I have migrated data from SQL spatial server to File GDB, I have given the correct primary key and used vertex function to create the points from lat-long values. Migration was done successfully but I couldn't find any spatial data in File GDB.
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Hello @96prasad,
I have a few questions for you:
1) Are you able to ensure the features were written correctly by looking at the log file?
2) Does the Geometry type of your Geodatabase Feature Type match the geometry of the features?
3) If you inspect the features directly before the Writer, do they display geometry?
4) Did any features get written to the Geodatabase, for example non-spatial features?
@96prasad, to add to @trentatsafe request, Can you confirm in the workspace you have File Geodatabase Feature type Geometry to allow geodb_point? If that is not the case, please try running it with this adjustment. 
@96prasad, to add to @trentatsafe request, Can you confirm in the workspace you have File Geodatabase Feature type Geometry to allow geodb_point? If that is not the case, please try running it with this adjustment.
I totally agree. Just a tiny detail: the user may need to force a table re-create, either by manually deleting the table/feature class in ArcCatalog, or by setting Table Handling = Drop and Create in FME.