For various sociocultural reasons ancient Egyptians are a big deal. The pyramids of Giza are about as distant from the time of Augustus as Classical Rome is from us. When the pyramids were rising the world was mostly prehistory. Africa was dominated by hunter-gatherers, as was much of Southeast Asia. The genetic cluster which we recognize as Northern Europeans was only coming into focus, while South Asians as we understand them today may not totally have been a coherent group.
It was a very different time. Down to the present day one population can plausibly claim a connection to ancient Egypt, and that population are the Copts. Though now extinct, their language was a direct descendant of ancient Egyptian, which was not a Semitic tongue. As Christians in a nation which as been Muslim for over 1,000 years, with the period after 1000 A.D. likely majority Muslim, they likely have experienced less genetic perturbation than other groups in the area.
The paper The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape has some Coptic, and other, samples. There are 175,000 markers on this chip. Merged with the HGDP populations you get about 30,000.
The PCA shows that Copts are mostly West Eurasian in ancestry. But they seem shifted to Northeast African Sub-Saharan groups The Mozabite Berbers are shifted toward West Africans, but their West Eurasian ancestry looks to be more like that of the Copts than West Asians. Though not shifted toward West Asians, the Copts do seem to have affinities with various Sudanese groups.
This TreeMix graph was run on 30,000 markers, with the Sudan skewed sample and some HGDP populations. Not surprisingly, there are gene flow arrows from the Copts to the others. In particular, the two Nubian groups, who have long been resident right to the south of Egypt. But, there is also gene flow from a position between the Copts and Sub-Saharan Africans. Finally, observe that Northeast African Bantus, who have some Nilotic admixture from the Bantu, receive gene flow from a more “European” like population, while the Copts receive gene flow from near the Sardinians. All this points to a complex population history.
It seems likely that the Eurasian backmigration into Sub-Saharan African over the Holocene involved several distinct events. Some of them probably date to the period of the Pleistocene.
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