It would be really great if there was a way to excuse a student from an assignment. You could place a X in the grade box or add an EX in the grade box. This would allow the teacher and students to know that the students does not deserve a 0 and they don't have to make it up.
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From what I've found, when a student is excused from an assignment, Canvas acts like that assignment does not exist for them. See How do I change the status of a submission in the Gradebook? , which mentions Excused assignments are not factored in the grade. So in your example, their grade would be 63/90. This also means if your assignment group is set up to drop the lowest grade, the Excused assignment does not count and it will drop a different assignment.