Total submissions: 3
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Ambry Genetics | RCV000166696 | SCV000217504 | uncertain significance | Hereditary cancer-predisposing syndrome | 2014-11-06 | criteria provided, single submitter | clinical testing | The p.V166I variant (also known as c.496G>A), located in coding exon 6 of the PTEN gene, results from a G to A substitution at nucleotide position 496. The valine at codon 166 is replaced by isoleucine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.002% (greater than 51000 alleles tested) in our clinical cohort. This amino acid position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to slightly weaken the efficiency of the native splice acceptor site; however, direct evidence is unavailable. In addition, this alteration is predicted to be possibly damaging by PolyPhen but tolerated by SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of p.V166I remains unclear. |
| Baylor Genetics | RCV003468791 | SCV004206693 | uncertain significance | Glioma susceptibility 2 | 2023-01-23 | criteria provided, single submitter | clinical testing | |
| Lupski Lab, |
RCV000166696 | SCV005402714 | likely benign | Hereditary cancer-predisposing syndrome | 2024-04-12 | criteria provided, single submitter | curation | Each variant was annotated with functional scores from MAVE data which was translated into functional evidence codes. All other evidence codes and combining criteria were adhered to as closely as possible based on the ClinGen VCEP (Variant Curation Expert Panel) gene-specific recommendations. See Supplemental Figure 34 of final paper (Supp Fig. 28 in preprint: doi:10.1101/2024.04.11.24305690) for a table to see which lines of evidence we did not have data for. The ClinGen VCEPs are highly regarded as the gold-standard for gene-specific variant curation and are developed after extensive evaluation of the evidence by clinical and scientific experts for the particular gene to classify genomic variants on a spectrum from pathogenic to benign using the 2015 ACMG/AMP Variant Interpretation Guidelines as a backbone (PMID: 25741868). Reclassification of these VUS variants from gnomAD or All of Us focused only on variants originally prescribed as VUS in ClinVar. To ensure reproducibility, transparency, and increased throughput, all the procedures for annotating variants and assigning evidence codes were codified using Python. All code has been made freely available and is linked in the Code Availability section and all reclassified variants with evidence codes used can be found in Tables S18-19 (preprint: doi:10.1101/2024.04.11.24305690). For the MAVE data, the clinical curation and clinical strength assignment as per the ClinGen recommendations in Brnich et al. (2020) (PMID: 31892348) for or against pathogenicity or benignity of each of these MAVE datasets utilized in this study were previously published in Fayer et al. (2021) (PMID: 34793697).For PTEN, two assays measuring activity and abundance were used. If the abundance was categorized as "wt-like" or "possibly wt-like," BS3_Supporting evidence was used. Furthermore, if the cumulative score was greater than -5, BS3_moderate evidence was used. This variant GRCh37:10:89711878:G>A was assigned evidence codes ['BS3_Supporting', 'BS1_Supporting'] and an overall classification of Likely Benign |