ClinVar Miner

Submissions for variant NM_024685.4(BBS10):c.1631A>G (p.Asn544Ser)

gnomAD frequency: 0.00618  dbSNP: rs34737974
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000152824 SCV000202220 benign not specified 2014-04-25 criteria provided, single submitter clinical testing
Invitae RCV001084157 SCV000261859 benign Bardet-Biedl syndrome 2021-12-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000152824 SCV000314383 likely benign not specified criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000438509 SCV000511659 likely benign not provided 2016-09-15 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000152824 SCV000699621 benign not specified 2021-09-03 criteria provided, single submitter clinical testing Variant summary: BBS10 c.1631A>G (p.Asn544Ser) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function and Asn544 is not located in a known functional domain of the Bardet-Biedl syndrome 10 protein. A functional study is consistent with the finding that this variant is a functional polymorphism (Zaghloul_2010) as the mutant was unable to rescue the morphant phenotype in zebrafish. The variant allele was found at a frequency of 0.0076 in 251414 control chromosomes, predominantly at a frequency of 0.016 within the South Asian subpopulation in the gnomAD database, including 6 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 13 fold of the estimated maximal expected allele frequency for a pathogenic variant in BBS10 causing Bardet-Biedl Syndrome phenotype (0.0012), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. Three ClinVar submitters (evaluation after 2014) cite the variant as benign (n=2) and likely benign (n=1). Based on the evidence outlined above, the variant was classified as benign.
Illumina Laboratory Services,Illumina RCV001112169 SCV001269805 benign Bardet-Biedl syndrome 10 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.
Genetic Services Laboratory,University of Chicago RCV000152824 SCV002068424 likely benign not specified 2018-05-11 criteria provided, single submitter clinical testing
Natera, Inc. RCV001112169 SCV002091752 benign Bardet-Biedl syndrome 10 2019-12-09 no assertion criteria provided clinical testing

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