why is gnomad2 not in the repository anymore?

A lot of software available in Ubuntu comes from Debian. Some of that software originates in Debian, but most is packaged in Debian and then imported through rather automated means into Ubuntu. See https://wiki.ubuntu.com/UbuntuDevelopment/NewPackages and https://wiki.ubuntu.com/DebianImportFreeze. gnomad2 was in Debian as of version 5.0 lenny, but was not packaged for Debian as of version 6.0 squeeze (which is the latest stable version, in the same general sense that 11.04 Natty is the latest stable version of Ubuntu).

So the answer to your question (though it raises other questions you might want answered) is this: gnomad2 ceased being packaged for Debian prior to the Debian import freeze for Ubuntu 10.10 Maverick, and continued not being in Debian through the import freeze for 11.04 Natty, which appears to be why it's not present in those two Ubuntu releases.

In Debian, sid is the perpetual codename for the testing branch, which perpetually undergoes development, and from which stable branches fork off (for lack of a better term). Searching for gnomad2 in Debian yields http://packages.debian.org/search?keywords=gnomad2&searchon=names&suite=all&section=all. At first glance I am inclined to say that gnomad2 is back (and thus, will be automatically imported into Ubuntu 11.10 Oneiric Ocelot in due time). I find it strange that it's only been packaged so far for the avr32 and m68k architectures (and, in particular, not packaged for *any* of the officially supported Debian architectures), but perhaps it's been newly added to Debian's testing branch and packages for other architectures simply haven't been produced yet.

If Oneiric's import freeze approaches (say, when it's a few months off) and there still aren't gnomad2 packages for amd64 and i386 (and whatever other architectures Oneiric supports) in Debian sid, then I'd recommend filing a bug report against gnomad2 in Ubuntu with the needs-packaging tag. Or you could just file such a bug now, if you want (if you do, you should make sure to mention that it looks like gnomad2 may be coming back to Debian sid). Before reporting any bugs in Ubuntu, please read https://help.ubuntu.com/community/ReportingBugs carefully if you haven't done so already. They you can search to see if the bug has already been reported (that page explains how, and also explains a lot of other important considerations), then file your bug report.