Starting
Initialising…
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CHEK1
Final classification
VUS
CHEK1 c.1148A>T · p.Lys383Ile
CHEK1

NM_001274.5:c.1148A>T (p.Lys383Ile) is a missense variant in CHEK1. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength.

Gene
CHEK1
Transcript
NM_001274.5
HGVS · transcript:coding
NM_001274.5:c.1148A>T
Consequence
N/A
GRCh38
chr11:125644558 A>T
GRCh37
chr11:125514453 A>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CHEK1 c.1148A>T

NM_001274.5:c.1148A>T (p.Lys383Ile) is a missense variant in CHEK1. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength.1 No pathogenic or likely pathogenic classifications exist in ClinVar. No functional studies, de novo reports, co-segregation data, or case-control evidence are available for this variant.2 In silico predictors are discordant: REVEL 0.433 is intermediate, BayesDel -0.14524 is benign-leaning, and SpliceAI predicts no splicing impact (max delta 0.01). The computational evidence does not meet PP3 or BP4 thresholds.3 CHEK1 lacks ClinGen-curated gene-disease validity, and no CSPEC or VCEP framework is available. Criteria dependent on established disease association (PP2, PP4) could not be reliably assessed. Applying the generic ACMG/AMP 2015 combination rules (PMID:25741868), the single supporting pathogenic criterion (PM2) is insufficient to reach Likely Pathogenic, and no benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 VUS
3 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001274.5 · variants mapped to exon structure
CHEK1 NM_001274.5
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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      Absent from gnomAD-Canada v1.0.
      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 = 0.01). REVEL score = 0.433. BayesDel score = -0.14524.
      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. CHEK1, an intracellular kinase, is overexpressed in various solid and hematologic malignancies.
      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
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots