Just to confirm - are you looking to incorporate this into the existing scene or save it as part of an OBJ file generated by Three.js?
If you want to add a point to the scene, you'll first need to establish a 'work plane' where you plan for the point (placed at the center of the sphere) to be located. By capturing the necessary coordinates based on the user's mouse position within the scene, you can then assign these values the appropriate X, Y, or Z coordinate, forming a vector and adding the Sphere to the scene.
On the other hand, if you're aiming to include this in an OBJ file, you'll either need to write out the file manually or programmatically generate an OBJ in memory before saving it, which could be more time-consuming.
To export your scene as an OBJ file, you may find useful information in this article: Exporting Threejs Scene to Obj Format