ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.920+5G>A (rs587780013)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000588193 SCV000149514 uncertain significance not provided 2014-06-27 criteria provided, single submitter clinical testing This variant is denoted STK11 IVS7+5G>A or c.920+5G>A and consists of a G>A nucleotide substitution at the +5 position of intron 7 of the STK11 gene. Multiple in silico models predict this variant to weaken the nearby natural donor site, and to possibly cause abnormal gene splicing. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. STK11 c.920+5G>A was not observed at significant allele frequency in the NHLBI Exome Sequencing Project. STK11 c.920+5G>A occurs at a position that is fully conserved across species. Based on the currently available information, we consider STK11 c.920+5G>A to be a variant of uncertain significance.
Ambry Genetics RCV000115605 SCV000186855 likely benign Hereditary cancer-predisposing syndrome 2019-10-08 criteria provided, single submitter clinical testing RNA Studies;Other data supporting benign classification
Invitae RCV000204699 SCV000261739 uncertain significance Peutz-Jeghers syndrome 2018-12-26 criteria provided, single submitter clinical testing This sequence change falls in intron 7 of the STK11 gene. It does not directly change the encoded amino acid sequence of the STK11 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs587780013, ExAC 0.05%). This variant has not been reported in the literature in individuals with an STK11-related disease. ClinVar contains an entry for this variant (Variation ID: 127709). Nucleotide substitutions within the consensus splice site are relatively common causes 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, but this prediction has not been confirmed by published transcriptional studies. In summary, this variant has uncertain impact on STK11 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000213026 SCV000602241 uncertain significance not specified 2017-03-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588193 SCV000696732 uncertain significance not provided 2015-10-16 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000213026 SCV000712641 uncertain significance not specified 2016-11-23 criteria provided, single submitter clinical testing The c.920+5G>A variant in STK11 has not been previously reported in individuals with Peutz-Jeghers syndrome, but has been identified in 1/2138 of African chromo somes by the Exome Aggregation Consortium (ExAC,; dbSNP rs587780013). This variant is located in the 5' splice region. Although n ucleotide substitutions at +5 position of the intron are relatively common cause s of aberrant splicing, computational tools do not suggest an impact to splicing . However, this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of the c.920+5G>A variant is uncertain.
Counsyl RCV000204699 SCV000784862 uncertain significance Peutz-Jeghers syndrome 2017-01-20 criteria provided, single submitter clinical testing
Mendelics RCV000204699 SCV000839422 uncertain significance Peutz-Jeghers syndrome 2018-07-02 criteria provided, single submitter clinical testing
Color RCV000115605 SCV000910053 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-30 criteria provided, single submitter clinical testing

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