Supplementary material J Med Genet Supplementary Table 4: Summary of inconclusive cancer cases ID Test indication Sex Age Gene; transcript Variant (cDNA, Zygosity Relatives ACMG OMIM phenotypes protein) class #T #P 003 Colorectal cancer F 48 APC c.3920T>A, Het 1 (a) 0 VUS Adenoma, periampullary, somatic; Adenomatous (NM_000038.5) (p.Ile1307Lys) polyposis coli (AD); Brain tumor-polyposis (AD) syndrome 2; Colorectal cancer, somatic; Desmoid disease, hereditary (AD); Gardner syndrome (AD); Gastric cancer, somatic; Hepatoblastoma, somatic 005 Lymphoma; mixed F 57 APC c.6724A>G, Het 1 (a) 0 VUS Adenoma, periampullary, somatic; Adenomatous polyposis; colorectal (NM_000038.5) (p.Ser2242Gly) polyposis coli (AD); Brain tumor-polyposis (AD) cancer syndrome 2; Colorectal cancer, somatic; Desmoid disease, hereditary (AD); Gardner syndrome (AD); Gastric cancer, somatic; Hepatoblastoma, somatic 008 Cholangiocarcinoma F 29 APC c.620G>A, Het 1 (a) 1 VUS Adenoma, periampullary, somatic; Adenomatous (NM_000038.5) (p.Cys207Tyr) polyposis coli (AD);Brain tumor-polyposis (AD) syndrome 2; Colorectal cancer, somatic; Desmoid disease, hereditary (AD); Gardner syndrome (AD);Gastric cancer, somatic; Hepatoblastoma, somatic 009 Colorectal cancer; M 75 BMPR1A c.729C>G, Het 1 (a) 0 VUS Juvenile polyposis syndrome, infantile form (AD); ameliogensis (NM_004329); (p.Gly243Gly) Hereditary mixed polyposis syndrome; Juvenile intestinal imperfecta polyposis (AD) MSH6 c.1273A>G, Het VUS Hereditary nonpolyposis colorectal cancer, type 5 (AD); (NM_000179) (p.Ile425Val) mismatch repair cancer syndrome 010 Colorectal cancer; F 53 MSH3 c.1992G>A Het 1(a) 1 VUS Endometrial carcinoma, somatic; familial adenomatous melanoma (NM_002439.4) (p.Gln664=) polyposis 4 011 Polyposis (40 F 68 POLD1 c.2570C>T, Het - - VUS Mandibular hypoplasia, deafness, progeroid features, and polyps); (NM_001308632) (p.Ala857Val) lipodystrophy syndrome (AD); Susceptibility to colon cancer type 10 (AD) 018 Ocular lymphoma; F 65 PTEN c.810G>T, Het - - VUS Cowden syndrome 1 (AD); Lhermitte-Duclos syndrome pancreatic cancer; (NM_000314) (p.Met270Ile) (AD); Macrocephaly/autism syndrome (AD); Prostate breast cancer cancer, somatic; Glioma susceptibility 2; Meningioma (AD) 020 Breast cancer F 54 PMS2 c.727G>T, Het - - VUS Hereditary nonpolyposis colorectal cancer type 4; (NM_000535) (p.Val243Phe) Mismatch repair cancer syndrome (AR) Shickh S, et al. J Med Genet 2020;0:1–9. doi: 10.1136/jmedgenet-2020-106936 Supplementary material J Med Genet Supplementary Table 5: Summary of inconclusive non-cancer cases Variant (cDNA, Relatives ACMG ID Test indication Sex Age Gene; transcript Zygosity OMIM phenotypes protein) #T #P class 016 Bilateral ectopia F 64 LTBP2 c.2541A>G, Het - - VUS Recessive Weill-Marchesani syndrome type 3 (AR); lentis NM_000428) (p.Arg847Arg) Primary congenital glaucoma 3D; Microspherophakia c.4964A>G, Het VUS and/or megalocornea, with ectopia lentis and with or (p.Tyr1655Cys) without secondary glaucoma (AR) 019 Achalasia, HL, F 20 CHD7 (NM_017780) c.2123G>A, Het 2 (u) 1 VUS CHARGE syndrome (AD); hypogonadotrophic corneal/ retinal (p.Ser708Asn) hypogonadism 5 with or without anosmia (AD) anomalies, c.7246G>C, 1 VUS delayed (p.Arg2449Thr) growth/puberty, RECQL4 c.520C>T, 1 VUS gastric (NM_004260) (p.His174Tyr) Baller-Gerold syndrome (AR); RAPADILINO syndrome dysmotility, c.3190C>T, 1 VUS (AR); Rothmund-Thomson syndrome (AR) dysmorphism (p.Arg1064Cys) 025 Duodenal F 50 NTHL1 c.527T>C, Het - - VUS Familial adenomatous polyposis 3 (AR) adenomas; IBS; (NM_002528) (p.Ile176Thr) GERD SEC23B c.1512T>C, Cowden syndrome 7 (AD); Dyserythropoietic anemia, (NM_001172745) (p.Asn504Asn) congenital, type 2 (AR) 026 Bilateral renal F 61 NEK8(NM_178170) c.450C>G, Het 4 (a) 4 VUS Nephronophthisis 9; Renal-hepatic-pancreatic dysplasia 2 cysts (p.Ile150Met) (AR) 027 Cerebellar ataxia, M 73 SUMF1 c.463T>C, Het 1 (a) 1 P Multiple sulfatase deficiency (AR) neuropathy (NM_001164675) (p.Ser155Pro) COL12A1 c.2956T>C Het VUS Ullrich congenital muscular dystrophy; Bethlem myopathy (NM_080645.2) (P.Tyr986His) 2 (AD) GAA(NM_000152.5) c.-32-13T>G Het P Glyogen Storage Disease Type II (Pompe) (AR) 028 Atrial septal M 27 PKD1 c.8293C>T, Het 3 (a) 3 LP† Polycystic kidney disease 1 (AD) defect; Aortic (NM_000296) (p.Arg2765Cys) † dilatation 032 Thin skin, unusual M 61 ABCC6 c.3823C>T, Het - - P Arterial calcification, generalized, of infancy type 2 (AR); scarring, absent (NM_001171) (p.Arg1275X) Pseudoxanthoma elasticum (AR); Pseudoxanthoma subcutaneous elasticum, forme fruste (AD) Shickh S, et al. J Med Genet 2020;0:1–9. doi: 10.1136/jmedgenet-2020-106936 Supplementary material J Med Genet tissue, bleeding disorder 033 Type A ascending M 76 NOTCH1 c.2734C>T, Het 1 (a) 1 VUS Adams-Oliver syndrome type 5 (AD); Aortic valve disease aortic dissection (NM_017617) (p.Arg912Trp) type 1 (AD) PKD2 c.484C>T, Het VUS Polycystic kidney disease 2 (AD) (NM_000297) (p.Pro162Ser) 035 Seizures; F 40 DHTKD1 c.2185G>A, Het 2 (u) 1 LP 2-aminoadipic 2-oxoadipic aciduria (AR); Charcot- dysmorphism; (NM_018706) (p.Gly729Arg) Marie-Tooth disease, axonal, type 2Q (AD) congenital microcephaly; severe ID; clubbed feet; hypertonia 058 Recurrent F 29 ATP2A1 c.733 G>A, Het - - VUS Brody myopathy (AR) rhabdomyolosis; (NM_173201.3) (p.Asp245Asn) cardiac CTDP1 c.227 C>A, (p. Het VUS Congenital cataracts, facial dysmorphism, and dysfunction (NM_004715.4) Pro76His) neuropathy (AR) 059 Memory loss, F 66 GALC c.334A>G Het - - P Krabbe disease (AR) seizures (P); (NM_000253.3) p.Thr96Ala white matter lesions 060 Progressive F 38 SYNE1 c.8003 A>G, Het 2 (u) 1 VUS Emery-Dreifuss muscular (AD); asymmetric (NM_1896.2) (p.Gln2668Arg) Spinocerebellar ataxia 8 (AR) muscle atrophy with weakness 068 Moyamoya F 38 LIPE c.3212delG Het - - LP Familial partial lipodystrophy type 6 (AR) vasculopathy; (NM_005357) (p.Gly1071fs) Cushing’s c.1252 G>A Het VUS disease; recurrent (p.Ala418Thr) kidney stones; MEGF8 c. 7409_7414del Het VUS Carpenter syndrome type 2 (AR) unilateral (NM_001410) (p.2470_2472del) postaxial Shickh S, et al. J Med Genet 2020;0:1–9. doi: 10.1136/jmedgenet-2020-106936 Supplementary material J Med Genet polydactyly; c.4233C>T Het VUS polycythemia; (p.Pro1411Pro) proptic eyes; partial bilateral RNF213 c.2745 A>C Het VUS Susceptibility to Moyamoya disease type 2 2,3 syndactyly (NM_001256071) (p.Arg915Arg) EVC2 c.3241T>G Het VUS Ellis-van Creveld syndrome (AR); Weyers acrofacial (NM_001166136) (p.Ser1081Ala) dysostosis (AD) 072 Mast cell F 42 CYBA c.467delC, Het - - LP Chronic granulomatous disease, autosomal, due to activation; (NM_000101.3) (p.Pro156Argfs*35) deficiency of CYBA (AR) postural IRF3 c.391G>A, Het VUS Susceptibility to acute, infection-induced (herpes-specific) orthostatic (NM_001197126.1) (p.Ala131Thr) encephalopathy type 7 AD) tachycardia syndrome OTULIN c.61C>A, Het VUS Autoinflammation, panniculitis, and dermatosis syndrome (NM_138348) (p.Pro21Thr) (AR) PDE4D c.79A>T, Het VUS Acrodysostosis 2, with or without hormone resistance (NM_001104631) (p.Lys27X) (AD); PEPD c.823delG, Het LP Prolidase deficiency (AR) (NM_001166056) (p.Val275fs) TPSAB1 c.422_423delinsTG, Het VUS Irritable bowel syndrome, cutaneous complaints, (NM_003294) (p.Thr141Met) connective tissue abnormalities, and dysautonomia (AD) TRPM4 c.1459_1495del, Het VUS Progressive familial heart block, type IB (AD) (NM_017636.3) (p.Arg499Glnfs*16) 074 Connective tissue M 60 ANK2 c.10339_10341del Het - - VUS Cardiac arrhythmia, ankyrin-B-related (AD); Long QT disorder NYD; (NM_001148) (p.3447_3447del) syndrome 4 (AD) aortic root KRAS (NM_033360) c.470A>G Het VUS Arteriovenous malformation of the brain, somatic; Bladder dilation (p.Tyr157Cys) cancer, somatic; Breast cancer, somatic Cardiofaciocutaneous syndrome 2; Gastric cancer, somatic; Leukemia, acute myeloid (AD, Smu); Lung cancer, somatic; Noonan syndrome type 3 (AD); Pancreatic carcinoma, somatic; RAS-associated autoimmune leukoproliferative disorder (AD); Shickh S, et al. J Med Genet 2020;0:1–9. doi: 10.1136/jmedgenet-2020-106936 Supplementary material J Med Genet Schimmelpenning-Feuerstein-Mims syndrome, somatic mosaic SPECC1L c.3310 G>A Het VUS Facial clefting (AD), oblique; Hypertelorism, Teebi type (NM_015330) (p.Val1104Met) (AD); Opitz GBBB syndrome, type II (AD) 077 Premenopausal F 38 GALNS c.1127G>A Het - - VUS Mucopolysaccharidosis IVA (AR) osteoporosis with (NM_001323544) (p.Arg376Gln) compression fractures; pulmonary issues; severe progressive scoliosis; AVM; unilateral hearing loss †hypomorphic allele Abbreviations: a=affected, u=unaffected, T =tested, P=positive Shickh S, et al. J Med Genet 2020;0:1–9. doi: 10.1136/jmedgenet-2020-106936.