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konradjk / exac_browser

Browser for ExAC consortium data
http://exac.broadinstitute.org
MIT License
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Definition of LoF #312

Closed tadafumikato closed 7 years ago

tadafumikato commented 7 years ago

In the FAQ section, the definition of LoF says "Nonsense, splice acceptor, and splice donor variants caused by single nucleotide changes". Frameshift is missing here, and because of this, the definition is discordant with that in your paper.

ksamocha commented 7 years ago

That definition of LoF only applies to the constraint analyses (e.g. pLI). Other analyses in the paper include frameshift variants.

tadafumikato commented 7 years ago

Thank you for your quick response! I was confused because the paper says "This metric - the probability of being loss-of-function (LoF) intolerant (pLI) - (p288)" just after the description of PTVs, which was later defined as "a stop codon, frameshift, or the disruption of an essential splice site (p.289)". But now I understand that the definition is different between these two. I appreciate your comments.