ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.11044+5C>T

gnomAD frequency: 0.00003  dbSNP: rs764708878
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000813050 SCV000953387 uncertain significance Cohen syndrome 2024-10-18 criteria provided, single submitter clinical testing This sequence change falls in intron 57 of the VPS13B gene. It does not directly change the encoded amino acid sequence of the VPS13B protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs764708878, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 656595). 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 is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV002298782 SCV002588037 uncertain significance not provided 2022-04-21 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002453843 SCV002738674 uncertain significance Inborn genetic diseases 2022-06-30 criteria provided, single submitter clinical testing The c.11119+5C>T intronic alteration consists of a C to T substitution nucleotides after coding exon 56 in the VPS13B gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV000813050 SCV005051997 pathogenic Cohen syndrome 2024-02-01 criteria provided, single submitter curation
Breakthrough Genomics, Breakthrough Genomics RCV002298782 SCV005196068 uncertain significance not provided criteria provided, single submitter not provided
Natera, Inc. RCV000813050 SCV001462034 uncertain significance Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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