Table 1. Different variations lead to the same alternative sequence and, therefore, the variations are equivalent.

	aligned sequences	unaligned sequences
reference sequence	TTGCAAAAAAAAAAATGCCTA	TTGCAAAAAAAAAAATGCCTA
rs34061715	TTGCAAAAAAAAAA TGCCTA	TTGCAAAAAAAAAATGCCTA	(start lost)
equivalent deletion	TTGCAAAAAAAAA ATGCCTA	TTGCAAAAAAAAAATGCCTA	(no effect)
equivalent deletion	TTGC AAAAAAAAAATGCCTA	TTGCAAAAAAAAAATGCCTA	(no effect)

The first variation is a deletion at position 15, the second variation is a deletion at position 14, and the third variation is a deletion at position 5.

This deletion is annotated in Ensembl as lying in the start codon of transcript HRNR-001 and therefore leads to the loss of the start codon. The equivalent indel has no effect on the protein. (Sequences are all shown as reverse complementary, because the transcript is located on the reverse strand.) Regular characters denote the upstream region and bold, italic characters the coding sequence.