.py
@@ -157,11 +157,16 @@ def test_five_prime_utr(self):
         hgvsp_expected = "MOCK:p.?"
         self._run_conversion(hgvsc, hgvsp_expected)
 
-    def test_three_prime_utr(self):
+    def test_sub_three_prime_utr(self):
         hgvsc = "NM_999999.1:c.*3G>A"
         hgvsp_expected = "MOCK:p.?"
         self._run_conversion(hgvsc, hgvsp_expected)
 
+    def test_ins_three_prime_utr(self):
+        hgvsc = "NM_999999.1:c.39_*1insA"
+        hgvsp_expected = "MOCK:p.?"
+        self._run_conversion(hgvsc, hgvsp_expected)
+
     def test_dup_three_prime_utr(self):
         hgvsc = "NM_999999.1:c.12_*1dup"
         hgvsp_expected = "MOCK:p.?"