For a more inclusive definition of mutations that may be of interest, we have grouped mutations into the following categories using the Variant_Classification column. The annotated category for each mutation has also been added to the maf file as the Variant_annotation column. The latest mutation data is available for download here.
Silent mutations are annotated in the Variant_annotation column as 'silent', but are not highlighted in the portal.
The portal colors mutations with the priority order of hotspot > damaging > other non-conserving > conserving. For instance, if a gene in a cell line has both hotspot and damaging mutations, it will be colored as hotspot. Hotspot mutations are defined as any mutation that is a hotspot in TCGA or COSMIC, and is not silent.