In rare disease research, sharing of individual health data is essential for advancing diagnostics and therapies, requiring robust and ethically sound informed consent processes. Within the Genomic Medicine Sweden Rare Diseases (GMS-RD) multicenter study, an electronic informed consent (eConsent) platform was developed to support data sharing, facilitate participation and enable research engagement. Tailored to the complex consent needs of rare disease contexts, the platform was piloted at three Genomic Medicine Centers in Sweden. A total of 2244 individuals were invited in the clinical routine cohort, with an overall eConsent rate of 18.6%. Uptake was highest among adult singletons (27.8%) and lowest in trios (14.3%). In contrast, the Undiagnosed Diseases Network (UDN) Sweden cohort achieved a 94% consent rate, attributed to targeted communication and active patient organization involvement. Key challenges included technical accessibility limitations, digital literacy deficits, comprehension and language barriers, and the burden of multi-step processes, especially for families. Findings underscore the need to improve usability, strengthen communication, and implement flexible consent management over time. eConsent can broaden participation in genomic research and promote responsible data sharing. However, in rare diseases contexts, it must be designed with inclusivity, clarity, and adaptability to meet the diverse participant needs.
Supplementary Information: The online version contains supplementary material available at 10.1038/s41598-025-32740-1.
Keywords: Electronic informed consent (eConsent); Genomics; Rare diseases; Whole-genome sequencing.