Gene filters

The Gene Filters allow filtering variants by specific genes or regions based on clinical relevance, functional significance, or enrichment kit.

• Disease-associated genes: Genes with a published disease association.

• Unknown genes: Genes of unknown clinical significance.

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• ACMG genes: Clinically actionable genes as defined by ACMG:

  • v100.39.0+: 84 genes (Lee et al. 2025)

  • ≤v38.0: 81 genes (Miller et al. 2023)

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• Cancer-associated genes: Genes that have a documented association with cancer.

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• LoF-intolerant genes: Extremely LoF-intolerant genes with gnomAD pLI ≥ 0.9.

  • If a variant is a CNV or insertion and overlaps multiple genes, it is included in the results as long as at least one of the overlapped genes has pLI ≥ 0.9.

  • mtDNA variants are excluded, because mitochondrial genes are not represented in the gnomAD pLI dataset.

  • Requires Knowledge base 26+.

• Established HI/TS genes: Genes with ClinGen haploinsufficiency and/or triplosensitivity score of 3.

  • mtDNA variants are excluded, because mitochondrial genes are not represented in the ClinGen dosage sensitivity dataset.

  • Requires Knowledge base 26+.

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• Coding regions: Protein-coding sequences.

• In targeted regions: Enrichment kit regions selected at case creation (falls back to RefSeq coding if no kit is provided).

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• Candidate genes: Gene list defined during case creation. The filter is not available in cases run without a gene list.

Default values

Cases without a gene list

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

Cases with a gene list

When filters are reset to default, the Gene filters are set to:

Filter	Setting
Candidate genes	Active
Other Gene filters	No restriction