Table 3 Results of clinical exome sequencing clinical reports for 426 assessed patients

Description of genetic variants in the clinical exome sequencing report

 Proportion of patients with at last one variant classified as LP or P—n/N, % (95% CI)

160/426

37.6%

(32.9–42.2)

 Proportion of patients with at last one variant classified as VUS, LP, or P—n/N, % (95% CI)

259/426

60.8%

(56.1–65.5)

 Number of genetic variants reported in the CES report per patient—n, median (IQR)

426

1

(0–2)

 Number of genetic variants classified as VUS, LP, or P per patient—n, median (IQR)

426

1

(0–1)

 Number of genetic variants classified as LP or P per patient—n, median (IQR)

426

0

(0–1)

Variant #1

 ACMG, pathogenic—n/N, % (95% CI)

78/426

18.3%

(14.6–22)

 ACMG, likely pathogenic—n/N, % (95% CI)

72/426

16.9%

(13.3–20.5)

 ACMG, uncertain significance—n/N, % (95% CI)

104/426

24.4%

(20.3–28.5)

 ACMG, likely benign—n/N, % (95% CI)

8/426

1.9%

(0.6–3.2)

 ACMG, benign—n/N, % (95% CI)

22/426

5.2%

(3.1–7.3)

 No variant retrieved—n/N, % (95% CI)

142/426

33.2%

(28.8–37.8)

 NGS-diag network scoring system—n, median (IQR)

284

4

(3–5)

Variant #2

 ACMG, pathogenic—n/N, % (95% CI)

24/426

5.6%

(3.4–7.8)

 ACMG, likely pathogenic—n/N, % (95% CI)

21/426

4.9%

(2.9–7.0)

 ACMG, uncertain significance—n/N, % (95% CI)

52/426

12.2%

(9.1–15.3)

 ACMG, likely benign—n/N, % (95% CI)

3/426

0.7%

(0–1.5)

 ACMG, benign—n/N, % (95% CI)

17/426

4.0%

(2.1–5.9)

 No variant retrieved—n/N, % (95% CI)

309/426

72.5%

(68.3–76.8)

 NGS-diag network scoring system—n, median (IQR)

117

3

(3–4)

Variant #3

 ACMG, pathogenic—n/N, % (95% CI)

1/426

0.2%

(0–0.6)

 ACMG, likely pathogenic—n/N, % (95% CI)

6/426

1.4%

(0.3–2.5)

 ACMG, uncertain significance—n/N, % (95% CI)

15/426

3.5%

(1.8–5.3)

 ACMG, likely benign—n/N, % (95% CI)

1/426

0.2%

(0–0.7)

 ACMG, benign—n/N, % (95% CI)

8/426

1.9%

(0.6–3.2)

 No variant retrieved—n/N, % (95% CI)

395/426

92.7%

(89.8–95.0)

 NGS-diag network scoring system—n, median (IQR)

31

3

(1–3)

Variant #4

 ACMG, pathogenic—n/N, % (95% CI)

0/426

0%

(—)

 ACMG, likely pathogenic—n/N, % (95% CI)

1/426

0.2%

(0–0.6)

 ACMG, uncertain significance—n/N, % (95% CI)

6/426

1.4%

(0.3–2.5)

 ACMG, likely benign—n/N, % (95% CI)

1/426

0.2%

(0–0.6)

 ACMG, benign—n/N, % (95% CI)

5/426

1.2%

(0.1–2.2)

 No variant retrieved—n/N, % (95% CI)

413/426

96.9%

(94.7–98.3)

 NGS-diag network scoring system—n, median (IQR)

13

3

(1–3)

Confirmation of the clinically suspected diagnosis—n/N, % (95% CI)

 Confirmation of the suspected diagnosis

183/426

43.0%

(38.2–47.7)

 Contribution to the suspected diagnosis

32/426

7.5%

(5.0–10.0)

 No contributive variant to the suspected diagnosis

211/426

49.5%

(44.8–54.3)

Therapy guided by NGS results—n/N, % (95% CI)

 Yes

62/426

14.6%

(11.2–17.9)

 No

263/426

61.7%

(57.1–66.4)

 No follow-up information

101/426

23.7%

(19.7–27.8)