GST vide Circular No. 129/48/2019 dated 24th December 2019 clarifies the issue and to ensure uniformity in the implementation of the provisions of the law across field formations with respect to appropriate procedure to be followed in case of non-furnishing of return under section 39 (monthly returns) or 44 (annual return) or 45 (final return) of the CGST Act, 2017.
The clarification is as follows,
As per section 46 of the CGST Act, 2017, It is required to issue a notice in FORM GSTR-3A to a registered person who fails to furnish return under section 39 or section 44 or section 45 (hereinafter referred to as the “defaulter”) requiring him to furnish such return within fifteen days. Further section 62 provides for assessment of non-filers of return of registered persons who fail to furnish return under section 39 or section 45 even after service of notice under section 46. As such, no separate notice is required to be issued for best judgment assessment under section 62 and in case of failure to file the return within 15 days of issuance of FORM GSTR3A, the best judgment assessment in FORM ASMT-13 can be issued without any further communication.
http://www.cbic.gov.in/resources//htdocs-cbec/gst/circular-cgst-125.pdf