Well it is possible that your dna is polymorphic and contains both the A and G sequence but aRMS used like this needs you to find a temperature where only one primer can work so that when the pcr works you can say that the normal or mutant sequence exists. AS you have a common R primer both normal and mutant primers amplify the same length amplimer so to say which sequence(s) exist you will have to run 2 PCRs at different temperatures to see if you have NN, MM or NM.

It might even be necessary to put the polymorphic base at the n-1 or n-2 positions to get better annealin temperature discrimination. What people often do is to have the sequence specific primers pointing in opposite directions then you can have 2 reverse primers giving different sized fragments so then a single reaction tube will tell you what sequences exist because the amplimers are different sizes

Article Discrimination of Primer 3′-Nucleotide Mismatch by Taq DNA P...

Some 3' mismatches are tolerated by the DNA polymerase.

It might be cheaper/faster to use Sanger sequencing for genotyping. Or see if your SNP add or removes a restriction site & use a digest for genotyping.

Good luck!

Thanks everyone, I redesigned my primer pair and succeeded in distinguishing the polymorphism

I want to ask a bit different question .......while i was using a standard kit for some specific mutation......everything was fine but in the no template control when i added the mastermix and nuclease free water i got no amplifications in the mutation channel and the channel specified for internal control (as mentioned in the kit insert) but when i loaded only the mastermix without making up the volume i got an amplification of around Ct 37 (The kit insert doesnt specify this) in the internal control channel ......the kit insert clearly specifies that for NTC there shouldnt be any kind of amplification in the mutation channel or the internal control channel.........can anybody please help me with the same.....are these primer dimers?

I am unclear from your question whether there is any added primer in the ntc as there should be but it may also be possible if you set the baseline too low and there is a small amount of signal released from the mastermix then it could look like amplification