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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 applied · 16 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_001274.5:c.157A>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0 in all populations (<0.1% threshold).
Absent from gnomAD v2.1 (AF=0). Absent from gnomAD v4.1 (AF=0). Absent from gnomAD-Canada v1.0 (AF=0.0).
Assessed · not applied
Pathogenic
PS3 No well-established functional studies evaluate the specific variant NM_001274.5:c.157A>G.
PS4 No case-control or cohort studies include this variant.
PM1 Position 53 lies within the CHEK1 kinase domain (residues ~1-265), but no VCEP/CSPEC defines this residue as a mutational hotspot or critical functional domain position.
PP1 No segregation data available.
PP2 HCI prior data not available for CHEK1.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No phenotype data available.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 Variant is absent from all gnomAD populations (AF=0).
BS1 Variant is absent from all gnomAD populations (AF=0).
BS2 No observations in healthy adult controls or homozygous state available.
BS3 No well-established functional studies have evaluated the specific effect of p.Lys53Glu on CHEK1 protein function.
BS4 No segregation data available to assess lack of cosegregation with disease.
BP1 Although CHEK1 loss-of-function is a supported disease mechanism with truncating variants implicated (PMID:38686193), insufficient evidence exists to determine that primarily truncating variants cause CHEK1-related disease such that a missense change should be downgraded.
BP2 No phase information available.
BP4 Computational evidence is mixed and does not meet the 'multiple lines suggesting no impact' threshold.
N/A · 8 PVS1 · PS1 · PS2 · PM5 · PM6 · BP5 · BP6 · BP7
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