I found an exonic SNP (rs35124509) significantly associated with my phenotype. In order to characterize it, I used 3 type of score:
The CADD: Combined Annotation Dependent Depletion score
The SIFT: sorting intolerant from tolerant
the Polyphen-2: polymorphism phenotyping v2
This variant is predicted as Polyphen = benign, SIFT = tolerated and CADD = 22.3.
It seem a bit contradictory ? the CADD score predict it as being deleteriouse however, both SIFT and polyphen as tolerated/benign.
Moreover, I couldn't properly interpret the Genomic Evolutionary Rate Profiling (GERP) score. It is estimated for this genomic position as neutral (3.84).
What does it mean ? What do you think ?
Thank you for your help,