I think the best answer to such issue is on the below link
The best way to remove value from SET field?
query should be like this which covers the ,value or value, or only value in the comma separated column
UPDATE yourtable
SET
categories =
TRIM(BOTH ',' FROM REPLACE(CONCAT(',', col, ','), ',2,', ','))
WHERE
FIND_IN_SET('2', categories)
Here you can have your condition in where clause. for more details refer above link.
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