I am an IT guy developing a database for genotype data of samples and I am confused when I look up a snp in NCBI, the genes listed for that SNP sometimes have multiple consequences (intron, missense, upstream, etc.) but on the data that I received only one of those consequences is listed. 
Hello ,

you have to get familiar with the concept of [transcripts][1] to understand this. In short: The sequence of the **gene** can encode for multiple (slightly) different **protein** sequences.

fin swimmer


  [1]: https://www.biostars.org/p/244850/