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.
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.
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.
When Filters are Reset to Default, the Variant Filters are set to:
Severity: High, Moderate, Low;
Known Variant - no filtering.
