VEP transcript CDS lenght

Question

[cristinaluengoagullo]

Hi,

I saw that VEP provides a 'transcript_consequences' annotation with 'cds_start' and 'cds_end' fields. But they do not indicate the amino acids length. Is there a way to get the amino acids length from the annotations? I haven't seen any possible field in the annotations structure:

"transcript_consequences": [
    {
      "variant_allele": "G",
      "consequence_terms": [
        "missense_variant"
      ],
      "gene_id": "ENSG00000135744",
      "gene_symbol": "AGT",
      "gene_symbol_source": "HGNC",
      "transcript_id": "ENST00000366667",
      "biotype": "protein_coding",
      "strand": -1,
      "cdna_start": 1018,
      "cdna_end": 1018,
      "cds_start": 803,
      "cds_end": 803,
      "protein_start": 268,
      "protein_end": 268,
      "codons": "aTg/aCg",
      "amino_acids": "M/T",
      "polyphen_prediction": "benign",
      "polyphen_score": 0,
      "sift_prediction": "tolerated",
      "sift_score": 1,
      "hgvsc": "ENST00000366667.4:c.803T>C",
      "hgvsp": "ENSP00000355627.4:p.Met268Thr"
    }

Thanks.

[cristinaluengoagullo]

Ok, thanks for the very fast reply!

Answer 1

[Emily]

I'll speak to our variation team about getting these added to the VEP output, maybe as an optional extra.