ClinVar Miner

Submissions for variant NM_022114.4(PRDM16):c.171C>T (p.Ser57=)

gnomAD frequency: 0.00004  dbSNP: rs369648897
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000615382 SCV000720834 likely benign not specified 2017-06-29 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000872185 SCV001013966 likely benign Left ventricular noncompaction 8 2022-06-13 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358181 SCV001553852 uncertain significance not provided no assertion criteria provided clinical testing The PRDM16 p.Ser57Ser variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs369648897), LOVD 3.0 and in ClinVar (classified as likely benign by GeneDx). The variant was identified in control databases in 23 of 277590 chromosomes at a frequency of 0.000083 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 11 of 19484 chromosomes (freq: 0.000565), South Asian in 6 of 30492 chromosomes (freq: 0.000197), Other in 1 of 7084 chromosomes (freq: 0.000141), African in 2 of 24008 chromosomes (freq: 0.000083) and European (non-Finnish) in 3 of 126116 chromosomes (freq: 0.000024); it was not observed in the Latino, Ashkenazi Jewish, and European (Finnish) populations. The p.Ser57Ser variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence however 3 of 4 in silico or computational prediction software programs (MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 5' splice site. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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