Table 1

Concepts relevant to the interpretation of variants for inherited genetic disorders, acquired somatic cancers and mitochondrial genome disorders

ApplicationsVariant interpretation concepts
Inherited germline variants
  • Variants are typically heterozygous or homozygous, in rare cases variants may be somatic mosaic (early post-zygotic event)

  • Assessment of variants for pathogenicity in diagnosis, prognosis, prevention, reproductive planning or treatment

  • Variants have utility for familial testing, including determining carrier status or identifying other at-risk family members. Variants may also be useful for determining genomic regions with absence of homozygosity (due to consanguinity or uniparental disomy)

Acquired somatic variants
  • Detectable variant allele frequency can have a wide range in tumour tissue

  • Assessment of variants for utility in diagnosis, or for prognostic or therapeutic purposes

  • Typically no familial risk, although variants at allelic frequencies consistent with germline heterozygous or homozygous variants may be identified

Mitochondrial genome variants
  • Detectable variant allele frequency can have a wide range in tissue tested (due to homoplasmy or heteroplasmy)

  • Assessment of variants for pathogenicity in diagnosis or prognosis requires haplogroup analysis

  • Familial risk via maternal inheritance only

  • Variants have utility for familial testing, including determining carrier status or identifying other at-risk family members