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STK11
Final classification
VUS
STK11 c.920+12C>T · p.?
STK11

NM_000455.5:c.920+12C>T is an intronic variant in STK11 located 12 base pairs downstream of exon 7.

Gene
STK11
Transcript
NM_000455.5
HGVS · transcript:coding
NM_000455.5:c.920+12C>T
Consequence
N/A
GRCh38
chr19:1222018 C>T
GRCh37
chr19:1222017 C>T
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: BP4 supporting; combination = 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: BP4 supporting; combination = 1 supporting benign, which maps to VUS.
Classification rationale
BP4 VUS
STK11 c.920+12C>T

NM_000455.5:c.920+12C>T is an intronic variant in STK11 located 12 base pairs downstream of exon 7. This variant is present in gnomAD at low frequency across multiple populations (0.006% overall in v2.1, 0.003% in v4.1), with the highest subpopulation frequency of 0.046% in the African/African American population, indicating it is a rare but known variant and not absent from population databases.1 SpliceAI predicts no splicing impact (max delta score = 0.00), providing computational evidence against a deleterious splicing effect for this intronic variant (BP4_supporting).2 ClinVar classifies this variant as Likely benign based on 4 clinical laboratory submissions, though the review status is 1-star (criteria provided, single submitter), which does not reach the expert panel threshold for BP6 application.3 No functional studies, de novo reports, segregation data, case-control studies, or variant-specific literature are available for this variant. The variant has not been reported in COSMIC and is not listed as a cancer hotspot. Based on the available evidence, only BP4 (supporting benign) is met. The overall evidence is insufficient to classify this variant as benign or likely benign; the variant remains a variant of uncertain significance (VUS) with a single supporting benign criterion.4

BP4 VUS
Gene diagram · NM_000455.5 · variants mapped to exon structure
STK11 NM_000455.5
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 18 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00). For a variant located at intron position +12 from exon 7, where altered splicing would be the primary plausible disease mechanism, this computational evidence supports a benign interpretation. No other in silico predictors contradict this finding.
SpliceAI max delta score = 0.00 (acceptor gain: nullacceptor loss: nulldonor gain: null
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data with confirmed parentage is available for this variant.
PS3 No functional studies have been reported for NM_000455.5:c.920+12C>T.
PS4 No case-control studies or patient cohort data demonstrating enrichment of this variant in affected individuals are available.
PM1 This intronic variant (c.920+12C>T) is not located in a known mutational hotspot or critical functional domain.
PM2 This variant is present in gnomAD at low frequency across multiple populations (12/201,762 alleles in v2.1, AF = 0.006%; 40/1,564,668 alleles in v4.1, AF = 0.003%).
PM6 No de novo occurrence data (without confirmed parentage) is available for this variant.
PP1 No co-segregation data with disease in affected family members is available for this variant.
PP3 No in silico prediction tools support a deleterious effect.
PP4 No patient-specific phenotype data or clinical information is available for assessment of this variant.
PP5 ClinVar reports this variant as Likely benign with a review status of 'criteria provided, single submitter' (1-star).
Benign
BA1 The highest observed allele frequency is 0.046% in the African/African American population (gnomAD v4.1), well below the BA1 threshold of 1%.
BS1 The highest observed allele frequency is 0.046% in the African/African American population (gnomAD v4.1), below the BS1 threshold of 0.3%.
BS2 No data on well-phenotyped healthy adults harboring this variant are available.
BS3 No well-established functional studies demonstrating no deleterious effect are available for this variant.
BS4 No segregation data are available to demonstrate lack of co-segregation with disease in affected families.
BP2 No data on observation of this variant in trans with a known pathogenic variant in a recessive disorder are available.
BP5 No cases have been reported in which this variant is found in a patient with an alternate molecular basis for disease.
BP6 ClinVar classifies this variant as Likely benign based on 4 clinical laboratory submissions (GeneDx, Mendelics, Color Health, Invitae), but the review status is 'criteria provided, single submitter' (1-star).
N/A · 6 PVS1 · PS1 · PM5 · PP2 · BP1 · 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= 2.55645e-05; MAF= 0.00256%, 40/1564668 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000461129; MAF= 0.04611%, 34/73732 alleles, homozygotes = 0); grpmax FAF= 0.00033884.
v2.1
This variant is present in gnomAD v2.1 (AF= 5.9476e-05; MAF= 0.00595%, 12/201762 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000453515; MAF= 0.04535%, 8/17640 alleles, homozygotes = 0); grpmax FAF= 0.00036738.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0026% · 40 / 1,564,668
0 hom · FAF 0.034%
African/African American
34 / 73,732
0.046%
Admixed American
3 / 53,118
0.0056%
Remaining individuals
1 / 60,600
0.0017%
South Asian
1 / 85,050
0.0012%
European (non-Finnish)
1 / 1,155,394
8.7e-05%
+ 5 not observed (European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.0059% · 12 / 201,762
0 hom · FAF 0.037%
African/African American
8 / 17,640
0.045%
Remaining individuals
1 / 5,728
0.017%
Admixed American
2 / 27,396
0.0073%
European (non-Finnish)
1 / 85,128
0.0012%
+ 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), 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). (ClinVarID = 234418)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Triaged references · 7 PMIDs not cited in assessment
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
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
26389505 ↗ Genetics of Colorectal Cancer (PDQ®): Health Professional Version. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR