Why did scientists think humans had 100,000 genes (before the Human Genome Project)?
Human genome is 3.2Gbp (giga=billions of basepairs). If you assume there are 100k genes, this yields around 32kbp (kilo=thousands base pairs) per gene.

Before human genome project, let's say before 1990, people were isolating a lot of genes from human-derived tissues. You can use google scholar to find relevant papers. From quick search, you can see that range is pretty large:


"186,000 base-pair (bp) human factor VIII gene"
"human TF gene spans 12.4 kbp"


So you can see how one might guess "average" size of the gene to be somewhere around 30kbp, if you haven't yet found too many genes. Whereas after genome sequencing, we know that genes are 100-10000 bp long. I think the issue was that there was no enough statistics yet to judge appropriately "average gene size". And as it turns out, the distribution is very funky. You need to isolate a lot of genes to reconstruct that distribution.

By the 1990 phenomenon of the alternative splicing was already known. What perhaps wasn't quite obvious, is how many genes there are, what their real sizes, and how many genes are overlapping