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

[Konrad Karczewski]

Oh, whoops! Indeed that's correct! If you visualize them on UCSC (click the UCSC link on the 3 pages: e.g. http://exac.broadinstitute.org/variant/1-245133629-A-C), you'll notice that they fall into splice variants that affect 3' and 5' UTRs, which are unlikely to be LoF (will not trigger nonsense-mediated decay).

This is a newer version of LOFTEE that hasn't been made into a full release yet, so hasn't been integrated into the ExAC browser yet.

-Konrad

On March 21, 2016 at 6:44:18 PM, Wei Zhao (mikezhaow at gmail.com) wrote:

Thank you, Konrad!

I listed the annotation for the three variant-transcript pairs below:

var273214       1:245133629     G       ENSG00000203666 ENST00000366523 Transcript      splice_acceptor_variant -       -       -       -       -       -       LoF=LC;LoF_flags=;IMPACT=HIGH;LoF_filter=5UTR_SPLICE;LoF_info=INTRON_SIZE:285;STRAND=1
var78183        8:130789839     C       ENSG00000147697 ENST00000276708 Transcript      splice_acceptor_variant -       -       -       -       -       -       LoF_filter=3UTR_SPLICE;IMPACT=HIGH;LoF_flags=;LoF=LC;LoF_info=INTRON_SIZE:8419;STRAND=-1
var113394       5:177474136     C       ENSG00000204677 ENST00000511189 Transcript      splice_donor_variant    -       -       -       -       -       -       LoF_info=INTRON_SIZE:1531;LoF_filter=3UTR_SPLICE;LoF_flags=;LoF=LC;IMPACT=HIGH;STRAND=1

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