What autoimmune diseases may cause raised ALT, ankle pain, chest pain, spine & shoulder pain without ANA, HLA B27 being positive?

Not many. Sounds like you have already had a "work-up" for your symptoms (ANA. HLA B27 are not :common" tests The raised ALT may or may not be associated with your other symptoms. Do you have a liver problem? Hepatitis B, C often cause associated joint problems. Get this checked out by the same Health Care Provider who obtained the blood tests you mention Hope this helps Dr Z.