The poor transferability of genetic risk scores (GRS) derived from European ancestry data in diverse populations is a cause of concern. We set out to evaluate if GRS derived from data of African American individuals and multi-ancestry data perform better in sub-Saharan Africa (SSA) compared to European ancestry-derived scores. Using summary statistics from the Million Veteran Program (MVP) we showed that GRS derived from data of African American individuals enhance polygenic prediction of lipid traits in SSA compared to European and multi-ancestry scores. However, our GRS prediction varied greatly within SSA between the South African Zulu (LDL-C, R2 = 8.14%) and Ugandan cohorts (LDL-C, R2= 0.026%). We postulate that differences in the genetic and environmental factors between these population groups might lead to the poor transferability of GRS within SSA. More effort is required to optimise polygenic prediction in Africa.