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 and advanced filtering modes operate independently.

Even with similar settings, results may differ due to variations in filtering logic and options available.

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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;

• Curate (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;

• gnomAD STR

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

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Default values

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

• Severity: High, Moderate, Low;

• Known Variant - no filtering.