Table 1 Deleteriousness and conservation scores for the CDKN2A variant c.256G > A
From: Informing patients about their mutation tests: CDKN2A c.256G>A in melanoma as an example
Tools | Score | Interpretation |
|---|---|---|
Deleteriousness Scores | ||
SIFT | Deleterious (D) | D – Damaging/Deleterious (>  0.05) T – Tolerated (<  0.05) |
PolyPhen-v2 | PolyPhen2_HDIV = 1.000 (D) PolyPhen2_HVAR = 0.945 (D) | D – Probably damaging (>  0.908) P – Possibly damaging (0.446 < score ≤ 0.908) B – Benign (≤ 0.446) |
MutationTaster | 0.957 (D) | A – Disease causing automatic D – Disease causing (>  0.5) N – Polymorphism (<  0.5) P – Polymorphism automatic |
MutationAssessor | No data | – |
FATHMM | No data | – |
VEST3 | No data | – |
PROVEAN | −3.711 (D) | D – Damaging/Deleterious (≤ −2.5) N – Neutral (> − 2.5) |
Reliability Index (RI) | 6 | D – Damaging (≥ 5) N – Neutral (<  5) |
CADD v1.5 | 33 | CADD > 10 = In top 10%, CADD > 20 = In top 1%, CADD > 30 = In top 0.1% of probable deleterious variants in the human genome |
Conservation Scores | ||
GerpN | 5.93 | Highly conserved (>  2) |
PhastCons | 0.999 | Highly conserved (>  0.3) |
PhyloP | 5.697 | Highly conserved (>  3.0) |