Clicking in the horizontal bar with the word Variants displays the information in a larger window.
Search variants: Search variants with keywords, such as TP53. Search only applies to the Variant column of the table.
Reset filters: If any filters have changed, a Reset filters button displays. Click to return all the filters to the default values.
Settings: Click the icon to customize the information displayed for the variants.
Display: Click the checkbox in the top row to include/uninclude all the variants in the analysis. Select individual variants by clicking the checkbox next to a variant’s name.
Information: Click the icon next to a variant to display more information about it. The Learn More button on that page will take you to the VarSome page for even more information.
Sort: Sort the data by ascending or descending order by clicking on the icon at the top of the columns. The columns can also be rearranged by dragging them to the right or left.
Note: A blank cell in the Variants Table denotes that a variant has no available annotations information for that column.
Variant: Lists all the variants in the sample. The format is
<gene name>:<chromosome number>:<position>:<allele>. For example:
Function*: Lists the variants function annotation – coding, intronic, splicing, 3' UTR, etc.
Protein*: Lists the protein nomenclature of the variant.
Coding impact*: Lists the variant’s impact annotation – frameshift, inframe, missense, nonsense, or synonymous.
ClinVar*: Lists variants with a ClinVar annotation version 20170801 – benign, likely benign, not provided, likely pathogenic, pathogenic, uncertain significance, and conflicting interpretations of pathogenicity.
DANN*: The DANN score ranges from 0 (low pathogenicity) to 1 (high pathogenicity).
Variant type*: Describes the variant type – SNV, MNV, insertion, deletion, or replacement.
RefSeq transcript id*: The id from the RefSeq annotations database.
Gene*: Displays the variant’s gene.
cDNA*: Nomenclature for the complementary DNA strand.
dbSNP rsids*: The id number for the variant in the SNP database.
Allele Freq (gnomAD)*: The allele frequency in the Genome Aggregation Database (gnomAD).
COSMIC ids*: The id number for the variant from the COSMIC database.
Whitelist: The variants listed in the optionally uploaded whitelist file. True means that the variant is whitelisted. List only the whitelisted variants by clicking the column sorting window icon next to the column’s header and unchecking False.
# Genotyped Cells: The number and percentage of genotyped cells for the variant.
# Mutated Cells: The number and percentage of mutated cells for the variant.
Sample: For each sample, it displays the number and percentage of cells genotyped and mutated and the VAF percentage by cell and read count per variant.
*This information comes from VarSome.