Genetic variants and how they change proteins

Coding DNA is the part of a gene that codes for the amino acids in a protein. Every three bases code for one amino acid.
If one base is swapped (a substitution), one amino acid may change. The protein may fold into a different shape. An enzyme's active site could change, so it works less well or not at all.
Some changes have no effect, because more than one triplet codes for the same amino acid.
If a base is added or deleted, every triplet after it is read differently, so many amino acids change.
Example: in sickle cell disease, one base change alters one amino acid in haemoglobin.

Before each gene there is non-coding DNA where RNA polymerase attaches to start making mRNA (transcription).
A variant here can make RNA polymerase bind more or less easily. Then more or less mRNA is made, so more or less protein is produced. This can change the phenotype even though the protein itself is normal.

Most mutations have no effect on the phenotype.
Some have a small effect, and a few have a big effect, which may be harmful.
Very rarely a mutation is beneficial, which gives natural selection something to act on.