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CHEK1
Final classification
VUS
CHEK1 c.157A>G · p.Lys53Glu
CHEK1

NM_001274.5:c.157A>G (p.Lys53Glu) in CHEK1 is a missense variant absent from all gnomAD population databases (v2.1, v4.1, Canada), meeting PM2 at supporting strength.

Gene
CHEK1
Transcript
NM_001274.5
HGVS · transcript:coding
NM_001274.5:c.157A>G
Consequence
N/A
GRCh38
chr11:125627698 A>G
GRCh37
chr11:125497593 A>G
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.157A>G

NM_001274.5:c.157A>G (p.Lys53Glu) in CHEK1 is a missense variant absent from all gnomAD population databases (v2.1, v4.1, Canada), meeting PM2 at supporting strength.1 No pathogenic or likely pathogenic variant has been reported at the same amino acid residue (Lys53) in ClinVar; PS1 and PM5 are not applicable.2 Multiple lines of in silico evidence do not support a deleterious effect: REVEL 0.271, BayesDel -0.154, SpliceAI max delta 0.00. PP3 is not met.3 PVS1 is not applicable as this is a missense variant not falling into null-variant buckets defined by ClinGen SVI PVS1 recommendations (PMC6185798).4 No functional studies (PS3/BS3), segregation data (PP1/BS4), de novo observations (PS2/PM6), case-control data (PS4), phenotype data (PP4), or ClinVar classifications (PS5/PP5/BP6) are available for this variant.5 With PM2_supporting as the sole met criterion, the variant is classified as a Variant of Uncertain Significance (VUS) under ACMG/AMP 2015 rules.6

PM2 VUS
2 pm5_candidates
3 revelbayesdelspliceai ↗
4 pvs1_variant_assessmentpvs1_generic_framework ↗
6 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
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar No data
      No ClinVar submissions were recorded for this variant.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.271. BayesDel score = -0.154117.
      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