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CHEK2
Final classification
VUS
CHEK2 c.715G>A · p.Glu239Lys
CHEK2

The CHEK2 c.715G>A (p.Glu239Lys, p.E239K) variant has been reported in ClinVar with predominantly uncertain significance submissions and one likely pathogenic submission.

Gene
CHEK2
Transcript
NM_007194.3
HGVS · transcript:coding
NM_007194.3:c.715G>A
Consequence
N/A
GRCh38
chr22:28711986 C>T
GRCh37
chr22:29107974 C>T
Basis Hereditary Breast, Ovarian and Pancreatic Cancer Specification v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate; combination = 1 moderate, which maps to VUS.
Hereditary Breast, Ovarian and Pancreatic Cancer Specification v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
CHEK2 c.715G>A

The CHEK2 c.715G>A (p.Glu239Lys, p.E239K) variant has been reported in ClinVar with predominantly uncertain significance submissions and one likely pathogenic submission.1 This variant is present in gnomAD at 0.00849% in v2.1 and 0.01091% in v4.1, with a highest observed subpopulation frequency of 0.03333%, which is below the 0.1% rarity threshold and does not reach BS1 or BA1 population thresholds.2 In a published yeast-based DNA-damage response assay, p.E239K had an intermediate score of 0.58 relative to 1.00 for wild type and 0.00 for a kinase-dead control, which is consistent with partial functional impairment but does not by itself establish a definitive functional criterion strength.3 Computational evidence is mixed: SpliceAI predicts no significant splice impact with a max delta score of 0.00, REVEL is 0.445, and BayesDel is 0.263648, so in silico evidence alone does not clearly support either a damaging or benign computational criterion.4

PM2 VUS
Gene diagram · NM_007194.3 · variants mapped to exon structure
CHEK2 NM_007194.3
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 0.000109053; MAF= 0.01091%, 176/1613900 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 0.000333289; MAF= 0.03333%, 20/60008 alleles, homozygotes = 0); grpmax FAF= 0.00022085.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 8.48794e-05; MAF= 0.00849%, 24/282754 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 0.000319183; MAF= 0.03192%, 8/25064 alleles, homozygotes = 0); grpmax FAF= 0.00011498.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.011% · 176 / 1,613,900
      0 hom · FAF 0.022%
      Admixed American
      20 / 60,008
      0.033%
      European (Finnish)
      15 / 63,940
      0.023%
      European (non-Finnish)
      134 / 1,179,920
      0.011%
      Remaining individuals
      3 / 62,506
      0.0048%
      East Asian
      1 / 44,864
      0.0022%
      South Asian
      2 / 91,078
      0.0022%
      African/African American
      1 / 75,010
      0.0013%
      + 3 not observed (Amish, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0085% · 24 / 282,754
      0 hom · FAF 0.011%
      European (Finnish)
      8 / 25,064
      0.032%
      Admixed American
      9 / 35,436
      0.025%
      European (non-Finnish)
      7 / 129,138
      0.0054%
      + 5 not observed (African/African American, Ashkenazi Jewish, East Asian, Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (17 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as uncertain significance (1 clinical laboratory). (ClinVarID = 5600)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.445. BayesDel score = 0.263648.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CHEK2, an intracellular kinase involved in control of the cell cycle, is altered in various cancer types.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 10 PMIDs not cited in assessment
      12533788 ↗ Mutations in CHEK2 associated with prostate cancer risk. CLINVAR
      16835864 ↗ Characterization of CHEK2 mutations in prostate cancer. CLINVAR
      22419737 ↗ Response to DNA damage of CHEK2 missense mutations in familial breast cancer. CLINVAR
      23298314 ↗ Proteome-wide analysis of amino acid variations that influence protein lysine acetylation. CLINVAR
      25525159 ↗ RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      26506619 ↗ Association of Germline CHEK2 Gene Variants with Risk and Prognosis of Non-Hodgkin Lymphoma. CLINVAR
      28166811 ↗ Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR