diff --git a/uk/ac/sanger/artemis/components/variant/VariantBase.java b/uk/ac/sanger/artemis/components/variant/VariantBase.java
index 0ffad2377ffe603c060f37ace3e8dfb7acbb4de3..c69637c9c0048a5fe7ce43d9260152f9f8e22fdb 100644
--- a/uk/ac/sanger/artemis/components/variant/VariantBase.java
+++ b/uk/ac/sanger/artemis/components/variant/VariantBase.java
@@ -109,7 +109,7 @@ public class VariantBase
 
   protected boolean isNonVariant()
   {
-    if (alt.equals(".") && record.getRef().length() == 1)
+    if ((alt.equals(".") ||  alt.equals("X")) && record.getRef().length() == 1)
       return true;
     return false;
   }