ClinVar Miner

Submissions for variant NM_004415.4(DSP):c.1140+6T>C (rs534740669)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000419203 SCV000521830 likely benign not specified 2016-08-22 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000786118 SCV000543240 likely benign not provided 2019-02-05 criteria provided, single submitter clinical testing
Stanford Center for Inherited Cardiovascular Disease,Stanford University RCV000786118 SCV000924779 uncertain significance not provided 2016-12-16 no assertion criteria provided provider interpretation c.1140+6T>C, Intron 9 in the DSP gene We have seen this variant in a person with HCM who also had a very likely pathogenic variant in MYBPC3. Given the lack of case data we consider this variant to be of uncertain significance and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The variant has not been reported in the literature. The variant does not change the amino acid sequence of the protein. Per the Invitae report, splicing algorithms suggest that this variant may alter RNA splicing. The variant was reported online in 11 of 60,632 individuals (0.009% MAF) in the Exome Aggregation Consortium Dataset (ExAC;, which currently includes variant calls on ~64,000 unrelated individuals of African, Asian, European, Latino descent. Specifically, the variant was observed in 4 of 4320 individuals of East Asian descent (0.046% MAF), 3 of 33,335 people of non-Finnish European descent (MAF: 0.0045%), 2 of 8,253 people of South Asian descent (MAF: 0.012%), 1 of 5,184 people of African descent (MAF: 0.009%) and 1 of 454 people of other descent (MAF: 0.11%). The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012).

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