ClinVar Genomic variation as it relates to human health

Observed in individuals with breast, endometrial, or ovarian cancer, but also in unaffected controls (PMID: 25186627, 27443514, 32546565, 31206626, 33471991, 34326862, 38061684); Published functional studies suggest no damaging effect: normal cell growth after exposure to DNA damage, and KAP1 and CHK2 kinase activity in the wild-type range in vitro (PMID: 30851065, 37449874); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27443514, 25186627, 32546565, 31398194, 32906215, 25085752, 37216304, 34326862, 31206626, 33471991, 38061684, 30851065, 37449874, 22419737, 19782031)

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].

Variant summary: CHEK2 c.1489G>A (p.Asp497Asn) results in a conservative amino acid change in 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 0.00024 in 233606 control chromosomes, predominantly at a frequency of 0.0009 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Hereditary Breast and Ovarian Cancer phenotype (0.00031), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. This variant has also been reported among women who are cancer free and older than age 70 (FLOSSIES database). c.1489G>A has been reported in the literature in individuals undergoing clinical genetic testing for breast cancer (example, Tung_2015, Vargas-Parra_2020), endometrial carcinoma (Ring_2016), and has also been reported in both cancer cohorts and control groups (Weitzel_2019, Dorling_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant based on a yeast based assay (Delimitsou_2019). The following publications have been ascertained in the context of this evaluation (PMID: 30851065, 27443514, 25186627, 32906215, 31206626, 33471991). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 (likely benign, n=5; VUS, n=3). Based on the evidence outlined above, the variant was classified as likely benign.

The CHEK2 c.1489G>A variant is predicted to result in the amino acid substitution p.Asp497Asn. This variant has been reported in an individual with endometrial cancer who also had other variants of uncertain significance (Ring et al. 2016. PubMed ID: 27443514, Supplemental Table 2, Study ID: 05-212), in an individual with breast cancer (Tung et al. 2015. PubMed ID: 25186627, supporting information 2), and in an individual with undefined hereditary cancer from a large cohort (Vargas-Parra. 2020. PubMed ID: 32906215). This variant is reported in 0.088% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/22-29085176-C-T) and has conflicting interpretations in ClinVar, ranging from likely benign to a variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/142445/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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.

According to the ACMG SVI adaptation criteria we chose these criteria: BP4 (supporting benign): spliceAI: CHEK2: 0.0, REVEL: 0.036, BS1 (strong benign): gnomAD v2.1.1 FAF Exom >0,05%, BS3 (strong benign): Delimitsou 2018/Stolarova 2023: benign

BP4

The CHEK2 p.Asp497Asn variant was not identified in the literature nor was it identified in the Cosmic and MutDB. The variant was identified in dbSNP (ID: rs143965148) as “With other allele”, ClinVar (classified as likely benign by Ambry Genetics, Invitae and Laboratory Corporation of America, and uncertain significance by GeneDx and Counsyl), Clinvitae (3x), Zhejiang University Database (1x), and in control databases in 57 of 260048 chromosomes at a frequency of 0.0002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 9 of 22562 chromosomes (freq: 0.0004), Other in 5 of 6274 chromosomes (freq: 0.0008), Latino in 32 of 34204 chromosomes (freq: 0.0009), European Non-Finnish in 7 of 121964 chromosomes (freq: 0.00006), Ashkenazi Jewish in 4 of 9954 chromosomes (freq: 0.0004); it was not observed in the East Asian, Finnish, and South Asian populations. The p.Asp497 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact of the variant Asn to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of 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.