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.

Simple mode

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, HGMD) and previous classifications by your organization or network.

Advanced mode

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.