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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 applied · 15 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at extremely low frequency in population databases: gnomAD v2.1 allele frequency 0.00227% (6/264,478 alleles), gnomAD v4.1 allele frequency 0.00187% (30/1,600,552 alleles), both well below the 0.1% PM2 threshold.
gnomAD v2.1 AF = 0.00227% (6/264478)gnomAD v4.1 AF = 0.00187% (30/1
BP4 supporting Benign
SpliceAI predicts no significant splicing impact for this intronic variant (max delta score = 0.01, well below the 0.1 threshold). Multiple lines of computational evidence suggest no impact on gene product or splicing.
SpliceAI max delta = 0.01no predicted donor/acceptor gain or loss.
BP6 supporting Benign
This variant has been classified as Likely benign by 4 clinical laboratories (Color Health, Genome-Nilou Lab, Rigshospitalet, Labcorp/Invitae) and Benign by 2 clinical laboratories (GeneDx, KCCC/NGS Laboratory) in ClinVar (Variation ID 379077), all with criteria provided.
ClinVar Variation ID 379077: Likely benign (4 clinical labs)Benign (2 clinical labs)criteria provided
Assessed · not applied
Pathogenic
PS2 No de novo evidence identified for this variant.
PS3 No functional studies were identified for this specific variant.
PS4 No case-control or case series data were identified for this variant.
PM6 No de novo evidence identified.
PP1 No segregation data were identified for this variant in the available literature.
PP3 SpliceAI predicts no significant splicing impact (max delta score = 0.01).
PP4 No phenotype specificity data are available for this variant.
PP5 No reputable source has recently reported this variant as pathogenic.
Benign
BA1 The allele frequency in gnomAD v2.1 (0.00227%) and v4.1 (0.00187%) is far below the 1% BA1 threshold for standing as a benign polymorphism.
BS1 The allele frequency in gnomAD v2.1 (0.00227%) and v4.1 (0.00187%) is far below the 0.3% BS1 threshold.
BS2 No specific evidence of this variant observed in healthy adults beyond its presence at low frequency in gnomAD population databases.
BS3 No well-established functional studies were identified demonstrating no damaging effect for this specific variant.
BS4 No segregation data are available to assess lack of segregation with disease.
BP2 No evidence of this variant observed in trans with a known pathogenic STK11 variant was identified in the available literature or databases.
BP5 No evidence was identified of this variant observed in a case with an alternate molecular basis for disease.
N/A · 10 PVS1 · PS1 · PM1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
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