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                   9434 Points
                   Joined December 2011
                
               
			  
			  
             
            
             Section 139 pertains to the filing of a return of income by an assessee. 
section 148 deals with the issuance of a notice for reassment or re-computation of income when the Assessing Officer has reason to believe that income has escaped assessment. 
Regarding the penalty calculation under section 270A, which deals with penalty for under reporting and miscreporting of income. 
A return filed under section 148 is considered for the purpose of determining the tax liability and penalities. 
The return filed under section 148 doesn't exactly "replace" the original return filed under Section 139 in all contexts but is considered for assessing income that might have escaped assessment. 
For penalty calculations under section 270A, the comparison might involve the income assessed versus the income reported in the return filed under section 139 or as per the reassessment under section 148. 
So for penalty calculation u/s 270A,, the return filed u/s 148 doesn't simply replace the one filed u/s 139 but is part of the assessment/reassessment process. The penalty would be based on the underreported income considereing the reassessment proceedings.