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Variant Filtering

The Variant Miner surfaces an order's variants for clinical review. Each order has its own variant set, populated from the analysis VCF that fed the order. This page covers how variants are classified, which ones are added to the report automatically, and how the per-variant detail view adapts to a variant's tier.

Classification: AMP / ASCO / CAP tiers

Somatic variants are classified using the AMP / ASCO / CAP four-tier system. The pipeline assigns an initial tier for each variant; a curator can change it during review.

Tier Meaning
IA Biomarkers that predict response or resistance to FDA-approved therapies for a specific type of tumor, or are included in professional guidelines, as diagnostic/prognostic for a specific type of tumor.
IB Biomarkers that predict response or resistance to therapies, or are of diagnostic/prognostic significance, for a specific type of tumor — based on well-powered studies with expert consensus.
IIC Biomarkers that predict response or resistance to therapies approved (by the FDA or professional societies) for a different tumor type, serve as clinical-trial inclusion criteria, or are of diagnostic/prognostic significance based on multiple small studies.
IID Biomarkers of plausible therapeutic significance from preclinical studies, or that may assist diagnosis/prognosis based on small studies or a few case reports.
III Variants of uncertain significance — absent or at extremely low frequency in somatic databases.
IV Benign or likely benign variants.

Auto-population

When the order's report is first opened, variants are auto-populated by tier:

  • Tier IA, IB, IIC, and IID (Tier I and II) are added automatically.
  • Tier III and IV are not auto-populated — a curator adds them manually when clinically relevant.

Auto-population runs once per report. A variant a curator later removes is not re-added on a subsequent visit.

Variant detail page

Opening a variant shows a detail page whose content adapts to the variant's tier — clinically actionable tiers surface more evidence, while lower tiers show a leaner view.

Section Tier IA Tier IB Tier IIC Tier IID Tier III Tier IV
Variant info & descriptions ✓ ✓ ✓ ✓ ✓ ✓
AMP tier & classification full full full full minimal minimal
Therapies & guidelines (FDA / NCCN) ✓ ✓ ✓ ✓ – –
Therapeutic & clinical-trial evidence ✓ ✓ ✓ ✓ – –

Fusion variants (e.g. PML::RARA, BCR::ABL1) use a layout tailored to gene pairs rather than single nucleotide variants, and omit the SNV-only evidence tables that don't apply to fusions.

See also