For a coding SNP, if it is non-synonymous and alters an amino acid in a protein resulting in a different protein structure (mis-sense, non-conservative change), or a non-sense change that results in a premature termination of the amino acid sequence (non-sense), then it will be assigned a high-risk or very high-risk ranking, because most known disease-causing SNPs are in these classes. A non-synonymous SNP that alters an amino acid in a protein to one with similar structural characteristics will be classified as ‘mis-sense, conservative change’ with a moderate risk ranking.
