diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index caf355ba1b95243c0cd4ca3a2b9511f37558a8d0..23a296b77ef74bf130fa8fa946463133d3f04321 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -522,7 +522,7 @@ class VCFRecord
     
     protected boolean isNonVariant()
     {
-      if(alt.equals("."))
+      if(alt.equals(".") && ref.length() == 1)
         return true;
       return false;
     }