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CHEK2
Final classification
Likely Pathogenic
CHEK2 c.1375+2T>G · p.?
CHEK2

The variant affects the canonical +2 donor position of CHEK2 and is expected to disrupt normal splicing, which supports PVS1 in a loss-of-function disease mechanism context.

Gene
CHEK2
Transcript
NM_007194.4
HGVS · transcript:coding
NM_007194.4:c.1375+2T>G
Consequence
N/A
GRCh38
chr22:28695125 A>C
GRCh37
chr22:29091113 A>C
Basis ACMG/AMP with CHEK2 VCEP framework context; applied criteria PVS1_VeryStrong + PM2_Supporting
ACMG/AMP with CHEK2 VCEP framework context; applied criteria PVS1_VeryStrong + PM2_Supporting
Classification rationale
PVS1PM2 Likely Pathogenic
CHEK2 c.1375+2T>G

The variant affects the canonical +2 donor position of CHEK2 and is expected to disrupt normal splicing, which supports PVS1 in a loss-of-function disease mechanism context.1 The reviewed CHEK2 framework mode is VCEP and the case workspace points to the CHEK2 ClinGen specification as the primary interpretive authority, although the local criterion table was not populated.2 Population data support rarity: the variant is absent from gnomAD v2.1 and observed only once in gnomAD v4.1 with no homozygotes, supporting PM2 at supporting strength.3 No convincing variant-specific case-control, segregation, de novo, or functional RNA evidence for this exact allele was identified in the reviewed workspace, so no additional criteria were added. Using ACMG/AMP combining rules, PVS1 plus PM2_Supporting supports a Likely Pathogenic classification.4

PVS1 + PM2 Likely Pathogenic
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 · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Allele frequency by ancestry
      three datasets · side by side
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.99).
      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.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:16199547
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      PMID PMID:21876083
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PVS1 supports · met
      Sources & reference links
      6Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB