GVs affecting the same protein-coding transcript must be assessed together to correctly predict their functional impact. Panel A shows an example where two neighboring frameshift indels (1-bp insertion and 1-bp deletion, indicated by arrows) cancel each others effect, restoring the original ORF. Panel B shows an example where an otherwise synonymous SNV (G->A, indicated by arrow) causes a missense mutation due to the effect of a neighboring SNV (A->G). In both panels, the first three rows show the reference nucleotide sequence on the forward strand, the reference nucleotide sequence from the reverse strand, and the reference protein sequence translation from the annotated ORF. Note that both ORFs are encoded on the reverse strand, so sequences must be read from right to left. The track below shows the variant sequence detected in human individual HG00732-200-37-ASM, with critical GVs highlighted by arrows. The blue horizontal bar represents the Ensembl protein-coding transcript spanning this genomic region.
Vergara et al. BMC Research Notes 2012 5:615 doi:10.1186/1756-0500-5-615