Classifying variants

Classification is the interpretive step between reviewing a variant and putting it on the report. You assign each variant a clinical significance on the five-tier ACMG/AMP scale, backed by the specific evidence criteria you applied. Only classified variants are eligible to become report findings.

Classifying variants requires the Classify Variants capability. Viewers can see classifications but not change them. See Workspaces & roles.

The five-tier scale

Every classification resolves to one category on the ACMG/AMP pathogenicity scale, shown as a visual gradient in the classification panel:

Category	Meaning
Benign	Not disease-causing.
Likely benign	Probably not disease-causing.
VUS	Variant of uncertain significance.
Likely pathogenic	Probably disease-causing.
Pathogenic	Disease-causing.

Automated vs. Your classification

A variant can carry two kinds of classification, and the panel distinguishes them:

• Automated classification — a starting suggestion computed by the platform from the annotations and criteria it can evaluate on its own.

• Your classification — the classification you commit as the interpreter. Your classification is what counts for the report; the automated one is only a starting point you can accept, adjust, or override.

Applying evidence criteria

You justify a classification by applying ACMG criteria. Each applied criterion has:

• a direction — whether it argues toward pathogenic or benign;

• a strength — Standalone, Very strong, Strong, Moderate, or Supporting; and

• an evidence note — free text recording why the criterion applies to this variant.

The set of criteria offered depends on the variant type — small variants, structural variants, tandem repeats, and paralogs each have their own criteria appropriate to how that variant type is assessed. Each criterion has a default strength, which you can override for a specific variant when the evidence warrants; overridden criteria are marked so a reviewer can see where you departed from the default.

Recording a classification

1. Open the variant and go to its Classification panel.

2. Review the automated suggestion, if present.

3. Apply the criteria that the evidence supports, setting strength and an evidence note on each.

4. Select the resulting ACMG/AMP category.

5. Add any overall notes for the variant.

Your classification is saved against the variant and becomes available to the report.

From classification to report

The report's candidate findings are derived live from your classifications: any variant with an active classification is eligible to be included as a finding. You curate which of those actually appear on the report from the report itself — see Generating a report. There is no separate "add to report" flag stored on the variant; inclusion is decided on the report.