Hi,
in those cases that snpEff returns different annotations, for example
ANN=T|synonymous_variant|LOW|Muc4|ENSMUSG00000079620|transcript|ENSMUST00000096106|protein_coding|2/27|c.2256C>T|p.Ser752Ser|2750/11277|2256/10413|752/3470||,T|upstream_gene_variant|MODIFIER|Muc4|ENSMUSG00000079620|transcript|ENSMUST00000135753|protein_coding||c.-3959C>T|||||3957|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|Muc4|ENSMUSG00000079620|transcript|ENSMUST00000132475|protein_coding||c.*1563C>T|||||1563|WARNING_TRANSCRIPT_NO_STOP_CODON,T|non_coding_transcript_exon_variant|MODIFIER|Muc4|ENSMUSG00000079620|transcript|ENSMUST00000142355|processed_transcript|2/25|n.2439C>T||||||
thanks