487dae9a4a149085ff20b7c73a399fce9c9c85ca
angie
  Thu May 22 09:47:41 2014 -0700
For intergenic variants, I was assuming that each variant would havea firstAltAllele -- but for reference-only "variants", that's not the
case so we need to check first.  If there's no actual variation,
drop the "variant".
fixes #13310 - thanks Jonathan for finding.

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index 5e35f3f..b421de9 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -41,21 +41,24 @@
 	    } nonCodingExon;
 	struct intron 		// intron_variant
 	    {
 	    uint intronNumber;	// 0-based intron number (from genePred, beware false "introns")
 	    } intron;
 	} details;
     };
 
 struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
 			    struct dnaSeq *transcriptSequence, struct lm *lm);
 // return the predicted effect(s) of a variation list on a genePred
 
 // number of bases up or downstream that we flag
 #define GPRANGE 5000
 
+boolean hasAltAllele(struct allele *alleles);
+/* Return TRUE if alleles include at least one non-reference allele. */
+
 char *firstAltAllele(struct allele *alleles);
 /* Ensembl always reports an alternate allele, even if that allele is not being used
  * to calculate any consequence.  When allele doesn't really matter, just use the
  * first alternate allele that is given. */
 
 #endif /* GPFX_H */