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CHEK2
Final classification
Likely Benign
CHEK2 c.1095+19G>A · p.?
CHEK2

NM_007194.4:c.1095+19G>A is an intronic variant in CHEK2 located at position +19 in intron 10.

Gene
CHEK2
Transcript
NM_007194.4
HGVS · transcript:coding
NM_007194.4:c.1095+19G>A
Consequence
N/A
GRCh38
chr22:28696882 C>T
GRCh37
chr22:29092870 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: BS2 supporting, BP4 supporting, BP6 supporting; combination = 3 supporting benign, which maps to Likely Benign.
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: BS2 supporting, BP4 supporting, BP6 supporting; combination = 3 supporting benign, which maps to Likely Benign.
Classification rationale
BS2BP4BP6 Likely Benign
CHEK2 c.1095+19G>A

NM_007194.4:c.1095+19G>A is an intronic variant in CHEK2 located at position +19 in intron 10. Computational evidence predicts no splicing impact: SpliceAI maximum delta score is 0.00 across all categories, consistent with a neutral intronic change (BP4_Supporting).1 A homozygous individual for this variant is observed in gnomAD v4.1, which is inconsistent with a highly penetrant autosomal dominant cancer predisposition variant (BS2_Supporting).2 ClinVar reports this variant as Likely benign by 9 clinical laboratories and Benign by 3 clinical laboratories (Variation ID: 371849), providing reputable source support for a benign interpretation (BP6_Supporting).3 The variant is observed at population frequencies of 0.017% (gnomAD v2.1) and 0.012% (gnomAD v4.1) with the highest subpopulation frequency of 0.237% in the Middle Eastern population (gnomAD v4.1), which approaches but does not exceed the BS1 threshold of 0.3%.4 No functional studies, segregation data, case-control enrichment, or variant-specific publications were identified for this variant. Three benign supporting criteria (BP4, BP6, BS2) are met. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two or more benign supporting criteria support a Likely Benign classification.5

BS2 + BP4 + BP6 Likely Benign
Gene diagram · NM_007194.4 · variants mapped to exon structure
CHEK2 NM_007194.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports benign
      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= 0.000120585; MAF= 0.01206%, 186/1542484 alleles, homozygotes = 1) and has highest observed frequency in the Middle Eastern population (AF= 0.00236887; MAF= 0.23689%, 14/5910 alleles, homozygotes = 0); grpmax FAF= 0.0014315.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000166616; MAF= 0.01666%, 47/282086 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.00094827; MAF= 0.09483%, 29/30582 alleles, homozygotes = 0); grpmax FAF= 0.00067758.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.012% · 186 / 1,542,484
      1 hom · FAF 0.14%
      Middle Eastern
      14 / 5,910
      0.24%
      South Asian
      81 / 89,542
      0.09%
      1 hom
      Remaining individuals
      10 / 60,092
      0.017%
      African/African American
      7 / 73,590
      0.0095%
      European (non-Finnish)
      72 / 1,115,072
      0.0065%
      Admixed American
      2 / 59,900
      0.0033%
      + 4 not observed (European (Finnish), Amish, East Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.017% · 47 / 282,086
      0 hom · FAF 0.068%
      South Asian
      29 / 30,582
      0.095%
      Remaining individuals
      3 / 7,190
      0.042%
      African/African American
      4 / 24,906
      0.016%
      European (non-Finnish)
      9 / 128,796
      0.007%
      Admixed American
      2 / 35,374
      0.0057%
      + 3 not observed (Ashkenazi Jewish, East Asian, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (9 clinical laboratories) and as Benign (3 clinical laboratories). (ClinVarID = 371849)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 7 PMIDs not cited in assessment
      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
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
      35802134 ↗ ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      40440438 ↗ CHEK2-Related Cancer Predisposition. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR