diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 67ade390f..3d9724ffb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -444,16 +444,10 @@ public class UnifiedGenotyperEngine {
         if ( alleleCountsofMLE.size() > 0 ) {
             attributes.put(VCFConstants.MLE_ALLELE_COUNT_KEY, alleleCountsofMLE);
             final int AN = builder.make().getCalledChrCount();
-
-            // let's sanity check that we don't have an invalid MLE value in there
-            for ( int MLEAC : alleleCountsofMLE ) {
-                if ( MLEAC > AN )
-                    throw new ReviewedStingException(String.format("MLEAC value (%d) is larger than AN (%d) at position %s:%d", MLEAC, AN, loc.getContig(), loc.getStart()));
-            }
-
             final ArrayList<Double> MLEfrequencies = new ArrayList<Double>(alleleCountsofMLE.size());
+            // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1)
             for ( int AC : alleleCountsofMLE )
-                MLEfrequencies.add((double)AC / (double)AN);
+                MLEfrequencies.add(Math.min(1.0, (double)AC / (double)AN));
             attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies);
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index 00a593768..2b1bd9c62 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -46,7 +46,8 @@ public class AlleleCount extends VariantStratifier {
             int AC = 0; // by default, the site is considered monomorphic
 
             if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && eval.isBiallelic() ) {
-                AC = eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0);
+                // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1)
+                AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom);
             } else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && eval.isBiallelic() ) {
                 AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
             } else if ( eval.isVariant() ) {
@@ -56,7 +57,7 @@ public class AlleleCount extends VariantStratifier {
 
             // make sure that the AC isn't invalid
             if ( AC > nchrom )
-                throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d " +
+                throw new UserException.MalformedVCF(String.format("The AC value (%d) at position %s:%d " +
                         "is larger than the number of chromosomes over all samples (%d)", AC,
                         eval.getChr(), eval.getStart(), nchrom));