ClinVar Miner

Submissions for variant NM_031885.5(BBS2):c.471G>A (p.Thr157=)

gnomAD frequency: 0.00001  dbSNP: rs749983428
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667073 SCV000791467 uncertain significance Bardet-Biedl syndrome 2 2017-05-16 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV000667073 SCV002073110 uncertain significance Bardet-Biedl syndrome 2 criteria provided, single submitter clinical testing The synonymous variant p.T157= in BBS2 (NM_031885.5) has been previously reported in an individual with retinis pigmentosa (Wang F et al). The variant has been submitted to ClinVar as Uncertain significance.The p.T157= variant is observed in 1/30,612 (0.0033%) alleles from individuals of South Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The variant affects an invariant splice nucleotide and hence may affect splicing. The p.T157= variant is predicted to disrupt splicing by 3 of 4 splice site algorithms. Since the variant is a synonymous change it is classified as Uncertain Significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV002532060 SCV003443601 likely pathogenic Bardet-Biedl syndrome 2023-03-14 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 551904). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. This sequence change affects codon 157 of the BBS2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the BBS2 protein. This variant also falls at the last nucleotide of exon 3, which is part of the consensus splice site for this exon. This variant is present in population databases (rs749983428, gnomAD 0.003%). This variant has been observed in individuals with Bardet-Biedl syndrome and/or retinitis pigmentosa (PMID: 24154662, 29588463; Invitae).
Baylor Genetics RCV000667073 SCV004214015 likely pathogenic Bardet-Biedl syndrome 2 2024-03-27 criteria provided, single submitter clinical testing

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