S.No | Variant Annotation Tools | Categorical Description | Database | Result |
---|---|---|---|---|
1. | Sort Intolerated From Tolerated (SIFT) | D: Deleterious (SIFT score ≤ 0.05); T: Tolerated (SIFT score >0.05) | DbSNP | Deleterious (SIFT score = 0.01) |
2. | Polymorphism Phenotyping v2 (Poly Phen v2) | D: Probably damaging (pp2_score ≥ 0.957), P: Possibly damaging (0.453 ≤ pp2_score ≤ 0.956) B: Benign (pp2_score ≤ 0.452) | PDB, DSSP, HumDiv, HumVar | Possibly damaging (pp2_score = 0.92) |
3. | Mutation Taster | A: Disease_causing_automatic; D: Disease_causing; N: Polymorphism [probably harmless]; P: Polymorphism_automatic [known to be harmless] | dbSNP / TGP / ClinVar / HGMD | Disease causing |
4. | Mutation Assessor | H: High; M: Medium; L: Low; N: Neutral. | OMIM, Uniprot, Refseq, Pfam, dbSNP | Medium |
5. | Functional Analysis Through Hidden Markov Models (FATHMM V2.3) | D: Deleterious (FATHMM score > 0.5); T: Tolerated ( FATHMM score < 0.5); | HGMD, SwissProt/TrEMBL | Deleterious (FATHMM_score = 0.99418) |
6. | Combined Annotation Dependent Depletion (CADD) | Pathogenic ; (>20) Likely pathogenic; (>15) Likely benign; (<15) Benign (<10) | 1000 Genomes, Ensembl | Pathogenic (CADD_Score = 28.2) |
7. | Mendelian Clinically Applicable Pathogenicity (M-CAP) | Pathogenic; (>0.025), Benign (<0.025) | Ensembl | Pathogenic (M-CAP_score = 0.721) |
8. | Likelihood Ratio Test (LRT) | D: Deleterious; N: Neutral; U: Unknown | HGMD | Deleterious |
9. | Protein Variation Effect Analyzer (PROVEAN) | Deleterious < -2.5 Neutral > -2.5 | Uniprot | Deleterious (Provean_score = -4.1) |
10. | CONsensusDELeteriousness (Condel) | D: Deleterious (1.0) N: Neutral (0.0) | Ensembl | Deleterious |
11. | Variant Effect Predictor (VEP) | HIGH; MODERATE; LOW | Ensembl | HIGH |