...
WHERE
  `POP1` IS NOT NULL
  && `VT`='ABC'
  && (`SOURCE`='HOME')
  && (`alt` RLIKE '^[AaCcGgTt]$')
  && (`ref` RLIKE '^[AaCcGgTt]$')
  && (`AA` RLIKE '^[AaCcGgTt]$')
  && (`ref` = `AA` || `alt` = `AA`)
LIMIT 10 ;

| id | select_type | table | type | possible_keys                          | key                 | key_len | ref         | rows     | Extra       |
|  1 | SIMPLE      | myTab | ref  | vt_source_pop1_pop2,pop1_vt_source,... | vt_source_pop1_pop2 | 206     | const,const | 20040021 | Using where |

CREATE TEMPORARY TABLE `myTab` (`notnul` FLOAT, `nul` FLOAT);
INSERT INTO `myTab` VALUES (1, NULL), (1, 2), (1, NULL), (1, 2), (1, NULL), (1, 2), (1, NULL), (1, 2), (1, NULL), (1, 2), (1, NULL), (1, 2);
SELECT * FROM `myTab`;

+--------+------+
| notnul | nul  |
+--------+------+
|      1 | NULL |
|      1 |    2 |
|      1 | NULL |
|      1 |    2 |
|      1 | NULL |
|      1 |    2 |
|      1 | NULL |
|      1 |    2 |
|      1 | NULL |
|      1 |    2 |
|      1 | NULL |
|      1 |    2 |
+--------+------+

CREATE INDEX `notnul_nul` ON `myTab` (`notnul`, `nul`);
CREATE INDEX `nul_notnul` ON `myTab` (`nul`, `notnul`);

SHOW INDEX FROM `myTab`;

+-------+------------+------------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| Table | Non_unique | Key_name   | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+-------+------------+------------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| myTab |          1 | notnul_nul |            1 | notnul      | A         |          12 |     NULL | NULL   | YES  | BTREE      |         |               |
| myTab |          1 | notnul_nul |            2 | nul         | A         |          12 |     NULL | NULL   | YES  | BTREE      |         |               |
| myTab |          1 | nul_notnul |            1 | nul         | A         |          12 |     NULL | NULL   | YES  | BTREE      |         |               |
| myTab |          1 | nul_notnul |            2 | notnul      | A         |          12 |     NULL | NULL   | YES  | BTREE      |         |               |
+-------+------------+------------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+

EXPLAIN SELECT * FROM `myTab` WHERE `notnul` IS NOT NULL;
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+
| id | select_type | table | type  | possible_keys | key        | key_len | ref  | rows | Extra                    |
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+
|  1 | SIMPLE      | myTab | index | notnul_nul    | notnul_nul | 10      | NULL |   12 | Using where; Using index |
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+


EXPLAIN SELECT * FROM `myTab` WHERE `nul` IS NOT NULL;
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+
| id | select_type | table | type  | possible_keys | key        | key_len | ref  | rows | Extra                    |
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+
|  1 | SIMPLE      | myTab | range | nul_notnul    | nul_notnul | 5       | NULL |    6 | Using where; Using index |
+----+-------------+-------+-------+---------------+------------+---------+------+------+--------------------------+

EXPLAIN SELECT * FROM `myTab` WHERE `nul` IS NULL && notnul=2;
+----+-------------+-------+------+-----------------------+------------+---------+-------------+------+--------------------------+
| id | select_type | table | type | possible_keys         | key        | key_len | ref         | rows | Extra                    |
+----+-------------+-------+------+-----------------------+------------+---------+-------------+------+--------------------------+
|  1 | SIMPLE      | myTab | ref  | notnul_nul,nul_notnul | notnul_nul | 10      | const,const |    1 | Using where; Using index |
+----+-------------+-------+------+-----------------------+------------+---------+-------------+------+--------------------------+


EXPLAIN SELECT * FROM `myTab` WHERE `nul` IS NOT NULL && notnul=2;
+----+-------------+-------+-------+-----------------------+------------+---------+------+------+--------------------------+
| id | select_type | table | type  | possible_keys         | key        | key_len | ref  | rows | Extra                    |
+----+-------------+-------+-------+-----------------------+------------+---------+------+------+--------------------------+
|  1 | SIMPLE      | myTab | range | notnul_nul,nul_notnul | notnul_nul | 10      | NULL |    1 | Using where; Using index |
+----+-------------+-------+-------+-----------------------+------------+---------+------+------+--------------------------+