A proband variant is heterozygous non-ref if it is heterozygous and neither allele is the reference allele. The variant is newly heterozygous non-ref if the genotypes of both parents contain the reference allele.
A proband variant is assigned the category IsNewlyHeterozygousNonRef if all of the following are true:
- The variant is heterozygous.
- Neither of the variant's alleles is the same as the reference.
- The father's genotype contains the reference allele at this variant position.
- The mother's genotype contains the reference allele at this variant position.
- The variant's functional annotations include at least one specified by newly_homozygous_nonref_functional_types.
- The frequency in the population of at least one of its alleles is at most newly_homozygous_nonref_max_population_allele_frequency.
This situation can indicate a recessive trait or condition, in which the parents carry the same deleterious mutations but are unaffected because they are heterozygous-ref.
Note: The parameters newly_homozygous_nonref_functional_types and newly_homozygous_nonref_max_population_allele_frequency are used in both the IsNewlyHomozygousNonRef and IsNewlyHeterozygousNonRef categories.