Gene filters

The Gene Filters allow filtering variants by specific genes or regions based on clinical relevance, functional significance, or targeted sequencing design. These filters help prioritize variants in genes associated with disease, dosage sensitivity, or coding regions.

Filter options

• All Disease Associated Genes: Variants in genes with a published disease association.

• All Unknown Genes: Variants in genes of unknown clinical significance.

• Candidate Genes: Variants in a gene list defined during case creation.

• All ACMG genes: Variants in clinically actionable genes defined by ACMGv3.3:

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

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

• Cancer Associated Genes: Variants in genes with published association with oncological disease.

• LoF Genes (Emedgene Knowledgebase 26+): Variants in extremely LoF-intolerant genes (gnomAD pLI ≥ 0.9).

  • If a variant is a CNV that overlaps more than one gene, it will appear in the filtering results if at least one of the genes has gnomAD pLI ≥ 0.9).

  • Variants of type mtDNA are excluded because they are not included in ClinGen dosage sensitivity dataset.

• Established HI/TS Genes (Emedgene Knowledgebase 26+): Variants in genes with sufficient evidence of dosage sensitivity (defined by having ClinGen's Haploinsufficiency and/or Triplosensitivity scores of 3).

  • Variants of type mtDNA are excluded because they are not included in ClinGen dosage sensitivity dataset.

• Coding regions: Variants restricted to the protein-coding sequences.

• In Targeted Regions: Variants in regions defined by the Enrichment Kit selected during case creation. RefSeq coding regions are used as a reference if no kit is provided.

Default values

When Filters are reset to default, Gene Filters remain disabled, except for cases launched in Virtual Panel mode. In such cases, the Candidate Genes filter is activated by default.