Table 1 Variant information and selected clinical data for samples with SMARCA2 sequence variants
From: New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome
Sample ID | Variant | Inheritance | PolyPhen Prediction Effect (score) | SIFT prediction effect | Mutation Taster prediction effect | CADD score | ExAC Total frequency | Diagnosis | ACMG classification | NCBRS-SMARCA2 score |
|---|---|---|---|---|---|---|---|---|---|---|
SMARCA2_1 | c.3493C > A, p.Gln1165Lys | de novo | Probably damaging (0.924) | Deleterious | Disease causing | 22.9 | – | NCBRS | Pathogenic | 0.37 |
SMARCA2_2 | c.3209 T > A, p.Leu1070Gln | – | Probably damaging (0.998) | Deleterious | Disease causing | 29.3 | – | NCBRS | Likely pathogenic | 0.27 |
SMARCA2_4 | c.2639 C > T, p.Thr880Ile | – | Probably damaging (0.999) | Deleterious | Disease causing | 28.2 | – | NCBRS | VUS | 0.25 |
SMARCA2_5 | c.2648C > T, p.Pro883Leu | – | Probably damaging (0.999) | Deleterious | Disease causing | 28.9 | – | NCBRS | Likely pathogenic | 0.24 |
SMARCA2_6 | c.2486C > T, p.Thr829Ile | de novo | Probably damaging (0.999) | Deleterious | Disease causing | 29.1 | – | NCBRS | Pathogenic | 0.22 |
SMARCA2_7 | c.2264A > G, p.Lys755Arg | – | Probably damaging (0.997) | Deleterious | Disease causing | 33.0 | – | NCBRS | Pathogenic | 0.36 |
SMARCA2_8 | c.3623C > G, p.Ser1208Cys | de novo | Probably damaging (0.999) | Deleterious | Disease causing | 27.0 | – | NCBRS | Likely pathogenic | 0.32 |
SMARCA2_9 | c.2348C > G, p.Ser783Trp | de novo | Probably damaging (1.0) | Deleterious | Disease causing | 34.0 | – | NCBRS | Likely pathogenic | 0.22 |
SMARCA2_10 | c.2564G > C, p.Arg855Pro | de novo | Probably damaging (0.999) | Deleterious | Disease causing | 28.7 | – | NCBRS | VUS | 0.24 |
SMARCA2_11 | c.2255G > C, p.Gly752Ala | – | Probably damaging (0.999) | Deleterious | Disease causing | 27.9 | – | NCBRS | Likely pathogenic | 0.27 |
SMARCA2_12 | c.3849G > T, p.Trp1283Cys | de novo | Probably damaging (0.999) | Tolerated | Disease causing | 34.0 | – | NCBRS | VUS | −0.04 |
SMARCA2_14 | c.2558G > T, p.Gly853Val | – | Probably damaging (0.83) | Deleterious | Disease causing | 29.7 | – | NCBRS | VUS | 0.29 |
SMARCA2_15 | c.400G > A, p.Val134Ile | – | Probably damaging (0.84) | Tolerated | Disease causing | 22.3 | 0.00001648 | – | VUS | −0.25 |
SMARCA2_16 | c.674A > C, p.Gln225Pro | – | Benign (0) | Tolerated | Benign | 14.7 | 0.0001821 | – | Benign | −0.32 |
SMARCA2_17 | c.689A > C, p.Gln230Pro | – | Benign (0) | Tolerated | Polymorphism | 12.7 | 0.0003702 | – | Benign | −0.31 |
SMARCA2_18 | c.695A > C, p.Gln232Pro | – | Benign (0) | Tolerated | Polymorphism | 12.7 | 0.0006005 | – | Benign | −0.30 |
SMARCA2_19 | c.1878-3 T > C, p.Gly626, | – | – | – | – | - | - | – | Benign | −0.24 |