No, it does not deduct the amount. If you enter the Medicare premiums that were deducted from your Social Security from your 1099-SA it will automatically flow to Schedule A and be included with your medical expense deduction. If you enter $10,000 of medical expenses (in addition to what's on your 1099-SA), you will end up with $12,385 on Schedule A, before it is adjusted for the AGI floor.