<?php

$timeString = '00:38:42,689';
$dateTime   = DateTime::createFromFormat('H:i:s,u', $timeString);

$milliseconds =
    $dateTime->format('H') * 3600000 +
    $dateTime->format('i') * 60000 +
    $dateTime->format('s') * 1000 +
    $dateTime->format('u') / 1000;

var_dump($milliseconds);