The reason is that DNA sequences code for certain amino acids. If you look at an amino acid chart there are more than one way to code for certain amino acids. For an example say GGTTA codes for a certain amino acid. But it got changed to GCTTA even though it changed this particular mutation was just another way to code for the same amino acid. So it wouldn't affect the phenotypic expression. It basically is a different way to code for the same things.
