What: Alnylam Pharmaceuticals (NASDAQ:ALNY) released earnings on Monday after the bell and fell 11.6% on Tuesday.

Of course, without any products on the market, the biotech's earnings don't really matter. But for the record, Alnylam recorded $7.3 million in revenue, mostly from partners Sanofi and The Medicines Company (NASDAQ:MDCO). The net loss for the quarter came in at $103 million, but much of that was non-cash GAAP expenses. Most importantly the company ended the quarter with $1.2 billion in the bank and increased its guidance for year-end cash to "over $1 billion," including $150 million of restricted marketable securities related to a credit agreement being used to the build-out of its new manufacturing plant.

Instead, it appears investors are worried about an update on the company's ALN-CC5, which caused three analysts to cut their price targets. It's all relative, of course, because all three analysts kept their buy or outperform ratings on the stock and the lowest of the new lower price targets is $107, substantially higher than where Alnylam trades today.

So what: Alnylam plans to present initial results from a phase 1/2 trial of ALN-CC5 in patients with paroxysmal nocturnal hemoglobinuria (PNH) at the European Hematology Association meeting next month, but management said the data point to developing the drug for PNH patients that are poor responders to Alexion's (NASDAQ:ALXN) already-approved Soliris or as a backup medicine in between doses of Soliris. Not having to compete for PNH patients is obviously good news for Alexion, which saw its stock end Tuesday up 2.7%.

Being a second-line drug will cut into the potential patients that ALN-CC5 could be used to treat. Alnylam thinks it might be 20% to 30% of PNH patients whose symptoms aren't adequately controlled on Soliris. On the plus side, there will be less competition for those patients. Alnylam plans to start a phase 2 trial by the end of 2016 in patients that need additional treatment beyond Soliris.

There's also the possibility to test ALN-CC5 in other complement-mediated diseases. Alexion, for instance, has also gotten Soliris approved for a disease called atypical hemolytic uremic syndrome (aHUS). Management mentioned aHUS and another complement disease called myasthenia gravis as potential targets for clinical trials starting in early 2017.

Now what: While investors seem to be focused on lower potential sales of ALN-CC5 years from now, keep in mind that Alnylam has four drugs that are further along in the clinic. We should get an update on the open label extension trials for both patisiran and revusiran in July at the International Symposium on Amyloidosis. Alnylam plans to start a phase 3 trial for fitusiran in hemophilia patients later this year. And The Medicines Company plans to present initial phase 2 data on ALN-PCSsc later this year. Given that they're all closer to market, progress on all four drugs is more important than ALN-CC5.

Alnylam Pharmaceuticals is anticipating the trials being positive and the drugs getting on the market with its investment in a manufacturing plant. The company expects the facility to be operational in 2018, which works out well with phase 3 data for patisiran expected to read out next year. Making drugs in house could give Alnylam a little boost to any licensing deals, perhaps collecting a manufacturing fee in addition to a royalty.

While the ALN-CC5 news is disappointing, there were no guarantees that every RNAi drug from Alnylam was going to be a blockbuster, and investors should focus on the bigger picture.