Molecular Vision: Asghar, Mol Vis 2025; 31:69-83. Table 3

Table 3. Curated classification of novel and previously reported likely pathogenic/variant of uncertain significance/benign variants as per ACMG guidelines.

Sr. No.	GENE		VARIANT	VARIANT INTERPRETATION
Sr. No.	ID	Accession number	VARIANT	Clin Var ID/Classification	Codes met	Curated Classification
1	PCDH 15	NM_001384140.1	CHR10:55996693T>C	NA	PM2, PVS1, PP4, PP1, PP3	Pathogenic
2	MYO7A	NM_000260.4	CHR11:76867137G>A	NA	PM2, PP2, PP4, PP3	Pathogenic
3	USH2A	NM_206933.4	CHR1:216498647C>G	NA	PM2, PP1, PP2, PP4	Likely pathogenic
4	BBS12	NM_152618.3	CHR4:123664102A>C	560,429/Likely Pathogenic	PM2, PP1, PP4	Likely Pathogenic
5	ARL6	NM_001278293.3	CHR3:97503891C>T	NA	PM2, PP1, PP4	Likely pathogenic
6	CLN5	NM_006493.2	CHR13:77570131 C>T	NA	PM2, PP1, PP2, PP3, PP4	Likely pathogenic
7	MFSD8/CLN7	NM_001371596.2	CHR4:128854177 A>C	3,294,568/Uncertain significance	PM2, PP1, PP2, PP3, PP4	Likely pathogenic
8	ARL2BP	NM_012106.4	CHR16:57280054 G>T	NA	PM2, PVS1, PP3, PP4, PP1	Pathogenic
9	COL2A1	NM_001844	CHR12.48393747C>T	964,324/Likely Benign	BS1, PP3, PP1, PP4	Likely pathogenic

PM2: Pathogenic moderate 2 [Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium] PVS1: Pathogenic very strong [null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene here LOF is a known mechanism of disease)] PP1:[ Cosegregation with disease in multiple affected family members in a gene definitively known to cause disease] PP2: Pathogenic supporting 2 [Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease] PP3: Pathogenic supporting 3 [Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)] PP4: Pathogenic supporting 4 [Patient's phenotype or family history is highly specific for a disease with a single genetic etiology] BS1: Benign Supporting 1 [Allele frequency is greater than expected for disorder].