ClinVar Miner

Submissions for variant NM_024649.5(BBS1):c.159+2del

dbSNP: rs1348187150
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002045926 SCV002304900 likely pathogenic Bardet-Biedl syndrome 2022-06-08 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with BBS1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change affects a splice site in intron 3 of the BBS1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BBS1 are known to be pathogenic (PMID: 12118255, 21520335, 27032803).
Baylor Genetics RCV003464390 SCV004217393 likely pathogenic Bardet-Biedl syndrome 1 2023-03-21 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004744211 SCV005351500 likely pathogenic BBS1-related disorder 2024-04-05 no assertion criteria provided clinical testing The BBS1 c.159+2delT variant is predicted to result in a deletion affecting a canonical splice site. This variant is predicted to interfere with splicing at the consensus donor site based on splicing prediction programs (SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751). This variant was documented in a study assessing the carrier frequency of autosomal recessive inherited retinal diseases (Table S3 in Hanany et al. 2020. PubMed ID: 31964843). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD and has been interpreted as likely pathogenic by submitters in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/1513499/). This variant is interpreted as likely pathogenic.

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