diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
index 81c5933526fbcb2a119588679fcbe1b127766a99..d45352b5919cd035e148cc230f999b9eb569e4c1 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -420,9 +420,9 @@ sub calc_overlap_score {
   #
   ## PENALTY:
   ## penalise by 10% if phase if different
-  #if ( $source_exon->phase != $target_exon->phase ) {
-  #$score *= 0.9;
-  #}
+  if ( $source_exon->phase != $target_exon->phase ) {
+    $score *= 0.9;
+  }
 
   # add score to scoring matrix if it's at least 0.5
   if ( $score >= 0.5 ) {