The possible functional consequence of a variant can be interrogated by comparing to a conservation score that tells how conserved this particular position is among a set of different species. The underlying line of thought is that conserved bases are functionally important - otherwise they would have been mutated during evolution. If a variant is found at a position that is otherwise well conserved, it is an indication that the variant is functionally important. Of course this is only a prediction, as non-conserved regions could have functional roles too.
Conservation scores can be computed by several tools e.g. PhyloP and PhastCons and can be downloaded as pre-computed scores from an whole genome alignment of different species from different sources. See how to find and import tracks with conservation scores in Import tracks.
Toolbox | Resequencing Analysis | Variant Annotation | Annotate with Conservation Scores
Select the variant track as input and when you click Next you will need to provide the track with conservation scores (see figure 27.30).
In the resulting track, all the variants will have quality scores annotated, and this can be used for sorting and filtering the track (see Showing a track in a table).