ClinVar Miner

Submissions for variant NM_152618.3(BBS12):c.116T>C (p.Ile39Thr)

gnomAD frequency: 0.00430  dbSNP: rs138036823
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000082656 SCV000114698 benign not specified 2013-11-20 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000082656 SCV000246780 benign not specified 2018-09-04 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082656 SCV000316216 benign not specified criteria provided, single submitter clinical testing
Invitae RCV001080843 SCV000558135 benign Bardet-Biedl syndrome 2020-12-08 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000513736 SCV000610341 likely benign not provided 2017-05-09 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000709646 SCV000743646 benign Bardet-Biedl syndrome 1 2014-12-22 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000626298 SCV000746959 uncertain significance Bardet-Biedl syndrome 12 2017-12-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000626298 SCV001305522 likely benign Bardet-Biedl syndrome 12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genome-Nilou Lab RCV000626298 SCV001653381 uncertain significance Bardet-Biedl syndrome 12 2021-05-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000082656 SCV002104097 likely benign not specified 2022-02-22 criteria provided, single submitter clinical testing Variant summary: BBS12 c.116T>C (p.Ile39Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0063 in 251186 control chromosomes in the gnomAD database, including 6 homozygotes. The observed variant frequency is approximately 8 fold of the estimated maximal expected allele frequency for a pathogenic variant in BBS12 causing Bardet-Biedl Syndrome phenotype (0.00076), strongly suggesting that the variant is benign. c.116T>C has been reported in the literature in individuals affected with Bardet-Biedl Syndrome. These report(s) do not provide unequivocal conclusions about association of the variant with Bardet-Biedl Syndrome. At-least one co-occurrence with other pathogenic variant(s) have been reported (BBS12 c.814C>T, p.Arg272*), providing supporting evidence for a benign role (example, Manara_2019). One publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Zaghoul_2010). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as likely benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000709646 SCV000745765 likely benign Bardet-Biedl syndrome 1 2017-04-19 no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000082656 SCV001924835 benign not specified no assertion criteria provided clinical testing
Natera, Inc. RCV000626298 SCV002082474 benign Bardet-Biedl syndrome 12 2019-11-13 no assertion criteria provided clinical testing

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