Exemption of Rs.100,000 on LTCG

There is a net LTCG of Rs.19,119 on sale of shares and MFs.  I have fed in the details in Sch 112A and it shows this amount correctly.  I also had a LTCG of 40,49,898 from sale of house property (after considering investment in CG Bonds).  In the computation statement, the IT shows total CG of 40,69,017 ie., it has added the full amount of CG on shares.  I understand that there is an exemption of 100,000 for LTCG from sale of shares.  The system has obviously not considered this.  How to get the benefit of this exemption?