InTransPhaseCompoundHeterozygote
A trans-phase compound heterozygote is a compound heterozygote in which one variant has a non-reference allele on the paternal homolog, and the other variant has a non-reference allele on the maternal homolog.
A trans-phase heterozygote is a pair of deleterious proband variants in a gene where:
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One of the two variants has a non-reference allele that is present in the father's genotype, and whose other allele is present in the mother's genotype, and
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The other variant has a non-reference allele that is present in the mother's genotype, and whose other allele is present in the father's genotype.
To determine the InTransPhaseCompoundHeterozygote category, for each gene, the trio analysis creates two lists of proband variants, fromFather and fromMother.
Both of the following apply to each variant in the fromFather list:
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Its functional annotations include at least one in compound_heterozygote_functional_types.
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It has a non-reference allele that is present in the father's genotype, and whose other allele is present in the mother's genotype at this variant's position.
Similarly, both of the following apply to each variant in the fromMother list:
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Its functional annotations include at least one in compound_heterozygote_functional_types.
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It has a non-reference allele that is present in the mother's genotype, and whose other allele is present in the father's genotype at this variant's position.
Any variant in the fromFather list paired with any variant in the fromMother list forms a trans-phase heterozygote pair, and any trans-phase heterozygous pair of variants has one variant in the fromFather list and the other in the fromMother list.
A proband variant is assigned the category InTransPhaseCompoundHeterozygote if either of the following are true: