There has been a gene variant discovered in 5% of the population that has been linked to the low blood levels of the active ingredient in hormonal contraceptives. This genetic variant is known as CYP3A7. This variant is mostly known to affect oral contraceptives as opposed to the implant forms of contraceptives. There were also two other gene variants discovered, however, those did not have as much of an impact on the hormonal contraceptives as the CYP3A7.
Source 1: https://www.the-scientist.com/news-opinion/gene-variant-linked-to-lower-levels-of-hormonal-birth-control-65600
Source 2: https://www.snpedia.com/index.php/CYP3A7