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STK11
Final classification
VUS
STK11 c.112C>G · p.Pro38Ala
STK11

NM_000455.5:c.112C>G (p.Pro38Ala) in STK11 is a missense variant with no functional, segregation, or case-control data available.

Gene
STK11
Transcript
NM_000455.5
HGVS · transcript:coding
NM_000455.5:c.112C>G
Consequence
N/A
GRCh38
chr19:1207025 C>G
GRCh37
chr19:1207024 C>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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
STK11 c.112C>G

NM_000455.5:c.112C>G (p.Pro38Ala) in STK11 is a missense variant with no functional, segregation, or case-control data available. The variant is extremely rare in population databases, absent from gnomAD v2.1 and present in gnomAD v4.1 at AF=5.58e-06 (9/1,613,804 alleles), meeting PM2 at supporting level.1 Multiple in silico tools predict no deleterious effect: SpliceAI max delta=0.0, REVEL=0.328, BayesDel=-0.085, meeting BP4 at supporting benign level.2 ClinVar reports the variant as Uncertain Significance by multiple clinical laboratories (Variation ID 458014) with no expert panel classification.3 The variant does not reside in a known functional domain or mutational hotspot. No same-residue pathogenic comparator (PM5) or de novo evidence (PS2/PM6) was identified. Overall, the available evidence is limited to population frequency data (PM2_supporting) and computational predictions (BP4_supporting_benign), which offset each other. The variant remains a Variant of Uncertain Significance.

PM2 + BP4 VUS
Gene diagram · NM_000455.5 · variants mapped to exon structure
STK11 NM_000455.5
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
      v4.1
      This variant is present in gnomAD v4.1 (AF= 5.57689e-06; MAF= 0.00056%, 9/1613804 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 3.12705e-05; MAF= 0.00313%, 2/63958 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00056% · 9 / 1,613,804
      0 hom · FAF 0.00025%
      European (Finnish)
      2 / 63,958
      0.0031%
      European (non-Finnish)
      7 / 1,179,868
      0.00059%
      + 8 not observed (Remaining individuals, Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (7 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 458014)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.328. BayesDel score = -0.0851511.
      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. STK11, a tumor suppressor and intracellular kinase, is frequently mutated in lung cancer.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      25645574 ↗ ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      31672839 ↗ Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      20301443 ↗ Peutz-Jeghers Syndrome. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR