55 1 c.161G>A p.C54Y DC c.2297G>T p.G766V DC 2 2 c.223T>G p.C75G DC c.5088C>G p.S1696R DC 2 3 c.740A>C p.N247T DC c.1433T>C p.I478T B c.2345G>A p.W782* DC 2 4 c.768G>T Splice site DC 1 5 c.1222C>T p.R408* DC c.2568C>A p.Y856* DC 2 6 c.1804C>T p.R602W DC c.859-9T>C Splice site PDC 2 7 c.1805G>A p.R602Q DC c.5113C>T p.R1705W DC 2 8 c.1922G>C p.C641S DC 1 9 c.1957C>T p.R653C DC 1 10 c.1957C>T p.R653C DC 1 11 c.2588G>C p.G863A DC c.655A>T p.R219* DC 2 Allele 2 (p.R219*) was APEX-false-negative 12 c.2588G>C p.G863A DC c.1906C>T p.Q636* DC 2 13 c.2588G>C p.G863A DC c.1906C>T p.Q636* DC 2 14 c.2588G>C p.G863A DC 1 15 c.2588G>C p.G863A DC 1 16 c.2894A>G p.N965S DC c.3322C>T p.R1108C DC 2 Allele 2 (p.R1108C) was APEX-false-negative 17 c.3064G>A p.E1022K DC c.6729&#fe;4_&#fe;18delAGTTGGCCCTGGGGC Splice site DC 2 18 c.3064G>A p.E1022K DC 1 19 c.3208_3209insGT p.S1071fs DC c.2942C>T p.P981L DC c.6529G>A p.D2177N B 2 20 c.3208_3209insGT p.S1071fs DC c.1519G>T p.D507Y DC 2 21 c.3208_3209insGT p.S1071fs DC c.4634G>A p.S1545N DC 2 22 c.3208_3209insGT p.S1071fs DC 1 23 c.3292C>T p.R1098C DC c.3299T>A p.I1100N DC 2 24 c.3322C>T p.R1108C DC c.4978delC p.L1661* DC 2 25 c.3386G>A p.R1129H DC c.3208_3209insGT p.S1071fs DC c.4634G>A p.S1545N DC 3 Allele 2 (p.S1071fs) was APEX false-negative and allele 1 (p.R1129H) was NGS false-negative 26 c.4139C>T p.P1380L DC c.3191-1G>T Splice site DC 2 27 c.4139C>T p.P1380L DC c.3398T>C p.I1133T PDC 2 28 c.4139C>T p.P1380L DC c.4070C>A p.A1357E DC 2 29 c.4139C>T p.P1380L DC c.4773G>C Splice site DC 2 30 c.4139C>T p.P1380L DC 1 31 c.4139C>T p.P1380L DC 1 32 c.4139C>T p.P1380L DC 1 33 c.4234C>T p.Q1412* DC 1 34 c.4319T>C p.F1440S DC 1 35 c.4328G>A p.R1443H DC c.180delG p.M61fs DC 2 36 c.4469G>A p.C1490Y DC c.1726G>C p.D576H DC 2 37 c.4469G>A p.C1490Y DC 1 38 c.4537_4538insC p.Q1513fs DC c.5578C>T p.R1860W DC 2 Allele 1 (p.Q1513fs) was NGS-false-negative 39 c.4577C>T p.T1526M DC 1 T ABLE 2. Continued Pt Allele 1 Detected by APEX Allele 2 Detected by NGS Allele 3 Detected by NGS Total N of DC Variants Comments DNA Change Protein Change/ Effect Pred. Patho. DNA Change Protein Change/ Effect Pred. Patho. DNA Change Protein Change/ Effect Pred. Patho.

X

ABCA4 p.Asp507Tyr 23982839:55:960

status: NEW

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103 Hum Var Score (0-1) Site Wt CV Mt CV CV % Variation 3 c.180delG p.M61fs 1 35 ND IVS7 c.859-9T>C Splice site 1 5 Acc. 78.18 76.99 Possibly site broken (1.52) ND Possibly disease-causing 11 c.1433T>C p.I478T 1 1 Tol. B 0.007 No change ND Benign 11 c.1519G>T p.D507Y 1 20 Del. 0.01 POD 0.641 No change 1/13006 dbSNP (rs148234178) 12 c.1749G>C p.K583N 1 68 Del. 0.04 POD 0.893 Acc. 66.17 37.22 Site broken (43.75) 1/13006 dbSNP (rs145265791) 14 c.1982_ 1983insG p.A662fs 1 69 ND 15 c.2297G>T p.G766V 1 1 Tol. NA POD 0.557 Don. 69.18 42.34 Site broken (38.79) ND 15 c.2345G>A p.W782* 1 3 ND 16 c.2510T>C p.L837P 1 72 Tol. NA POD 0.905 No change ND 16 c.2568C>A p.Y856* 1 5 ND 18 c.2686A>G p.K896E 1 53 Tol. NA B 0.002 ND Benign 20 c.2942C>T p.P981L 1 19 Del. 0.00 POD 0.813 No change 1/13006 dbSNP (rs147826775) 20 c.2972G>T p.G991V 1 70 Del. NA PRD 0.998 Donor 64.62 91.45 New site (41.53) ND IVS20 c.3050&#fe;1G>C Splice site 1 54 Acc. 86.43 57.49 Site broken (33.49) ND IVS21 c.3191-1G>T Splice site 1 26 Acc. 94.38 65.44 WT site broken (30.67) ND 22 c.3289A>T p.R1097* 1 71 ND 22 c.3299T>A p.I1100N 1 23 Del. NA PRD 0.986 No change ND 23 c.3370G>T p.D1124Y 1 62 Del. NA PRD 0.998 No change ND 23 c.3392delC/ 3393C>G p.A1131Gfs 1 55 ND 23 c.3398T>C p.I1133T 1 27 Del. NA B 0.100 No change ND Possibly disease-causing 27 c.4070C>A p.A1357E 1 28 Del. NA PRD 0.94 Acc. 40.92 69.86 New site (&#fe;70.74) ND IVS30 c.4539&#fe;2T>G Splice site 1 56 Don. 79.18 52.35 WT site broken (33.89) ND 31 c.4552A>C p.S1518R 1 57 Del. NA POD 0.871 Acc. 76.3 47.36 Site broken (37.94) ND 31 c.4634G>A p.S1545N 2 21, 25 Tol. NA B 0.253 Acc. 80.04 51.1 Site broken (36.16) ND 5. Continued Exon/ IVS DNA Change Protein Change/ Effect N of Alleles Identified Pt SIFT Polyphen2 HSF Matrix Allele Freq. by EVS Reference Comments Pred. Tol. Index (0-1) Pred.

X

ABCA4 p.Asp507Tyr 23982839:103:259

status: NEW

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