Question

When I run this it doesn’t throw an error however it doesn’t insert/delete an entry either. I don’t know why it’s not working.

DECLARE @trAction VARCHAR(5)
  SET @trAction = 'addTR'

  IF EXISTS (SELECT TransgeneID
            FROM tbl_MT
            WHERE MouseID = '3' AND TransgeneID = '3')
    IF (@trAction = 'rmvTR')    
      DELETE
      FROM tbl_MT
      WHERE MouseID = '3' AND TransgeneID = '3'
  ELSE
    IF (@trAction = 'addTR')  
      INSERT INTO tbl_MT 
      VALUES ('3', '3')

Answer 1

First, put BEGIN and END on the IF's:

  DECLARE @trAction VARCHAR(5)
  SET @trAction = 'addTR'

  IF EXISTS (SELECT TransgeneID
            FROM tbl_MT
            WHERE MouseID = '3' AND TransgeneID = '3')
  BEGIN
    IF (@trAction = 'rmvTR')    
    BEGIN
      DELETE
      FROM tbl_MT
      WHERE MouseID = '3' AND TransgeneID = '3'
    END
  END
  ELSE
  BEGIN
    IF (@trAction = 'addTR')  
    BEGIN
      INSERT INTO tbl_MT 
      VALUES ('3', '3')
    END
  END

Second and final, if the first IF is true, the inner IF (@trAction = 'rmvTR') will fail and nothing will be done.