ClinVar Miner

Submissions for variant NM_207122.2(EXT2):c.889C>T (p.Arg297Cys)

gnomAD frequency: 0.00014  dbSNP: rs146098187
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001102609 SCV001259294 benign Exostoses, multiple, type 2 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV001102609 SCV001659272 likely benign Exostoses, multiple, type 2 2024-01-25 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003396747 SCV004112399 uncertain significance EXT2-related condition 2023-03-02 criteria provided, single submitter clinical testing The EXT2 c.889C>T variant is predicted to result in the amino acid substitution p.Arg297Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.12% of alleles in individuals of Ashkenazi Jewish descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-44146484-C-T). A different variant affecting the same amino acid (p.Arg297His) was reported in one individual with multiple osteochondromas (Table 1, Ishimaru. 2016. PubMed ID: 26961984). In CalinVar, this variant is interpreted as benign/likely benign (https://preview.ncbi.nlm.nih.gov/clinvar/variation/877127/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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