chr22-28725372-A-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6BS2_Supporting
The NM_007194.4(CHEK2):c.320-5T>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000579 in 1,614,106 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_007194.4 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- CHEK2-related cancer predispositionInheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
- hereditary breast carcinomaInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
- Li-Fraumeni syndrome 2Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
- acute myeloid leukemiaInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- hereditary nonpolyposis colon cancerInheritance: AD Classification: LIMITED Submitted by: ClinGen
- familial ovarian cancerInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CHEK2 | NM_007194.4 | c.320-5T>A | splice_region_variant, intron_variant | Intron 2 of 14 | ENST00000404276.6 | NP_009125.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CHEK2 | ENST00000404276.6 | c.320-5T>A | splice_region_variant, intron_variant | Intron 2 of 14 | 1 | NM_007194.4 | ENSP00000385747.1 |
Frequencies
GnomAD3 genomes 0.000663 AC: 101AN: 152224Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000570 AC: 143AN: 250794 AF XY: 0.000553 show subpopulations
GnomAD4 exome AF: 0.000570 AC: 833AN: 1461764Hom.: 1 Cov.: 32 AF XY: 0.000569 AC XY: 414AN XY: 727184 show subpopulations
Age Distribution
GnomAD4 genome 0.000663 AC: 101AN: 152342Hom.: 1 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74500 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1Benign:4
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.
CHEK2 c.320-5T>A is an intronic variant located close to a canonical splice site. This variant is found in 142/267712 alleles at a frequency of 0.043% in the gnomAD v2.1.1 database, non-cancer dataset. The SpliceAI algorithm predicts no significant impact on splicing . Functional RNA studies (PMID: 32906215, PMID: 27616075) showed an in-frame transcript lacking exons 3 and 4 (r.320_592del; p.Glu107Lys197del). The proportion of transcripts suggested that the variant allele also produces full-length transcript, although no tag-SNP was available to confirm it. CHEK2 c.320-5T>A was identified in individuals affected with breast cancer, colorectal cancer, pancreatic cancer, ovarian cancer and Hodgkin lymphoma (PMID: 18058223, 18996005, 20643596, 21744992, 27067391,27616075, 38075173). This variant has been reported in the ClinVar database (1x pathogenic, 5x uncertain significance, 11x likely benign, 4x benign) and in LOVD (4x uncertain significance, 2x likely benign). Based on currently available information, the variant c.320-5T>A should be considered an uncertain significance variant according to ACMG/AMP classification guidelines.
not provided Uncertain:1Benign:3Other:1
The CHEK2 c.320-5T>A variant was identified in 40 of 33888 proband chromosomes (frequency: 0.001) from individuals or families with breast, ovarian, pancreatic, and colon cancer, as well as non-Hodkin lymphoma and the variant was present in 1 of 10976 control chromosomes (frequency: 0.00009) from healthy individuals (Decker 2017, Havranek 2015, Mucaki 2016, Yurgelun 2015, Kraus 2017, Kleibl 2008, Kleibl 2009, Mohelnikova-Duchonova 2010). The variant was also identified in dbSNP (ID: rs121980700) as “With uncertain significance”. The variant was also identified in ClinVar (as benign by Invitae, likely benign by University of Washington, LabCorp, and Ambry and uncertain significance by Quest, ARUP and Gene Dx). The variant was not identified in Cosmic, MutDB or Zhejiang University databases. The variant was identified in control databases in 151 of 276520 chromosomes (1 homozygous) at a frequency of 0.0005 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 6 of 6458 chromosomes (freq: 0.009), Latino in 33 of 34412 chromosomes (freq: 0.001), European Non-Finnish in 71 of 126074 chromosomes (freq: 0.0006), Ashkenazi Jewish in 40 of 10146 chromosomes (freq: 0.004), and South Asian in 1 of 30776 chromosomes (freq: 0.00003). The variant was not observed in the African, East Asian, or Finnish populations. The c.320-5T>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. Reverse transcription PCR analysis on blood from an individual with breast or ovarian cancer demonstrated that this variant leads to an in frame transcript lacking exon 3 and 4; however the shortened transcript was present at levels less than 20% that of the wild-type transcript suggesting that this variant does not abolish normal splicing (Kraus, 2017). However, 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In addition the variant was identified as co-occurring with a pathogenic BRCA2 variant (c.5857G>T, p.Glu1953X) by our laboratory in an affected individual, indicating that the variant c.320-5T>A may not have clinical significance. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Patient RNA studies demonstrate aberrant splicing resulting in an in-frame transcript lacking exons 3 and 4 present at approximately 20%, as well as full-length transcript (Kraus 2017, Vargas-Parra 2020); In-silico analysis is inconclusive as to whether the variant alters gene splicing; Also known as IVS1-5T>A; This variant is associated with the following publications: (PMID: 18058223, 20643596, 21744992, 25980754, 24549055, 18996005, 27067391, 27616075, 27621404, 26506619, 29596542, 25186627, 30306255, 31422574, 28779002, 30374176, 29337092, 32906215)
The CHEK2 c.320-5T>A variant has been described in the literature in individuals affected with different cancers, including breast and/or ovarian cancer, Hodgkin lymphoma, and colorectal cancer (Castera 2014, Hampel 2018, Havranek 2011, Kleibl 2008, Kleibl 2009, Kraus 2017, Tung 2015). However, several affected individuals with this variant were found to carry an additional pathogenic variant (Hampel 2018, Tung 2015). The c.320-5T>A variant is found in the general population with an overall allele frequency of 0.05% (152/282198 alleles, including one homozygote) in the Genome Aggregation Database, including an increased frequency of 0.37% (38/10362 alleles) in the Ashkenazi Jewish population. This is an intronic variant in a moderately conserved nucleotide, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical acceptor splice site. Functional analyses of patient RNAs show exon skipping in a small minority of transcripts (Casadei 2019, Kraus 2017); however, it is unclear that these splicing alterations are clinically significant. While existing evidence suggests this variant is unlikely to cause disease in all carriers, given the possibility of a low penetrance effect, the clinical significance of the c.320-5T>A variant is uncertain at this time. References: Casadei S et al. Characterization of splice-altering mutations in inherited predisposition to cancer. Proc Natl Acad Sci U S A. 2019;116(52):26798-26807. Castera L et al. Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes. Eur J Hum Genet. 2014 Nov;22(11):1305-13. Hampel H et al. Assessment of Tumor Sequencing as a Replacement for Lynch Syndrome Screening and Current Molecular Tests for Patients With Colorectal Cancer. JAMA Oncol. 2018;4(6):806-813. Havranek O et al. Alterations of CHEK2 forkhead-associated domain increase the risk of Hodgkin lymphoma. Neoplasma. 2011;58(5):392-5. Kleibl Z et al. Analysis of CHEK2 FHA domain in Czech patients with sporadic breast cancer revealed distinct rare genetic alterations. Breast Cancer Res Treat. 2008 Nov;112(1):159-64. Kleibl Z et al. The CHEK2 gene I157T mutation and other alterations in its proximity increase the risk of sporadic colorectal cancer in the Czech population. Eur J Cancer. 2009 Mar;45(4):618-24. Kraus C et al. Gene panel sequencing in familial breast/ovarian cancer patients identifies multiple novel mutations also in genes others than BRCA1/2. Int J Cancer. 2017;140(1):95-102. Mucaki EJ et al. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics. 2016 Apr 11;9:19. Tung N et al. Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Cancer. 2015;121(1):25-33.
CHEK2: BP4, BS1
Familial cancer of breast Uncertain:1Benign:3
The CHEK2 variant designated as NM_007194.3:c.320-5T>A is classified as likely benign. Cosegregation analysis of one observed family was performed using analyze.myvariant.org (Rañola et al, 2018, PMID:28965303) and shows a likelihood ratio of 1.38 to 1 (Thompson, et al., 2003, PMID:12900794). This likelihood ratio indicates weak evidence that the allele co-segregates disease in this family. However, RNA studies in two individuals unrelated from different families show no significant change in RNA splicing or protein transcripts, thus providing strong evidence that this variant does not alter the CHEK2 protein. This variant has been classified as likely benign by other laboratories (ClinVar Variation ID: 128070). Bayesian analysis integrating all of this data (Tavtigian et al, 2018, PMID:29300386) gives less than 1% probability of pathogenicity, which is consistent with a classification of likely benign. This variant is not predicted to alter CHEK2 function or modify cancer risk. This reclassification analysis was performed in conjunction with the family studies project as part of the University of Washington Find My Variant Study.
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].
This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com.
not specified Benign:4
Variant summary: CHEK2 c.320-5T>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict the variant slightly weakens a 3 acceptor site. An in silico analysis also predicted the variant to result in a reduced splicing efficiency that could activate pre-existing cryptic acceptor 92 nucleotide upstream of the natural site, leading to the inclusion of 92 nucleotide of the intron. However this effect was predicted to be partial, with the variant mRNA relatively less abundant compared to the wild type (Mucaki 2016). Two publications reported experimental evidence evaluating splicing impact: one identified an in frame transcript variant lacking exon 3 and 4, however, the amount of the shortened transcript compared to wild type was less than 20%, suggesting that this variant reduces but does not eliminate the usage of the consensus splice acceptor and can therefore be regarded as a hypomorphic allele (Kraus 2017); whereas the other study reported splice analysis from 2 patients showing no significant change in RNA splicing, however without providing experimental evidence (Tsai 2018). The variant allele was found at a frequency of 0.00053 in 288862 control chromosomes (gnomAD and publication data), including 1 homozygote. The observed variant frequency is approximately 1.7 fold of the estimated maximal expected allele frequency for a pathogenic variant in CHEK2 causing Breast Cancer phenotype (0.00031), strongly suggesting that the variant is benign. In addition, this variant has been reported in 10/9884 American women who are older than age 70 and cancer free (FLOSSIES database). c.320-5T>A has been reported in the literature in individuals affected with various tumor phenotypes, including breast-/ovarian-, colorectal- and pancreas cancer, non-Hodgkin lymphoma and Lynch syndrome (Kleibl 2008, Kleibl 2009, Mohelnikova-Duchonova 2010, Havranek 2015, Castera 2014, Tung 2015, Yurgelun 2015, Kraus 2017, Decker 2017, Bonache 2018, Hampel 2018). These reports however do not provide unequivocal conclusions about association of the variant with Breast Cancer. In addition, in two of these patients co-occurrences with other pathogenic variants have been reported (CHEK2 exon 2 deletion, Tung 2015; MLH1 c.1381A>T/K461X, Hampel 2018), providing supporting evidence for a benign role. Though one case-control study suggested that the variant might be associated with breast cancer, the carrier frequency in healthy controls recruited in this study was much lower than observed in population datasets, therefore this postulation might be the result of sampling error (Decker 2017). Nine other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (6 calling it a VUS, 2 classifying as likely benign, and 1 as benign). Based on the evidence outlined above, the variant was classified as benign.
Familial cancer of breast;C5882668:CHEK2-related cancer predisposition Pathogenic:1
CHEK2-related disorder Uncertain:1
The CHEK2 c.320-5T>A variant is predicted to interfere with splicing. This variant has been reported in individuals with breast and colorectal cancer and Hodgkin lymphoma (Kleibl et al. 2008. PubMed ID: 18058223; Kleibl et al. 2009. PubMed ID: 18996005; Havranek et al. 2011. PubMed ID: 21744992). RNA studies on blood from a patient carrying this variant identified a novel CHEK2 transcript with in-frame omission of exons 3 and 4. However, this transcript was detected at a level <20% of normal, prompting the authors to conclude it may be a hypomorphic allele (Kraus et al. 2017. PubMed ID: 27616075). This variant is reported in 0.37% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant has also been reported in ClinVar with conflicting interpretations from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/128070/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Breast and/or ovarian cancer Uncertain:1
Hereditary cancer Benign:1
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at