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STK11
Final classification
VUS
STK11 c.734+17C>G · p.?
STK11

NM_000455.5:c.734+17C>G is an intronic variant in STK11 at position +17 of intron 5. No CSPEC/VCEP framework exists for STK11; classification follows generic ACMG/AMP 2015 rules (PMID:25741868).

Gene
STK11
Transcript
NM_000455.5
HGVS · transcript:coding
NM_000455.5:c.734+17C>G
Consequence
N/A
GRCh38
chr19:1220734 C>G
GRCh37
chr19:1220733 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, BP6 supporting; combination = 1 supporting + 2 supporting benign, which maps to VUS because the evidence is conflicting.
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, BP6 supporting; combination = 1 supporting + 2 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM2 BP4BP6 VUS
STK11 c.734+17C>G

NM_000455.5:c.734+17C>G is an intronic variant in STK11 at position +17 of intron 5. No CSPEC/VCEP framework exists for STK11; classification follows generic ACMG/AMP 2015 rules (PMID:25741868).1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 allele frequency 0.00227% (6/264,478 alleles) and gnomAD v4.1 allele frequency 0.00187% (30/1,600,552 alleles), with no homozygotes observed (PM2_Supporting).2 SpliceAI predicts no significant splicing impact (max delta score = 0.01), and multiple lines of computational evidence suggest no effect on gene product or splicing (BP4_Supporting).3 This variant has been independently classified as Likely benign by 4 clinical laboratories and Benign by 2 clinical laboratories in ClinVar (Variation ID 379077), all with criteria provided (BP6_Supporting).4 No functional studies, de novo observations, segregation data, or case-control data were identified for this specific variant in the available literature. The 15 PubMed-indexed references associated with this ClinVar entry are practice guidelines and review articles that do not mention NM_000455.5:c.734+17C>G. Applying generic ACMG/AMP 2015 final combination rules: 1 supporting pathogenic criterion (PM2_Supporting) and 2 supporting benign criteria (BP4_Supporting, BP6_Supporting). With ≥2 supporting benign criteria, this variant is classified as Likely Benign.5

PM2 + BP4 + BP6 VUS
1 generic_acmg_combination_rules
5 generic_acmg_combination_rules
Gene diagram · NM_000455.5 · variants mapped to exon structure
STK11 NM_000455.5
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 1.87435e-05; MAF= 0.00187%, 30/1600552 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000227285; MAF= 0.02273%, 17/74796 alleles, homozygotes = 0); grpmax FAF= 0.00014401.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 2.26862e-05; MAF= 0.00227%, 6/264478 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000172073; MAF= 0.01721%, 4/23246 alleles, homozygotes = 0); grpmax FAF= 3.983e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0019% · 30 / 1,600,552
      0 hom · FAF 0.014%
      African/African American
      17 / 74,796
      0.023%
      Ashkenazi Jewish
      1 / 29,062
      0.0034%
      Remaining individuals
      2 / 61,708
      0.0032%
      South Asian
      1 / 90,096
      0.0011%
      European (non-Finnish)
      9 / 1,172,834
      0.00077%
      + 5 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern)
      gnomAD v2.1
      0.0023% · 6 / 264,478
      0 hom · FAF 0.004%
      African/African American
      4 / 23,246
      0.017%
      Ashkenazi Jewish
      1 / 9,440
      0.011%
      European (non-Finnish)
      1 / 117,360
      0.00085%
      + 5 not observed (Admixed American, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (2 clinical laboratories). (ClinVarID = 379077)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      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.
      COSMIC ↗
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      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