ClinVar Miner

Submissions for variant NM_007194.4(CHEK2):c.47G>A (p.Ser16Asn)

dbSNP: rs1060502705
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000470829 SCV000550497 uncertain significance Familial cancer of breast 2023-05-24 criteria provided, single submitter clinical testing 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. This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 16 of the CHEK2 protein (p.Ser16Asn). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 410038). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated.
Ambry Genetics RCV003278816 SCV004006470 uncertain significance Hereditary cancer-predisposing syndrome 2023-04-18 criteria provided, single submitter clinical testing The p.S16N variant (also known as c.47G>A), located in coding exon 1 of the CHEK2 gene, results from a G to A substitution at nucleotide position 47. The serine at codon 16 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV003278816 SCV004361419 uncertain significance Hereditary cancer-predisposing syndrome 2023-05-08 criteria provided, single submitter clinical testing This missense variant replaces serine with asparagine at codon 16 of the CHEK2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with CHEK2-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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