[ensembl-dev] Different LOFTEE Annotations by Standalone and ExAc

Konrad Karczewski konradk at broadinstitute.org
Mon Mar 21 22:27:08 GMT 2016

Hi Wei,

Sorry for the delay, I had an email typed out, but got stuck because I couldn't figure out what was going on with the first variant (which is missing from ExAC). I see now that it's probably a typo and you probably meant 245133629.

In any case, indeed I'm getting different results.  Can you post your annotated output of the variants here? Specifically, why they get an LC mark. If it's NON_CAN_SPLICE, I suspect there may be an issue with the FASTA index that is sending LOFTEE a sequence of "NN" for the splice site and making it think it's a non-GT/AG splice site.


On March 13, 2016 at 6:14:52 PM, Wei Zhao (mikezhaow at gmail.com) wrote:

Dear Konrad,

I have some variant-transcript pairs and the LOFTEE annotations I got by running it locally and checking ExAc website are different: ExAc reported "high-confidence" while I got "LC".  It seems to me that all of these variants are related to splicing and I listed three examples below.  Could you please kindly take a look?  Hope I didn't miss anything obvious.  I was running VEPv83 and downloaded LOFTEE on March 9th.

Thank you for you help.


1:2451336129_A/G, ENST00000366523
5:177474136_T/C, ENST00000511189
8:130789839_T/C, ENST00000276708

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