Variant effect filters

Variant effect filters allow you to filter variants by consequence, ACMG pathogenicity class, and prior classifications in both internal and external 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.

Simple mode

Severity

Filter variants by the severity of their effect:

• High

• Moderate

• Low

• Modifier

• Unknown

Known variant

• Known variants: Variants that have been curated in public or private variant databases.

• Drug response: Variants classified in ClinVar as impacting drug response.

• Known pathogenic: Variants classified as pathogenic or likely pathogenic in public or private variant databases.

Advanced mode

Main effect

Filter variants by their specific functional effect.

Results include variants matching any selected effect.

ACMG classification

Filter SNV variants by ACMG pathogenicity class:

• Pathogenic

• Likely Pathogenic

• Uncertain Significance

• Likely Benign

• Benign

Note: Only tagged variants have an ACMG classification.

ClinVar known variants

Filter variants by pathogenicity class in ClinVar:

• Pathogenic

• Likely Pathogenic

• VUS

• Likely Benign

• Benign

• Other

Curate

Filter variants by pathogenicity class in your Curate variant database:

• Pathogenic

• Likely Pathogenic

• VUS

• Likely Benign

• Benign

• Other

Curated organization databases

Filter variants by pathogenicity class in a curated variant database maintained by your organization:

• Pathogenic

• Likely Pathogenic

• VUS

• Likely Benign

• Benign

• Other

If your institution maintains multiple curated databases, each database will have its own filter.

gnomAD STR

Filter STR variants by gnomAD STR pathogenicity category:

• Pathogenic

• Intermediate

• Normal

• Unknown

Manually сlassified variants

Limit results to variants with established pathogenicity in prior cases.

Default values

When Filters are reset to default, the Variant effect filters are not applied.