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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
  1. Cases used to generate the NCBRS-SMARCA2 DNAm signature are in bold. CADD score > 20 indicates a variant in the top 1% of deleterious variants in the human genome, > 30 in the top 0.1%. ACMG classification was made by the referring clinical laboratory for each sample. NCBRS-SMARCA2 score was generated in this study based on the DNAm signature (see Methods). Detailed clinical data are presented in Additional file 2: Table S1