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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
      Population frequency
      Overall AF
      27 / 1,501,478
      0.0018%
      Highest · South Asian
      0.029%
      Homozygotes
      0
      grpmax FAF
      0.02%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      South Asian 26 / 89,040 0.029% 0
      Admixed American 0 / 59,846
      European (Finnish) 0 / 48,486
      Amish 0 / 912
      East Asian 0 / 44,364
      Middle Eastern 0 / 4,252
      Ashkenazi Jewish 0 / 28,994
      African/African American 0 / 73,012
      European (non-Finnish) 0 / 1,093,508
      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.
      Overall AF
      15 / 233,494
      0.0064%
      Highest · South Asian
      0.049%
      Homozygotes
      0
      grpmax FAF
      0.03%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      South Asian 15 / 30,334 0.049% 0
      African/African American 0 / 14,608
      Admixed American 0 / 34,370
      Ashkenazi Jewish 0 / 9,866
      East Asian 0 / 18,002
      European (Finnish) 0 / 11,758
      European (non-Finnish) 0 / 108,620
      Remaining individuals 0 / 5,936
      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.
      This variant is absent from gnomAD-Canada.
      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