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CHEK2
Final classification
VUS
CHEK2 c.1376-23G>C · p.?
CHEK2

NM_007194.4:c.1376-23G>C is a deep intronic variant in CHEK2 intron 12, located 23 bases upstream of exon 13.

Gene
CHEK2
Transcript
NM_007194.4
HGVS · transcript:coding
NM_007194.4:c.1376-23G>C
Consequence
N/A
GRCh38
chr22:28694140 C>G
GRCh37
chr22:29090128 C>G
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 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CHEK2 c.1376-23G>C

NM_007194.4:c.1376-23G>C is a deep intronic variant in CHEK2 intron 12, located 23 bases upstream of exon 13. This variant is present at extremely low frequency in population databases: gnomAD v2.1 allele frequency = 0.0064% (15/233,494 alleles) and gnomAD v4.1 allele frequency = 0.0018% (27/1,501,478 alleles), with all observations restricted to the South Asian population and no homozygotes observed (PM2_Supporting).1 Computational splicing analysis with SpliceAI predicts no impact on splicing (max delta score = 0.00; all four delta scores for acceptor gain, acceptor loss, donor gain, and donor loss are 0.00), consistent with a benign computational profile (BP4_Supporting).2 The variant does not fall into any PVS1 null-variant category (not a nonsense, frameshift, or canonical splice variant), and SpliceAI confirms no predicted cryptic splice alteration.3 No functional studies, segregation data, de novo observations, case-control data, or ClinVar classifications are available for this variant. Applying the generic ACMG/AMP 2015 final combination rules (PMID:25741868), the evidence profile consists of one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4). With only one supporting criterion on each side, the evidence is indeterminate, resulting in a classification of Variant of Uncertain Significance (VUS).4

PM2 + BP4 VUS
3 pvs1_variant_assessmentspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_007194.4 · variants mapped to exon structure
CHEK2 NM_007194.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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= 1.79823e-05; MAF= 0.00180%, 27/1501478 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000292004; MAF= 0.02920%, 26/89040 alleles, homozygotes = 0); grpmax FAF= 0.00020457.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 6.42415e-05; MAF= 0.00642%, 15/233494 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000494495; MAF= 0.04945%, 15/30334 alleles, homozygotes = 0); grpmax FAF= 0.00030425.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0018% · 27 / 1,501,478
      0 hom · FAF 0.02%
      South Asian
      26 / 89,040
      0.029%
      Remaining individuals
      1 / 59,064
      0.0017%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.0064% · 15 / 233,494
      0 hom · FAF 0.03%
      South Asian
      15 / 30,334
      0.049%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      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
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC