Mutation Annotations

Hotspot

  • Is a hotspot in TCGA
  • Is a hotspot in COSMIC
  • Not silent

Damaging

  • Start_Codon_SNP
  • Start_Codon_Del
  • Start_Codon_Ins
  • Splice_Site
  • Frame_Shift_Del
  • Frame_Shift_Ins
  • Nonsense_Mutation
  • De_novo_Start_OutOfFrame

Other non-conserving

  • Missense_Mutation
  • In_Frame_Del
  • In_Frame_Ins
  • Nonstop_Mutation
  • Stop_Codon_Del
  • Stop_Codon_Ins

Other conserving

  • 5'Flank
  • Intron
  • IGR
  • 3'UTR
  • 5'UTR

Silent

  • Silent

In visualizations and tools

The portal colors mutations with the priority order of hotspot > damaging > other non-conserving > other conserving. For instance, if a gene in a cell line has both hotspot and damaging mutations, it will be colored as hotspot. Silent mutations are not colored.

The mutation dataset is also available to plot on an axis in data explorer. Note that this uses a binarized defintion of mutation, which includes any "hotspot", "damaging", or "other non-conserving" mutation.

In the MAF file download

For a more inclusive definition of mutations that may be of interest, we have added a Variant_annotation column that groups mutations into "damaging", "other non-conserving", "other conserving" or "silent" using the Variant_Classification column. "Hotspot" is not in the Variant_annotation column, but can be obtained from the isTCGAhotspot and isCOSMIChotspot columns. The latest mutation data is available for download here.