diff --git a/csq.c b/csq.c
index c3fbb337..6cbaa5c9 100644
--- a/csq.c
+++ b/csq.c
@@ -1110,7 +1110,9 @@ fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%
                 {
                     if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
                     if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
-                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+
+                    int noff = N_SPLICE_REGION_INTRON - N_SPLICE_DONOR;
+                    if ( ref && alt && noff<splice->kref.l && noff<splice->kalt.l && !strncmp(ref+noff,alt+noff,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
                 }
             }
         }
diff --git a/test/csq/ENSCAFT00000047742/test.txt b/test/csq/ENSCAFT00000047742/test.txt
index 603cdbef..9f0258e2 100644
--- a/test/csq/ENSCAFT00000047742/test.txt
+++ b/test/csq/ENSCAFT00000047742/test.txt
@@ -1,3 +1,3 @@
-104	CA	C	synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
-104	CA	C	synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+104	CA	C	splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+104	CA	C	splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
 
diff --git a/test/csq/ENSCAFT00000047742/test.vcf b/test/csq/ENSCAFT00000047742/test.vcf
index ff2493d4..188fc29f 100644
--- a/test/csq/ENSCAFT00000047742/test.vcf
+++ b/test/csq/ENSCAFT00000047742/test.vcf
@@ -4,4 +4,4 @@
 ##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
 ##INFO=<ID=EXPL,Number=1,Type=String,Description="Expected consequence with bt/csq -l">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-chr9	104	.	CA	C	.	PASS	EXP=synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+chr9	104	.	CA	C	.	PASS	EXP=splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding