Utility of CADD Scores

Question

[john.ozborn]

Can anybody here comment on the utility of CADD scores? Specifically do people treat them as anything other than a fishing expedition?

I have only recently been using them and was surprised to see that among the highest ranked SNPs the non-coding high scoring sequences often outscored likely deleterious missense mutations. Although there are obviously many more non-coding mutations than coding mutations (in the human genome) I was surprised to see so many high scoring non-coding variants.

[Zev.Kronenberg]

What quality control steps have you taken to ensure that your variants calls are high quality? False variant calls are often classified as deleterious by variant prioritizers. If you have a biological expectation (e.g: pathway or phenotype) you can apply that knowledge using https://www.sanger.ac.uk/resources/software/exomiser/ or http://www.yandell-lab.org/software/phevor.html

Answer 1

[Kevin Blighe]

The best way to think about CADD is that it measures functional variants, which may be either damaging or beneficial to the organism. They may also have absolutely no effect on the phenotype but are likely to be altering some type of functionality.

CADD scores should be used as just 1 line of evidence toward gauging pathogenicity.