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What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the reference sequence?

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The difference between the two depends on to whom you talk ;)

You are right: both refer to one base difference from the sequence. Usually the term "mutation" is used if the change has an impact on the phenotype. The "P" in "SNP" means "polymorphism". A lot of people use this term if more than 1% of the individual in a given population have this variant.

My recommendation: only use "mutation" if you are sure that your variant has an important impact on the phenotype. Only use "SNP" if you are sure that it is a commonly occurring variant. In any other case just use "variant". It is slowly becoming more common to talk about "SNV" (Single Nucleotide Variant) than about "SNP".

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    $\begingroup$ I would add that "mutation" is best used when it has an important negative impact on the phenotype. There's a lot of baggage that goes along with the word "mutation", so even when we talk about patients we usually prefer "deleterious variant" or something like that. $\endgroup$
    – Devon Ryan
    Jan 15 '19 at 8:08
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    $\begingroup$ Personally, I only use "mutation" when talking about it actually happening. So somatic mutations are mutations, or de novo mutations where the child had a variant but the parent doesn't are mutations. But if it's germline, I always call it a variant. The other advantage of saying "variant" over "SNP" is that "variant" can be used to describe insertions and deletions larger than one base. $\endgroup$ Jan 15 '19 at 8:54
  • $\begingroup$ @DevonRyan But consider "silent mutation" or "adaptive mutation", these are not negative in their impact and people studying molecular evolution would not consider that the default; indeed most mutations are neutral $\endgroup$ Jan 15 '19 at 13:05
  • $\begingroup$ I think SNP is only really used at the population level while a point mutation may imply either population level (SNP) or between-species (substitution). Also sometimes, a point mutation is used for a single base pair insertion/deletion (although personally I wouldn't use it like that), while SNP is never an indel $\endgroup$ Jan 15 '19 at 13:06
  • $\begingroup$ @Chris_Rands I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying. $\endgroup$
    – Devon Ryan
    Jan 15 '19 at 13:16

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