Answers.Body: <p>The difference between the two depends on to whom you talk ;)</p>
  
  <p>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.</p>
  
  <p>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".</p>
  
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Answers.Text: 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.
Answers.UserDisplayName: Devon Ryan
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Answers.Text: 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.
Answers.UserDisplayName: Emily_Ensembl
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Answers.Text: @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
Answers.UserDisplayName: Chris_Rands
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Answers.Text: 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
Answers.UserDisplayName: Chris_Rands
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Answers.Text: @Chris_Rands I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying.
Answers.UserDisplayName: Devon Ryan
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Answers.Text: @Chris_Rands When I was working on comparative genomics and sequence evolution, I and those around me would use "SNP" for any form of single nucleotide change. Using the term specifically for common ones is something I only saw when I started looking at NGS data in a clinical context. I think this is one of those things that really change depending on your specific sub-field.
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Body: <p>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?</p>
  
Tags: <snp><terminology><variation>
Title: SNP vs Point Mutation
ThreadText: # SNP vs Point Mutation
  
  (Asked by: username_0 on 2019-01-15)
  
  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?
  
  **Tags:** snp, terminology, variation
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-01-15. Score: 6 | Accepted answer
  
  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".
  
  > **Comments:**
  > **username_2**: 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.  
  > **username_3**: 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.  
  > **username_4**: @username_2 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  
  > **username_4**: 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  
  > **username_2**: @username_4 I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying.  
  > **username_5**: @username_4 When I was working on comparative genomics and sequence evolution, I and those around me would use "SNP" for any form of single nucleotide change. Using the term specifically for common ones is something I only saw when I started looking at NGS data in a clinical context. I think this is one of those things that really change depending on your specific sub-field.  
  
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