To run mysql under different port than default port 3306 we have the dboptions-array in config.php.
But dboptions['dbport'] is ignored when creating the mysqli connection.

I changed line 265 in lib/dml/mysqli_native_moodle_database.php
from

$this->mysqli = new mysqli($dbhost, $dbuser, $dbpass, $dbname);

to

$this->mysqli = new mysqli($dbhost, $dbuser, $dbpass, $dbname, $dboptions['dbport']);

to solve this problem