What is the Variant Effect Predictor?
This tool allows you to input coordinates of any alleles you have identified, and determine the effect on relevant Ensembl transcripts and proteins. An example input file is available. For example, if a variant that you enter as input causes a change in the protein sequence, Ensembl will calculate the possible amino acids at that position. The variant would be given a consequence type of "non-synonymous". Have a look at other possible consequence types in the variation documentation.