Submissions for variant NM_000321.3(RB1):c.501-2A>G

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV003123180	SCV003798832	likely pathogenic	not provided	2023-02-02	criteria provided, single submitter	clinical testing	Observed in an individual with unilateral retinoblastoma (Abouzeid et al., 2007); Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 36497448, 17960112, 27535533)
Ambry Genetics	RCV003294636	SCV003998739	uncertain significance	Hereditary cancer-predisposing syndrome	2023-06-13	criteria provided, single submitter	clinical testing	The c.501-2A>G intronic variant results from an A to G substitution two nucleotides upstream from coding exon 5 in the RB1 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in a transcript predicted to lead to a protein with an in-frame deletion of 13 amino acids. Another alteration impacting this same exon (c.539+1G>A) has been shown to have a similar impact on splicing and has been reported in patients with unilateral retinoblastoma and sarcoma (Ambry internal data; Sánchez F et al. J Med Genet, 2000 Aug;37:615-20; Chai P et al. Exp Eye Res, 2021 Apr;205:108456; Singh J et al. Mol Vis, 2016 Aug;22:1036-47; Personal communication). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp	RCV003626809	SCV004461404	uncertain significance	Retinoblastoma	2023-11-03	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 4 of the RB1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RB1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2428939). Studies have shown that disruption of this splice site results in skipping of exon 5 (loss of 13 amino acid residues), but is expected to preserve the integrity of the reading-frame (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.