There is no such thing as potential SNPs, either it exists or it doesn't.

If you are trying to understand if an a certain SNP is influencing biological function, that would be useful. If so, if the polymorphism exists in the coding region, and if it does not cause a change in AA, it would be safe to ignore. Beyond that things get a little more complex. generally, AA substitution to another one in similar class may or may not matter but if it is drastically different type of AA, you may need to look at it further.

In non-coding region things are similarly complex - in certain well-known motifs, changes can make some to a drastic difference. 

I think that you would benefit from a literature review and read through a few recent review articles to get a better understanding. 

in addition to Tausif's answer, depending on your bioinformatics expertise and the genome you are interested in, there are a number of programs that predict or give a probability that a change in coding DNA sequence will lead to a deleterious protein product (e.g. as Tausif mentioned, a base change may lead to a non-conservative amino acid change which would be predicted to affect protein folding or function, and in a particularly bad case, the base change may result in formation of a STOP codon, in which case the protein product would be truncated or not even translated). Two commonly used programs are Polyphen http://genetics.bwh.harvard.edu/pph2/ and SIFT http://sift.jcvi.org/ both of which give a score as to the likelihood that a coding change will affect protein function. If the SNP is a known SNP, it will probably be catalogued in dbSNP https://www.ncbi.nlm.nih.gov/SNP/ - you would have to already have some information about the labelling of the SNP for this. If your SNP is in a non-coding region, as Tausif mentioned above, you would probably be best to do a bit of reading - there are a whole load of articles on this subject e.g. PMC3167619 PMID26781813 PMID26474488 PMID24916300 ... Good luck

Thank you Tousif and Philip for your valuable explanation. Your comments are leading to me my destination. Basically i have sequenced type of GPCR in some subjects which basically involve in itch . I am studying itch whether these SNPs may be involve in itch process or not.  Both SNPs are in coding region ie One SNP is not changing amino acid while one SNP change AA but to same AA. Wether i can go for it or not as it is the same AA substitution and bioinfo tools suggest that it not pathogenic.

SNP refers to the variation in genomic DNA sequence at a specific position in the population of individuals of the same species. Hence,  the following statements are nonsensical: "SNP is not changing", "SNP may be involved", "one SNP changes AA" .

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G. πολύµορϕ-ος = of many forms.

Hi Arif,

I think as suggested by others, it will be helpful for you to go through recent review articles on the study area you are trying to investigate SNPs. This would give you information about the rationale for selecting your SNPs.

Thank you for your kind suggestion

 As i have got 4 kind of Missense Variants while some basic tools suggest it is SNPs and not pathogenic so i have to to decide that which will be more potential to investigate further..