diff --git a/src/pheval/prepare/prepare_corpus.py b/src/pheval/prepare/prepare_corpus.py
index d749d0dd..df0beda2 100644
--- a/src/pheval/prepare/prepare_corpus.py
+++ b/src/pheval/prepare/prepare_corpus.py
@@ -57,6 +57,11 @@ def prepare_corpus(
                     f"Removed {phenopacket_path.name} from the corpus due to missing variant fields."
                 )
                 continue
+            elif phenopacket_util.check_variant_alleles():
+                info_log.warning(
+                    f"Removed {phenopacket_path.name} from the corpus due to identical "
+                    "reference and alternate allele fields."
+                )
         if gene_analysis:
             if phenopacket_util.check_incomplete_gene_record():
                 info_log.warning(