Variants Table

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TI_Variants_Table.png

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 TI_Settings_Icon.png icon to customize the information displayed for the variants.

Display: Click the TI_Variant_Box.png 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 TI_Info_Icon.png 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 TI_Column_Icon.png 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:

TP53:chr17:7578211:C/T

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 TI_Column_Icon.png icon next to the column’s header and unchecking False.

TI_Whitelist_Filter.png

# 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.

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