diff --git a/genie/process_mutation.py b/genie/process_mutation.py
index b2846ffd..fe27d647 100644
--- a/genie/process_mutation.py
+++ b/genie/process_mutation.py
@@ -342,6 +342,7 @@ def check_annotation_error_reports(
         maf_table_synid (str): synapse_id of the narrow maf table
         full_error_report (pd.DataFrame): the failed annotations error report
         center (str): the center this is for
+
     """
     maf_table_df = extract.get_syntabledf(
         syn=syn,
@@ -351,10 +352,11 @@ def check_annotation_error_reports(
             "Annotation_Status = 'FAILED'"
         ),
     )
-    assert len(maf_table_df) == len(full_error_report), (
-        "Genome nexus's failed annotations error report rows doesn't match"
-        f"maf table's failed annotations for {center}"
-    )
+    if len(maf_table_df) != len(full_error_report):
+        logger.warning(
+            "Genome nexus's failed annotations error report rows doesn't match"
+            f"maf table's failed annotations for {center}"
+        )
 
 
 def store_annotation_error_reports(
diff --git a/tests/test_process_mutation.py b/tests/test_process_mutation.py
index 5895dee3..94e03d3f 100644
--- a/tests/test_process_mutation.py
+++ b/tests/test_process_mutation.py
@@ -264,25 +264,26 @@ def test_check_annotation_error_reports_passes_if_match(
                 "Annotation_Status = 'FAILED'",
             )
 
-    def test_check_annotation_error_reports_throws_assertion_if_no_match(
-        self, syn, test_error_report
+    def test_check_annotation_error_reports_raises_warning_if_no_match(
+        self, syn, test_error_report, caplog
     ):
         with patch.object(
             extract,
             "get_syntabledf",
             return_value=pd.DataFrame({"test": [1], "test2": [2]}),
         ):
-            with pytest.raises(
-                AssertionError,
-                match="Genome nexus's failed annotations error report rows doesn't match"
-                "maf table's failed annotations for SAGE",
-            ):
-                process_mutation.check_annotation_error_reports(
-                    syn=syn,
-                    maf_table_synid="synZZZZ",
-                    full_error_report=test_error_report,
-                    center="SAGE",
-                )
+            process_mutation.check_annotation_error_reports(
+                syn=syn,
+                maf_table_synid="synZZZZ",
+                full_error_report=test_error_report,
+                center="SAGE",
+            )
+            assert (
+                "Genome nexus's failed annotations error report rows doesn't match"
+                "maf table's failed annotations for SAGE" in caplog.text
+            )
+            # check that at least one is a warning
+            assert any(record.levelname == "WARNING" for record in caplog.records)
 
     def test_concat_annotation_error_reports_returns_expected(self, test_error_report):
         compiled_report = process_mutation.concat_annotation_error_reports(