It seems to be quite difficult to find an answer to this. Are SNPs the same thing as alleles?


1 Answer 1


Alleles are variations of a same locus that codes for a protein (gene). These alleles can come in different forms, one of which is SNP. For example, sickle cell anemia arises from an allele of the beta-globin gene which has had a change from A to T. Meanwhile, for the ABO gene that determines your blood group, the O allele has a missing nucleotide (G) that leads to a frameshift in the gene and a loss of function. So alleles are caused by SNPs, but can also be due to deletions, additions, insertions and other genetic changes. Note that SNPs not always lead to new alleles. Sometimes they occur in non-coding areas and nothing happens.


SNPs do not need to be gene specific, but this was for simplicty.

@Artem added nicely to the answer, I'm quoting it here:

"Single Nucleotide Polymorphisms (SNPs) are Single Nucleotide Variants (SNVs) at a population allele frequency greater then 1%. Alleles are any variants of the same position of DNA, which includes SNVs, insertion/deletions, or structural variants and at any frequency." - @Artem

  • $\begingroup$ Allele doesn't have to be in the coding region $\endgroup$
    – SmallChess
    Commented Mar 19, 2017 at 12:29
  • $\begingroup$ I have two comments: 1. An SNP is just a substitution, correct? 2. AN allele can be more generally defined as a variation in a section of a gene, correct? I assume that that's why @student states that alleles can happen in non-coding regions of the DNA, and that makes sense now that we know that these sections are actually useful. $\endgroup$ Commented Mar 19, 2017 at 13:28
  • $\begingroup$ @Mathematician SNP is also known as substation. 2. Yes, but that doesn't have to be in a gene coding area. Anywhere in the genome is okay. $\endgroup$
    – SmallChess
    Commented Mar 19, 2017 at 13:34
  • $\begingroup$ Please add some references to your answer. $\endgroup$ Commented Mar 19, 2017 at 13:37
  • $\begingroup$ What is the basis for assertion by @Artem that SNPs have to occur at a frequency of greater than 1%? It may be a general agreement in the field — I don't know — but if so a reference is needed to back this up. $\endgroup$
    – David
    Commented Sep 13, 2018 at 22:59

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