diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm
index 136c486eb..07c963a81 100644
--- a/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm
+++ b/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm
@@ -289,7 +289,7 @@ sub annotate_InputBuffer {
         $parser->next();
       }
 
-      while($parser->{record} && $parser->get_start <= $vf_end + 1) {
+      while($parser->{record} && $parser->get_seqname eq $self->get_source_chr_name($chr) && $parser->get_start <= $vf_end + 1) {
         $self->annotate_VariationFeature($vf);
         $parser->next();
       }