Annotate genomic variants with variant effect

This "Variant Effect Predictor" seems like a useful tool:

http://uswest.ensembl.org/info/docs/variation/vep/index.html

would be useful to run against any genomic source's variants during some part of the data ingest, in order to classify the types of variation. i've noticed that resources will sometimes do their own classification, although i have absolutely no idea what vocabulary they are drawing on. in this case, i believe they are using SO (does SO have enough types for us?)

this can use VCF file format, and looks like it compares against the ENSEMBL genome databases...an arguments for pulling in the ENSEMBL genomic annotations.