We don't know. And we cannot answer this question. First, lets quote the Wikipedia: "In the past,
SNPs with a minor allele frequency of greater than or equal to 1% (or 0.5%, etc.) were given the
title SNP. Some used mutation to refer to variations with low allele frequency. With the advent
of modern bioinformatics and a better understanding of evolution, this definition is no longer
necessary, e.g., a database such as dbSNP includes SNPs that have lower allele frequency than
one percent". Further, suppose we find a SNP in the Mongolian population that occurs at a too low
frequency in the rest of the world to be entered in SNP databases. What do we do then?
At the HGPI information page I find: Single nucleotide polymorphisms, or SNPs (pronounced "snips"), are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. For example a SNP might change the DNA sequence AAGGCTAA to ATGGCTAA. For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. Two of every three SNPs involve the replacement of cytosine (C) with thymine (T). SNPs can occur in coding (gene) and noncoding regions of the genome. Many SNPs have no effect on cell function, but scientists believe others could predispose people to disease or influence their response to a drug.
Although more than 99% of human DNA sequences are the same, variations in DNA sequence can have a major impact on how humans respond to disease; environmental factors such as bacteria, viruses, toxins, and chemicals; and drugs and other therapies. This makes SNPs valuable for biomedical research and for developing pharmaceutical products or medical diagnostics. SNPs are also evolutionarily stable—not changing much from generation to generation—making them easier to follow in population studies.
Scientists believe SNP maps will help them identify the multiple genes associated with complex ailments such as cancer, diabetes, vascular disease, and some forms of mental illness. These associations are difficult to establish with conventional gene-hunting methods because a single altered gene may make only a small contribution to the disease.
Several groups worked to find SNPs and ultimately create SNP maps of the human genome. Among these were the U.S. Human Genome Project (HGP) and a large group of pharmaceutical companies called the SNP Consortium or TSC project. The likelihood of duplication among the groups was small because of the estimated 3 million SNPs, and the potential payoff of a SNP map was high.
In addition to pharmacogenomic, diagnostic, and biomedical research implications, SNP maps are helping to identify thousands of additional markers in the genome, thus simplifying navigation of the much larger genome map generated by HGP researchers.
At some places it is written that SNPs do not cause diseases. That is a bit confusing, because they do. But we don't call disease causing SNPs SNPs but we rather call them mutations...