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That information should be present in your TF tree, so you should not need to explicitly tell amcl what that transform is.

The LaserScan messages that amcl subscribes to should have a frame id in the header of each message. amcl will then transform the data in the scan message from the message frame id, to whatever frame is specified in the amcl parameter base_frame_id. The transform predicted by amcl (i.e. your pose in the global frame) will hence be relative to the base_frame_id.

So, make sure you are publishing transforms from your scanner frame id, to the base frame id, and that those transforms represent the appropriate offset of the physical scanner from the base frame (where the base frame origin should be the centre of rotation of your robot).