You can use Mfold for estimating the conformation of single-stranded DNA and RNA molecules.

http://unafold.rna.albany.edu/?q=mfold

it can affect all - but is it relative to which mutation you are talking about, 

1) Missense are most studied - where amino acid change is evident. 

2) at splice site, even synonyomous which have RNA structural changes can be deleterious.

3) 3UTR, 5UTR, in promoters and in enhancers may serve critical. 

uses of folding tools like unafold are recommended.

Hi,

I would suggest you to search for some mutations prediction effects tool online (such as mutation tasting) or some official database (exome variant server).

I hope this could be helpful.

Cheers,

Giulia

Thank you Guilia. I will try these.

Thank you all for your suggestions