No, do not ignore information on your W-2 - a copy is sent to the IRS who will eventually compare it to your return and write you a letter if they see an unexplained difference.
Instead, ask your employer why the amount that the HSA administrator says that they received for 2017 is different than what they reported on the W-2 in box 12 with a code of W. Sometimes, employers mistakenly add their contributions to the code W, but not the employee's contributions by payroll deduction, and vice versa.
May I assume that box 1 on the 5498-SA is blank, and that box 2 reflects all the contributions that were made? If so, ask the employer why their W-2 number is different - and if they discover a problem, ask for a corrected W-2, so that the IRS is updated and you can correctly finish your return.
