616; 41c.2453G>A; c.5824G>Cp. G818E (D); p. E1942Q (B;N)46c.6384A>Gp.H2128R (D)Compound heterozygous

Table S2. ABCA4 variant categorization:

Summary genetic testing data is available on the eyeGENE website (eyeGENE.nih.gov/data), including the number of participants for each of the 38 diagnostic categories, variants detected per gene, and variant classification by gene. As of the time of this writing, 3,448 eyeGENE participants have been reported to have at least one pathogenic or likely pathogenic genetic variant. The 10 most frequently reported genes were ABCA4 (1799, 37%), USH2A (316, 7%), RPGR (283, 6%), CHM (219, 5%), PRPH2 (161, 3%), RS1 (142, 3%), RHO (130, 3%), BEST1 (114, 2%), EYS (67, 1%), and PRPF31 (62, 1%). These 10 genes represent 68% of all pathogenic and likely pathogenic variants in eyeGENE. Two thousand one hundred and four participants have genetic results where no pathogenic or likely pathogenic variant was found. Variants of uncertain significance were identified in 1,712 individuals.

Screening of reported pathogenic variants in ABCA4 for Stargardt (STGD) The disease prevalence of STGD is estimated as 1 in 10000 individuals4. It has been estimated that about 70% of STGD patients carry variants in ABCA45. Therefore, this represents the scenario of a recessive disease with a relatively homogeneous genetic cause. We screened 945 reported pathogenic variants in ABCA4 genes collected in HGMD. Among them, 11 variants are likely benign, as their population AF in is higher than 0.7% (1/20000‾‾‾‾‾‾‾‾√)<math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M11"><mrow><mrow><mo>(</mo><mrow><msqrt><mrow><mn>1</mn><mo>/</mo><mn>20000</mn></mrow></msqrt></mrow><mo>)</mo></mrow></mrow></math>, the cutoff based on STGD disease prevalence, therefore were excluded from further analysis. The remaining 934 variants were subjected to our test model. As a result, 26 variants with the AF in the range of 0.46% to 0.03% were identified as likely benign (Binomial test1, Bonferroni correction p-value ≤ 0.05/934 and test2 Bonferroni correction p-value > 0.05/934) (Figure 3A).