ClinVar Miner

Submissions for variant NM_031885.4(BBS2):c.1511C>T (p.Ala504Val) (rs16957538)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000203892 SCV000260909 benign Bardet-Biedl syndrome 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000245072 SCV000314810 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001094290 SCV000398055 benign Bardet-Biedl syndrome 2 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.
Integrated Genetics/Laboratory Corporation of America RCV000086984 SCV000699653 likely benign not provided 2016-01-11 criteria provided, single submitter clinical testing Variant summary: This c.1511C>T variant affects a non-conserved nucleotide, resulting in amino acid change from a small size and hydrophobic residue (A) to medium size and hydrophobic residue (V). 3/4 in-silico tools predict this variant to be benign; however, functional studies have not been carried out to confirm these predictions. This variant is found in 741/121412 control chromosomes (including 19 homozygotes) at a frequency of 0.0061032, which is about 7 times greater than the maximal expected frequency of a pathogenic BBS2 allele (0.0008452), suggesting this variant is benign. It was found to co-occur in patients with 2 pathogenic variants in the BBS1 gene, and did not co-segregate in a manner consistent with BBS (Mykytyn_2003). This finding is consistent with its co-occurrence with two confirmed pathogenic BBS1 variants (p.M390R and c.607delA) in a subject tested in our laboratory. This variant has also been reported in patients with thrombosis mechanistic phenotype; however, it was not significantly associated with increased odds ratio (Mosley_2013). There are no functional studies reported for this variant. A digenic and tri-allelic locus interactions have been reported in patients with BBS. This variant's role in such interaction and whether this variant plays a modifier role for another pathogenic variant has not been fully explored. The variant has not been reported in reputable databases. Based on currently available information this variant has been classified as Likely Benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000709639 SCV000743749 benign Bardet-Biedl syndrome 1 2014-12-23 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000709639 SCV000745153 benign Bardet-Biedl syndrome 1 2015-09-21 criteria provided, single submitter clinical testing
NEI Ophthalmic Genomics Laboratory,National Institutes of Health RCV000086984 SCV000119237 not provided not provided no assertion provided not provided

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