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Correct way of reading nomenclature of polymorphisms


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#1 jamestoon

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Posted 09 June 2014 - 10:38 AM

Hi all, 

 

I just wonder, what is the correct way of reading nomenclature of polymorphisms.

For example, i have this polymorphism: TNF -308G>A

Do I pronounce it as:

- TNF minus three zero eight G to A polymorphism

- TNF minus three zero eight GA polymorphism

- TNF minus three hundred and eight G to A polymorphism

- TNF minus three hundred and eight GA polymorphism

- TNF negative three zero eight G to A polymorphism

- TNF negative three zero eight GA polymorphism

- TNF negative three hundred and eight G to A polymorphism

- TNF negative three hundred and eight GA polymorphism

or others?

 



#2 bob1

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Posted 09 June 2014 - 01:10 PM

That appears to be a promoter polymorphism (that's what the "-" indicates) so it would be referred to as minus.  How you say the number is up to you, and  usually it would be "G to A" for the substitution.



#3 jamestoon

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Posted 10 June 2014 - 05:04 AM

Thanks a lot!



#4 Trof

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Posted 10 June 2014 - 06:46 AM

I would say "G to A substitution at the position minus 308 from translation start (or ATG) of TNF gene". That's what it is.

If it's in the promoter or not, that depends.

 

See HGVS nomenclature.

 

BTW "Polymorphism" is generaly some substitution, that is polymorphic in the population, so there are more than one "common" variants.  It's also used when meaning "without effect", though also term "functional SNP" exists, that indicates a "polymorphism" with a function".

"Mutation" is sometimes used when decribing a rare, functional variant, but it's not prefered.

 

"Substitution" or "sequence variant" is more neutral.


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