Standard deduction u/s 16 (ia)

Please guide me about Standard Deduction U/s 16 (ia)

Tax Calculation for FY 18-19 for Govt. Employer

Annual Working Case 1

Pay- 342232

Grade pay - 64800

DA - 563040

HRA - 40704

Transport Allowance - 12640

DA Diffarance- 25426

Then What is the Standard Deduction U/s 16 (ia) - 40000 or 12640?

Annual Working Case 2

Pay- 342232

Grade pay - 64800

DA - 563040

HRA - 40704

Transport Allowance - 12640

DA Diffarance- 25426

Medical Reimbursement - 68541

Then What is the Standard Deduction U/s 16 (ia) - 40000 or (12640 + 15000)

Thanks In Advance.