A proband variant is newly homozygous if it is homozygous but genotypes of both of the parents are heterozygous.

A proband variant is assigned the category IsNewlyHomozygousNonRef if all of the following are true:

  • The variant is homozygous.

  • The variant's allele is not the same as the reference.

  • The father's genotype is heterozygous at this variant position.

  • The mother's genotype is heterozygous at this variant position.

  • The variant's functional annotations include at least one specified by newly_homozygous_nonref_functional_types.

  • The frequency of the allele in the population is at most newly_homozygous_nonref_max_population_allele_frequency.

This situation can indicate a recessive disease or condition, in which the parents carry the same deleterious mutation but are unaffected because they are heterozygous. The trio analysis later examines the variant's functional annotations to help determine if the variant is deleterious.