When looking through stained glass, you are unable to see rain. This effects both full blocks and panes. Interestingly, this does not affect regular glass
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Duplicate of MC-188529, which is unfortunately resolved as won't fix. Playing on the fabulous graphics setting solves the problem.
I find that the bug fixes itself when the graphics options are set to Fabulous! in settings, sadly lower settings might not be able to handle transparency issues like this. Also relates to MC-210760