Gene sequence from transcript sequence

[Phantom123]

I have variation information for SNPs and small indels together with the position of the variation relative to the transcript. I also have the transcript sequence because i have the NM_ID of the transcript. Two questions:
1. Given the above, how do i obtain the position of the variation relative to the gene.
2. How do i handle cases where the transcript sequence has been 'updated' by NCBI as compared to the transcript sequence data i have.(do an alignment of new transcript sequence data with earlier transcript sequence data?)