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?
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".