MySQL 8.0

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CREATE TABLE t(
  provenance_country VARCHAR(100), 
  provenance_locality VARCHAR(100), 
  provenance_place VARCHAR(100)
)
INSERT INTO t VALUES 
  ('Unknown', 'Unknown', 'Unknown'),
  ('Known1', 'Unknown', 'Known3');
SELECT
  IFNULL(CONCAT_WS(', ',
      IF(provenance_country = 'Unknown' OR provenance_country = 'Not Applicable', NULL, provenance_country),
      IF(provenance_locality = 'Unknown' OR provenance_locality = 'Not Applicable', NULL, provenance_locality),
      IF(provenance_place = 'Unknown' OR provenance_place = 'Not Applicable', NULL, provenance_place)
  ), '-') AS provenance_loc
FROM t;  


provenance_loc




Known1, Known3


SELECT
  IFNULL(NULLIF(CONCAT_WS(', ',
      IF(provenance_country = 'Unknown' OR provenance_country = 'Not Applicable', NULL, provenance_country),
      IF(provenance_locality = 'Unknown' OR provenance_locality = 'Not Applicable', NULL, provenance_locality),
      IF(provenance_place = 'Unknown' OR provenance_place = 'Not Applicable', NULL, provenance_place)
  ), ''), '-') AS provenance_loc
FROM t;


provenance_loc


-

Known1, Known3