Variant Effect Filters

The Variant Effect Filters allow filtering variants by consequence, ACMG pathogenicity classes, and whether/how the variant has been classified internally or in clinical variation databases. The filters can operate in a Simple or Advanced mode.


Modes

Simple

Filter variant list by:

  • Severity of variant effect (High, Moderate, Low, Modifier);

  • CNV Severity is set according to the image below;

  • Known Variant (Known Variants, Known Pathogenic Variants) - variant status in clinical variation databases (ClinVar) and previous classifications by your organization or network.

Advanced

Further restrict analysis results by:

  • Specific Main effect of the variant on protein structure and function;

  • ACMG Classification (Pathogenic, Likely Pathogenic, Uncertain Significance, Likely Benign, Benign)- ACMG pathogenicity class assigned manually or automatically. Note: applicable only for Candidate and Most Likely variants;

  • ClinVar Known Variants (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign, Other) - variant status in ClinVar;

  • Custom database Known Variants (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign, Other) - variant status in your own curated variant database, including CNVs detected by means of NGS and/or chromosomal microarray;

  • Manually Classified Variants - select this option to restrict results to variants from previous cases with user-assigned Pathogenicity.


Default values

When Filters are Reset to Default, the Variant Filters are set to:

  • Severity: High, Moderate, Low;

  • Known Variant - no filtering.

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