We describe an interesting case of a 23 year old female with known primary ovarian failure, who was diagnosed with abdominal adenocarcinoma of gastrointestinal origin. She experienced severe and prolonged chemotherapy side effects, and was eventually diagnosed with Fanconi anaemia due to biallelic BRCA2 variants. We highlights hurdles that were encountered during diagnosis, including initial false negative chromosome instability testing, and the uncertainty generated for individuals, families and clinicians when variants of uncertain significance are encountered. Gastrointestinal cancer has been described in only 2 other adults with BRCA2-related Fanconi anaemia and is worthy of further investigation, given the availability of effective screening for these types of cancers. (By Emilia Ip, https://jmg.bmj.com/content/early/2021/10/24/jmedgenet-2021-108072 )