Threshold limit of 40l

You have to maintain books of accounts as per section 44AA of the income tax Act , because as per section 44 AA of the income tax Act one has to maintain books of accounts if your turnover crosses 25 lacs in Case of individual in other Cases it's 10 Lacs In the previous year, So my opinion you maintain the books of accounts , get audit done of the books of accounts ( even though Audit is not required )   and find out Correct turnover for GST registration  which  may be less  then  38 lacs or  more than 38 lacs  or  38 Lacs  . If  you are not maintaining books of accounts which is required as per income tax Act and neither the audit  has been done therefore.  your Turnover may not be correct , 

Take others opinion as well.