Core rule: apply eligible income deductions before calculating tax. Apply qualifying tax credits at the tax stage, subject to their own limits. The same NPR amount can therefore have very different effects.
Example: assume an entire NPR 20,000 deduction falls within the 10% marginal band. It saves NPR 2,000 tax, not NPR 20,000. A permitted NPR 1,500 medical credit instead reduces tax by NPR 1,500, subject to the available tax liability and statutory conditions.
Qualifying retirement contributions, insurance premiums and tuition relief are income-side deductions. Approved medical expenditure produces a tax credit; non-final TDS is reconciled as tax already paid. Final withholding has its own treatment and is not automatically a credit against ordinary salary tax.
Keep deductions, rebates and credits on separate lines in the annual calculation. Never deduct the same amount from income and again from tax.