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NM_001127510.3:c.6873A>T
p.Gln2291His · APC
0%
complete
Final classification
VUS
BP1
APC
c.6873A>T
p.Gln2291His
missense · exon 17

APC is a tumor suppressor gene whose protein acts as a key brake on the Wnt signaling pathway by helping mark the growth-promoting protein beta-catenin for destruction; it also participates in cell migration, adhesion, and apoptosis. Inherited mutations in APC cause familial adenomatous polyposis (FAP), an autosomal dominant condition characterized by numerous colorectal polyps and a very high risk of colorectal cancer, with related forms including attenuated FAP and gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS). Somatic APC mutations are found in roughly 50-80% of sporadic colorectal cancers, where they act as early tumor-initiating events, and are also observed in some breast, stomach, and prostate cancers. Loss of APC function leaves Wnt signaling abnormally active, driving uncontrolled cell growth, which makes APC a central tumor suppressor in colorectal cancer.

This variant

This APC variant affects a tumor-suppressor gene whose loss of Wnt pathway control causes familial adenomatous polyposis and contributes to colorectal tumor initiation.

Transcript
NM_001127510.3
HGVS · transcript:coding
NM_001127510.3:c.6873A>T
GRCh38
chr5:112842467 A>T
GRCh37
chr5:112178164 A>T
VUS: BP1 supporting is the only met criterion, and no APC VCEP Version 2.1 pathogenic or benign combination rule is satisfied.
Classification rationale
BP1 VUS
APC c.6873A>T missense · exon 17

BP1 supporting: p.(Gln2291His) is an APC missense change at codon 2291, outside the excluded codons 1021-1035.

BP1 VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_001127510.3 · variants mapped to exon structure
APC NM_001127510.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 16 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
BP1 supporting Benign
Met, supporting: codon 2291 lies outside the VCEP's BP1 exception at codons 1021-1035.
The APC InSiGHT VCEP BP1 rule applies to APC missense variants except those in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035.The assessed variant is p.(Gln2291His) at codon 2291, which is outside codons 1021-1035.
Assessed · not applied · 2 not met · 14 not assessed
Pathogenic
PS1 Not met: p.(Gln2291His) has no documented same-amino-acid APC comparator among the VCEP's two established missense variants.
PS2 Not assessed: no proband-level parental testing or confirmed maternity and paternity evidence is documented.
PS3 Not assessed: no variant-specific validated damaging assay was available, and the APC protein-assay route is restricted to codons 959-2129 while this variant affects codon 2291.
PS4 Not assessed: no usable phenotype-point total, case-control enrichment estimate, or exact-variant affected-individual evidence is available for PS4.
PM2 Not assessed: required gnomAD v2.1.1 non-cancer AF is unavailable; all-comers AFs are 0.000145204 and 0.000231727, above the VCEP PM2 threshold.
PM5 Not assessed: zero p.Gln2291 comparator candidates were retrieved, but the comparator search recorded an HTTP 429 failure.
PM6 Not assessed: no assumed-de-novo observation or de novo score is documented.
PP1 Not assessed: no affected relatives, informative pedigree, or countable segregating meioses are documented.
PP3 Not met: SpliceAI max delta 0.00 and Pangolin scores 0.001/-0.006 do not support the APC VCEP's deleterious-splicing requirement.
Benign
BA1 Not assessed: the required gnomAD v2.1.1 non-cancer Popmax AF is unavailable; available all-comers grpmax FAFs are 0.00022755 and 0.00027477 versus 0.001.
BS1 Not assessed: the required gnomAD v2.1.1 non-cancer Popmax AF is unavailable; available all-comers grpmax FAFs exceed the 0.00001 threshold but are not the specified source.
BS2 Not assessed: available all-comers gnomAD v2.1 and v4.1 report zero homozygotes, but the VCEP-specified non-cancer homozygote dataset is unavailable.
BS3 Not assessed: no variant-specific benign functional assay was available, and the APC protein-assay route is restricted to codons 959-2129 while this variant affects codon 2291.
BS4 Not assessed: no affected, variant-negative relative with an APC phenotype score is documented.
BP2 Not assessed: no documented phase, affected-proband observation, or second (Likely) Pathogenic APC variant is available for this case.
BP5 Not assessed: no documented alternate pathogenic polyposis-gene finding with the required colorectal polyposis phenotype establishes BP5.
N/A · 11 PVS1 · PM1 · PM3 · PM4 · PP2 · PP4 · PP5 · BP3 · BP4 · BP6 · 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= 0.000231727; MAF= 0.02317%, 374/1613966 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000300869; MAF= 0.03009%, 355/1179916 alleles, homozygotes = 0); grpmax FAF= 0.00027477.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000145204; MAF= 0.01452%, 41/282362 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000294972; MAF= 0.02950%, 38/128826 alleles, homozygotes = 0); grpmax FAF= 0.00022755.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.023% · 374 / 1,613,966
0 hom · FAF 0.027%
European (non-Finnish)
355 / 1,179,916
0.03%
Remaining individuals
12 / 62,498
0.019%
Admixed American
3 / 60,002
0.005%
European (Finnish)
2 / 64,030
0.0031%
East Asian
1 / 44,858
0.0022%
African/African American
1 / 75,016
0.0013%
+ 4 not observed (Amish, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.015% · 41 / 282,362
0 hom · FAF 0.023%
European (non-Finnish)
38 / 128,826
0.029%
Remaining individuals
1 / 7,210
0.014%
European (Finnish)
1 / 25,088
0.004%
Admixed American
1 / 35,388
0.0028%
+ 4 not observed (African/African American, Ashkenazi Jewish, East Asian, 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 (14 clinical laboratories) and as Uncertain significance (4 clinical laboratories) and as Benign (1 clinical laboratory) and as Likely Benign (1 clinical laboratory). (ClinVarID = 41534)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.147. BayesDel score = -0.36177.
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. APC, a tumor suppressor involved in WNT signaling, is recurrently altered in colorectal 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 previously been reported in somatic cancers (COSMIC; COSV105854020, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 PMIDs not cited in assessment
22703879 ↗ Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. CLINVAR
22855150 ↗ Guidelines for biomarker testing in colorectal carcinoma (CRC): a national conse CLINVAR
23429431 ↗ Recommendations from the EGAPP Working Group: can testing of tumor tissue for mu CLINVAR
23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and CLINVAR
24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants CLINVAR
24310308 ↗ ACMG technical standards and guidelines for genetic testing for inherited colore CLINVAR
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting CLINVAR
25479140 ↗ Prevalence of germline mutations in cancer predisposition genes in patients with pancreatic cancer. CLINVAR