ClinVar Miner

Submissions for variant NM_031885.4(BBS2):c.1864C>T (p.Arg622Ter) (rs201196733)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000424669 SCV000337475 pathogenic not provided 2015-12-08 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000424669 SCV000511629 likely pathogenic not provided 2017-01-05 criteria provided, single submitter clinical testing
Invitae RCV000531316 SCV000636526 pathogenic Bardet-Biedl syndrome 2019-07-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg622*) in the BBS2 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs201196733, ExAC 0.02%). This variant has been reported in individuals affected with Bardet-Biedl syndrome (PMID: 21344540, 26078953). ClinVar contains an entry for this variant (Variation ID: 284737). Loss-of-function variants in BBS2 are known to be pathogenic (PMID: 11285252). For these reasons, this variant has been classified as Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000335732 SCV000916672 pathogenic Bardet-Biedl syndrome 2 2018-03-02 criteria provided, single submitter clinical testing Variant summary: BBS2 c.1864C>T (p.Arg622X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. A truncation downstream of this position has been classified as likely pathogenic by our laboratory, c.2107C>T (p.Arg703X). The variant has been observed with an allele frequency of 2.8e-05 in 246196 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in BBS2 causing Bardet-Biedl Syndrome (2.8e-05 vs. 8.5e-04), allowing no conclusion about variant significance. The variant, c.1864C>T, has been reported in the literature in individuals affected with Bardet-Biedl Syndrome (Bee 2015, Deveault 2011). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) have classified the variant as "likely pathogenic/pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.
Counsyl RCV000335732 SCV000486377 likely pathogenic Bardet-Biedl syndrome 2 2016-11-02 no assertion criteria provided clinical testing

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