CADD score

[zdw...@gmail.com]

Hello Kyoko,

Thanks for your prompt fix of FUMA after last weekends expansion it works like a charm. Can you help me with these questions.

1.) Per FUMA CADD score, 12.37 is the suggested threshold by Kircher et al. (2014), but I cannot find that number in the paper or supplements. Could you please point me to the source (page number, paragraph) for citation.
2.) Also, what percent deleteriousness does 12.37 associate with? (i.e. CADD 10 = 10%, CADD 20 = 1%).
3.) Is there a table that lists range of CADDs with their associated percentage?

Thanks very much,
Zach

[Kyoko Watanabe]

Hi Zach,

1) I'm sorry for the confusion but I should have referenced this paper, https://genome.cshlp.org/content/25/3/305.full

12.37 is the minimum value for pathogenic SNPs and has been used as a threshold for highly deleterious SNPs.

But, it's up to you to use different threshold like 10 to include top 10% of SNPs though.

2) and 3), I don't think there is a table of percentage of SNPs with binned CADD score, but what I got from my data is 7.5% for SNPs with CADD >=12.37.

Hope it helps.

Best,

Kyoko