How to rectify mannual return filed

You need  to file revised return  for  a)     

if only b) & c) were present then you could have asked for rectification of return. 

Now for all three a),b) c)-  request for filing revised return under condonation 

With forwarding letter attach Form 16 , Traces 26AS copy and xerox copy of 80C investment.  Your forwarding letter will be reply to tax demand also and  request for for filing revised return also. In fact you should fill revise return with all details mention exemption against sec 10, deductions for 80C and Tax credits as in 26AS.

As soon as permission is granted plz file return 

Keep fingers crossed.