diff --git a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
index 9f2f628a59c0607ea7fd0f3b644d15c9a764efc8..8434ae6f1beda57527c98d820ad9223de9986083 100644
--- a/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
+++ b/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
@@ -172,10 +172,19 @@ sub calculate_same_codon{
 sub type_variation {
   my $tr  = shift;
   my $var = shift;
+
+  my $UPSTREAM = 5000;
+  my $DOWNSTREAM = 5000;
+
   if (!$var->isa('Bio::EnsEMBL::Variation::ConsequenceType')){
       throw("Not possible to calculate the consequence type for ",ref($var)," : Bio::EnsEMBL::Variation::ConsequenceType object expected");
   }
 
+  if (($var->start < $tr->start - $UPSTREAM) || ($var->end  > $tr->end + $DOWNSTREAM)){
+    #since the variation is more than UPSTREAM and DOWNSTREAM of the transcript, there is no effect in the transcript
+    return [];
+  }
+
   my $tm = $tr->get_TranscriptMapper();
   my @coords = $tm->genomic2cdna($var->start,
                                  $var->end,