Relates an allele (hla molecule) to residues that are parts of it, that are different from the chosen reference allele. There are three cases: Either a) relating to a residue that is different from the reference sequence. b) Relating to a deletion relative to the reference allele, represented as an instance of sc:SequenceGap or c) Recording that the allele is truncated relative to the reference sequence, represented as the target of the relation being a sc:StopCodon