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Variant detail

Variant Detail Page

  • Variant Details
    • CKB – dot tells if it’s in the CBK and if it’s a gene match, variant match, or affects alternate tanscript
    • Gene
    • Effect
    • Position
    • Copy Number
    • Lab Reported Significance
  • Drug Associations table
    • CKB – Gene Match, Variant Match, or Affects Alternate Transcript
    • Gene – Gene name
    • Feature - Mutation
    • Source – Source database (civic, cosmic_resistmut.civic, pmkb)
    • Drug – Drug name
    • Response Type – Tells how responsive it is to the drug. (Resistant, responsive, better outcome, poor outcome)
    • Evidence Level – AB, A (clinical practice/standard of care), B (some sort of clinical trial/off-label use data), C (early clinical trials/one case showed benefit), D (preclinical/mouse studies)
    • Source Evidence – 1, 2, 3, clinical evidence, preclinical evidence, validated association, case study, early trials
    • Disease – disease information (location/type)
    • Publication – links out to pubmed article regarding any gene drug association
    • Comment
  • Alternate Transcripts
    • Transcript ID – Most canonical transcripts have a blue info dot beside it. If there isn’t, it means there is no canonical transcript identified because the way it was annotated did not specify it was part of this same gene.
    • NC Damage
    • AA Change
    • Variant Class
    • EXON Number
  • Gene Details
    • Gene
    • Name
    • Aliases
    • Cytoband
    • Summary
  • Needle Plot Note: If there is a gene match, but when you click on the Variant Detail and there is no info under drug, it means while the gene is known to have a gene drug association, this particular variant in this patient sample didn’t have an exact match but it may be of interest to know this gene has a drug association.

Another example of Affects Alternate Transcript: If we have a blue dot beside a missense Variant Class and a blue dot beside the AA Change. If you hover over “missense” you’ll see missense is in the canonical transcript, but as you hover over it, “intron variant” appears, meaning there is another transcript that labels this mutation as an intron variant and not a missense. When we hover over the AA Change, we’ll see 2 different AA changes from the canonical AA change shown in the table. If we click on the row to view the Variant Detail we see 4 transcripts, there is an “I” beside the canonical transcript and that is the one displayed in the table. There are 2 other transcripts with a missense mutation. There is also an intron variant (seen in the Variant Class) but since it’s an intron, there is no AA Change.

Blue dots alone in the table – If we filter on a missense variant and see a blue dot in a blank field under AA Change and Variant Class, that’s because the canonical transcript does not have a missense variant but if we hover over it, it shows the alternate transcript does have a missense variant, and that’s why it came through as a result for that missense filter.

Pardon Our Dust

Last update: 2020-09-03