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. 2024 Oct 9;15:8741. doi: 10.1038/s41467-024-52939-6

Fig. 3. Contribution of protein-altering and non-protein altering SNVs to the observed heritability of CAD.

Fig. 3

a Absolute (left) and relative (right) contribution per variant of each LD score-MAF-Impact bin to the global CAD heritability estimate. Each label in the legend represents a combination of: i) MAF (UR: ultra-rare (MAF ≤ 0.1%), R: rare (0.1% <MAF ≤ 1%), UC: uncommon (1% <MAF ≤ 10%), C: common (10% < MAF ≤ 50%)); ii) LD score (LO: Low, HI: High); and iii) Impact (High: protein-altering variants, Low: non-protein-altering variants). Error bars show ± one SE from each contribution point estimate. Absolute SEs (left) are calculated by GCTA and are proportional to the effective number of independent variants in each bin and inversely proportional to the total sample size (4949 cases + 17,494 controls). Relative SEs (right) are obtained by dividing the corresponding absolute SEs by the square root of the number of variants. b Log impact ratio of protein-altering over non-protein-altering variants in each LD score-MAF bin. Each label on the y-axis is defined as in (a). Error bars represent ± one SE from each log impact ratio estimate. SEs are calculated from GCTA’s output of the covariance matrix of contribution estimates to heritability in each bin and their corresponding number of SNVs (see Supplementary “Methods” for derivation details). CAD, coronary artery disease; LD, linkage disequilibrium; MAF, minor allele frequency; SE, standard error; SNV, single nucleotide variant.