Add variant region condition for dups ending in UTR

genomoncology · Jan 4, 2024 · 0e4eeb2 · 0e4eeb2
1 parent 2781a4b
commit 0e4eeb2
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Showing 4 changed files with 16 additions and 0 deletions.
diff --git a/src/hgvs/utils/altseqbuilder.py b/src/hgvs/utils/altseqbuilder.py
@@ -185,6 +185,11 @@ def _get_variant_region(self):
             and self._var_c.posedit.pos.end.datum == Datum.CDS_END
         ):
             result = self.T_UTR
+        elif (
+            self._var_c.posedit.edit.type == "dup"
+            and self._var_c.posedit.pos.end.datum == Datum.CDS_END
+        ):
+            result = self.T_UTR
         elif self._var_c.posedit.pos.start.base < 0 and self._var_c.posedit.pos.end.base < 0:
             result = self.F_UTR
         elif (

diff --git a/tests/data/cache-py3.hdp b/tests/data/cache-py3.hdp
diff --git a/tests/test_hgvs_variantmapper.py b/tests/test_hgvs_variantmapper.py
@@ -118,6 +118,12 @@ 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_dup_three_prime_utr(self):
+        hgvs_c = "NM_153223.3:c.2959_*1dup"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_694955.2:p.?")
+
 
 if __name__ == "__main__":
     unittest.main()

diff --git a/tests/test_hgvs_variantmapper_cp_sanity.py b/tests/test_hgvs_variantmapper_cp_sanity.py
@@ -164,6 +164,11 @@ def test_three_prime_utr(self):
         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.?"
+        self._run_conversion(hgvsc, hgvsp_expected)
+
     def test_deletion_into_three_prime_utr_frameshift(self):
         hgvsc = "NM_999999.1:c.27_*3del"
         hgvsp_expected = "MOCK:p.(Lys9XaafsTer?)"