$re = '/(?P<reference_sequence>(NM|NR|XM|XR)_[0-9]{4,12}|ENST[0-9]{1,11})(\.(?P<version>([0-9]?[0-9])))?(:(?P<prefix>c|n)\.(?P<start>-?[1-9][0-9]{0,7})(?P<start_offset>[+-][1-9][0-9]{0,7})?(?P<ref>[ACTG])>(?P<alt>[ACTG]))?/m';
$str = 'NM_12345.5:c.1999+500C>A
NR_12345.5:c.1999+500C>A
XM_12345.5:c.1999+500C>A
XR_12345.5:c.1999+500C>A
ENST12334455677:c.1999+500C>A';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php