Adjustment u/s 143(1)(a)- itr3

Hello Guys,

I have recieved notice from ITD 143(1) due to Salary difference in form 16 and 26as. Actually I have filled ITR3 from ClearTax website and I have deducted HRA and TransPort Allowance from my salary income and mentioned it as Gross Income (As there was no option to declare it seperatly on clearTax). 

Now what should i do ? Do i need to submit revised ITR3 with all salary details in 'Schedule S' or Do I need to Disagree with it ?

Thanks,

Aniket