Provide mutation info with StartLosses

[joaoe]

Both VEP and ANNOVAR mark start losses but include the information regarding changes in the coding sequence and aminoacids. For instance, the json from VEP with variant chr10 58224929 A G:

{
"allele_string": "A/G",
"assembly_name": "GRCm38",
"end": 58224929,
"id": "10_58224929_A/G",
"input": "chr10\t58224929\t.\tA\tG\t4567\t.",
"most_severe_consequence": "start_lost",
"seq_region_name": 10,
"start": 58224929,
"strand": 1,
"transcript_consequences": [{
  "amino_acids": "M/T",
  "cdna_end": 2,
  "cdna_start": 2,
  "cds_end": 2,
  "cds_start": 2,
  "codons": "aTg/aCg",
  "consequence_terms": ["start_lost"],
  "gene_id": "ENSMUSG00000058537",
  "impact": "HIGH",
  "protein_end": 1,
  "protein_start": 1,
  "source": "Ensembl",
  "strand": -1,
  "transcript_id": "ENSMUST00000204003",
  "variant_allele": "G",
}],

Would perhaps be nice to annotate these as regular annotations (Substitution, Insertion, Deletion), and then wrap them with a StartLoss in a property called alternate_effect the same way it happens for ExonicSpliceSite. Or just include aa_ref and aa_alt. (which is not that useful if the annotation has other consequences, like being a Frameshift or PrematureStop

[ijhoskins]

I concur with @joaoe 's suggestion above. It'd be nice to have the aa_alt attribute for this effect class, instead of the p.M1? annotation.