<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>

CC BY-SA 4.0
2019-01-15T08:08:13.513Z
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.
Devon Ryan
CC BY-SA 4.0
2019-01-15T08:54:45.737Z
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.
Emily_Ensembl
CC BY-SA 4.0
2019-01-15T13:05:58.173Z
@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
Chris_Rands
CC BY-SA 4.0
2019-01-15T13:06:13.007Z
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
Chris_Rands
CC BY-SA 4.0
2019-01-15T13:16:57.847Z
@Chris_Rands I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying.
Devon Ryan
CC BY-SA 4.0
2019-01-15T13:44:07.980Z
@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.
terdon
CC BY-SA 4.0
2019-01-15T04:48:06.523Z
2019-01-15T14:21:15.530Z
2019-01-15T14:21:15.530Z
finswimmer
<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>

<snp><terminology><variation>
SNP vs Point Mutation
# 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**: @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  
> **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**: @Chris_Rands I suspect this comes more from my human genetics background, where we worry about how patients will interpret what we're saying.  
> **username_5**: @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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