Learn more about VarSome Clinical's host of customization options.
Custom Variant Classifications and Comments
As mentioned in the article Custom Variant Classification, if you have your own, custom pathogenicity classifications for certain variants or wish to add information in the form of a comment, you can send us a file with this information. We will then include this information and display it in any of your analyses where the relevant variants appear. However, the provided file needs to fulfill certain requirements in order to be processed correctly:
- The file provided by the user should be in CSV (comma-separated values) format with content in the following order: chr,position,ref,alt,classification,comment(s). The classification should be one of 'P' (pathogenic), 'LP' (likely pathogenic), 'VUS' (variant of unknown significance), 'LB' (likely benign) or 'B' (benign).
- Multiple comments should be separated by semi column ( ; ) and the size of each comment is limited to 2000 characters.
- One classification per variant is expected.
- Each CSV file corresponds to one specific user. Multiple files need to be provided for multiple users.
- It is essential that the corresponding reference genome (hg19 or hg38) is specified by the user along with the provided file(s).
This is an example of a valid CSV file:
chr5,125562,C,T,P,found in a young adult with melanoma;
Standard classifications must be declared with the following names to comply with the nomenclature used by VarSome Clinical. They can be referred to either by the full name or its code:
B or Benign
LB or Likely Benign
VUS or Uncertain Significance
LP or Likely Pathogenic
P or Pathogenic
CA or Common Artefact
DR or Drug Response
DA or Disease Association
RF or Risk Factor
PR or Protective
Local Variant Frequencies
You may import also your local variant/allele frequencies, and use them for filtering using Algorithmic filters, for example.
Please note this is different from the Sample cross-referencing feature.
Although VarSome Clinical annotates your variants by default against all the transcripts from RefSeq and Ensembl, you may specify your preferred transcript for Germline Variant Classification of pathogenicity.