Total submissions: 2
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Invitae | RCV001314252 | SCV001504777 | uncertain significance | not provided | 2020-12-10 | criteria provided, single submitter | clinical testing | This sequence change deletes 3 nucleotides from exon 11 of the RINT1 mRNA (c.1671_1671+2delTGT), corresponding to the last nucleotide of exon 11 and the donor splice site in intron 11. 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. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in RINT1 cause disease. Nucleotide substitutions at the last nucleotide of the exon and donor splice site in the intron are relatively common causes of aberrant splicing (PMID: 17576681). However, according to multiple splice site algorithms this variant does not result in a significant splicing alteration. An adjacent GT dinucleotide (c.1669_1670) has the potential to serve as a new donor splice site that, if used, would result in an in-frame deletion of Val557. There is also the possibility that this alternate site is not used, which may result in aberrant splicing. Neither of these predictions has been confirmed by published functional studies. This variant has not been reported in the literature in individuals with RINT1-related disease. ClinVar contains an entry for this variant (Variation ID: 224920). This variant is present in population databases (rs774457611, ExAC 0.01%). |
| Ambry Genetics | RCV002390565 | SCV002703081 | uncertain significance | Hereditary cancer-predisposing syndrome | 2021-09-22 | criteria provided, single submitter | clinical testing | The c.1671_1671+2delTGT variant results from a deletion of three nucleotides between positions 1671 and 1671+2 and involves the canonical splice donor site after coding exon 11 of the RINT1 gene. The canonical splice donor site is well conserved through mammals. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. However, the gene-disease association for RINT1 is limited. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. |