ClinVar Genomic variation as it relates to human health

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Variant summary: CHEK2 c.1336A>G (p.Asn446Asp) results in a conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 7.5e-05 in 253306 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in CHEK2 causing Hereditary Breast and Ovarian Cancer (7.5e-05 vs 0.00031), allowing no conclusion about variant significance. The variant was reported in breast cancer, colorectal cancer or Non-Hodgkin Lymphoma patients, without strong evidence for causality (Kraus 2016, Havranek 2015, Pearlman 2016), and was also found in healthy controls (Le Calvez-Kelm 2011). These reports however, do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Co-occurrence with another likely pathogenic variant has been reported in an internal sample (APC c.4873delC, p.Gln1625fsX25). In an in vivo, yeast based functional assay, the variant was classified as benign (Delimitsou_2019). Six other ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign until additional evidence becomes available.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 446 of the CHEK2 protein (p.Asn446Asp). This variant is present in population databases (rs121908705, gnomAD 0.03%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with breast cancer, non-Hodgkin lymphoma, and/or rectal cancer (PMID: 26506619, 27616075, 27978560, 34326862). ClinVar contains an entry for this variant (Variation ID: 126909). 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. Experimental studies have shown that this missense change does not substantially affect CHEK2 function (PMID: 30851065, 34903604). 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.

Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with breast cancer, rectal cancer, or lymphoma and in unaffected controls (Le Calvez-Kelm 2011, Havranek 2015, Kraus 2016, Pearlman 2017); Published functional study demonstrates no damaging effect: normal cell growth after MMS-induced DNA damage (Delimitsou 2019); This variant is associated with the following publications: (PMID: 26506619, 21244692, 27978560, 27616075, 26787654, 28873162, 29596542, 30851065, 31398194, 31422574, 19782031, 22419737, 34903604)

The CHEK2 p.Asn446Asp variant was identified in 3 of 10018 proband chromosomes (frequency: 0.0003) from individuals or families with Non-Hodgkin Lymphoma, breast cancer and colorectal cancer (Havranek 2015, Kraus 2017, Le Calvez-Kelm 2011, Pearlman 2017) and was present in 1 of 3208 control chromosomes (frequency: 0.0003) from healthy individuals (Havranek 2015, Le Calvez-Kelm 2011).The variant was also identified in dbSNP (ID: rs121908705) as With Uncertain significance allele, ClinVar (classified as uncertain significance by GeneDx, Invitae, Color Genomics, Ambry Genetics and 3 clinical laboratories), Clinvitae (classified as uncertain significance by Clinvar and Invitae), MutDB, databases. The variant was not identified in Cosmic, Zhejiang Colon Cancer Database, databases. The variant was identified in control databases in 19 of 276858 chromosomes at a frequency of 0.000069 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include European Non-Finnish in 9 of 126372 chromosomes (freq: 0.0001), and South Asian in 10 of 30776 chromosomes (freq: 0.0003), while the variant was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, populations. The p.Asn446 residue is conserved in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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.