It is possible, however, that pop-ups could impact your bounce rate, irritating users and causing them to leave your site quickly. It is believed that search engines judge sites by the dwell time (time spend on site before returning to the results), so a high bounce rate could impact SEO.
Google now penalises sites that use pop-ups covering a large portion of the page. Currently, this is for Mobile only, but I expect it will move over to desktop too. I advise using pop-ups with caution: select a suitable delay (45 seconds), a position at the bottom of pages, or slide in from the side just before the exit.