diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index fc9752629..6650f99ea 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -248,8 +248,8 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
     }
 
     public double getNonRefAlleleFrequency() {
-        if ( !isBiallelic() )
-            throw new StingException("This VCF record is not bi-allelic.");
+        if ( isReference() )
+            throw new StingException("This VCF record is not variant.");
 
         if ( mInfoFields.containsKey(ALLELE_FREQUENCY_KEY) ) {
             return Double.valueOf(mInfoFields.get(ALLELE_FREQUENCY_KEY));