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NM_001127510.3:c.4072G>A
p.Ala1358Thr · APC
0%
complete
Final classification
Likely Benign
BS1BP1
APC
c.4072G>A
p.Ala1358Thr
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 underlies inherited familial adenomatous polyposis and contributes to colorectal tumor initiation.

Transcript
NM_001127510.3
HGVS · transcript:coding
NM_001127510.3:c.4072G>A
GRCh38
chr5:112839666 G>A
GRCh37
chr5:112175363 G>A
Likely Benign: BS1 strong for population frequency plus BP1 supporting for an APC missense variant outside codons 1021-1035 satisfy APC VCEP Rule26.
Classification rationale
BS1BP1 Likely Benign
APC c.4072G>A missense · exon 17

BS1 strong: gnomAD v4.1 grpmax FAF 0.0001909 exceeds the APC threshold of 0.00001. BP1 supporting: p.Ala1358Thr is an APC missense change at codon 1358, outside the excluded codons 1021-1035.

BS1 + BP1 Likely Benign
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 · 2 applied · 15 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 · 2
Strength Supporting Moderate Strong Very strong
BS1 strong Benign
Met, strong: gnomAD v4.1 grpmax FAF 0.0001909 exceeds the APC BS1 threshold of 0.00001.
The APC VCEP specifies BS1 at gnomAD Popmax Filtering Allele Frequency >= 0.001% (0.00001).gnomAD v4.1 reports grpmax FAF 0.0001909 and European non-Finnish AF 0.000212706; gnomAD v2.1 reports grpmax FAF 0.00010915, all above 0.00001.
BP1 supporting Benign
Met at supporting: APC BP1 excludes only codons 1021-1035, and p.Ala1358Thr is at codon 1358.
The APC 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.(Ala1358Thr), placing it at codon 1358 and outside the stated exception.
Assessed · not applied · 5 not met · 10 not assessed
Pathogenic
PS1 Not met: APC VCEP examples are p.Asn1026Ser and p.Ser1028Arg, whereas this variant produces p.Ala1358Thr.
PS2 Not assessed: no proband-level parental testing or confirmed maternity and paternity evidence is available to calculate an APC de novo score.
PS3 Not assessed: no variant-specific RNA or protein assay result is available to demonstrate a damaging functional effect for p.Ala1358Thr.
PS4 Not assessed: exact-variant colorectal cancer reports lack the individual phenotype details required to calculate the APC VCEP PS4 phenotype-point score.
PM2 Not met: gnomAD v4.1 AF 0.000158614 with allele count 256 exceeds the APC PM2 threshold of 0.000003 for counts above one.
PM5 Not met: no useful same-residue comparator was identified for p.Ala1358Thr, while APC PM5 examples are limited to codons 1026 and 1028.
PM6 Not assessed: no assumed-de-novo proband observation or parental testing details are available to calculate the APC PM6 score.
PP1 Not assessed: no affected relatives, transmitting relatives, or meioses are reported to meet the APC PP1 thresholds.
PP3 Not met: SpliceAI maximum delta 0.001 is below the 0.2 supporting threshold and does not support a deleterious splice effect.
Benign
BA1 Not met: gnomAD v4.1 grpmax FAF 0.0001909 is below the APC BA1 threshold of 0.001.
BS2 Not assessed: gnomAD v4.1 reports zero homozygotes, but no qualifying healthy-individual point count is available for the APC BS2 rule.
BS3 Not assessed: no variant-specific benign RNA or protein assay with wild-type comparison and required controls is available for p.Ala1358Thr.
BS4 Not assessed: no affected noncarrier with an APC phenotype score is reported to satisfy the BS4 non-segregation thresholds.
BP2 Not assessed: no qualifying in-trans observation or three unknown-phase observations with different pathogenic APC variants is documented.
BP5 Not assessed: no qualifying (Likely) Pathogenic alternate-gene variant is documented for a colorectal polyposis phenotype.
N/A · 11 PVS1 · PM1 · PM3 · PM4 · PP2 · PP4 · PP5 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency · supports benign
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= 0.000158614; MAF= 0.01586%, 256/1613982 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000212706; MAF= 0.02127%, 251/1180032 alleles, homozygotes = 0); grpmax FAF= 0.0001909.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.79782e-05; MAF= 0.00780%, 22/282130 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000155569; MAF= 0.01556%, 20/128560 alleles, homozygotes = 0); grpmax FAF= 0.00010915.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.016% · 256 / 1,613,982
0 hom · FAF 0.019%
European (non-Finnish)
251 / 1,180,032
0.021%
African/African American
3 / 74,900
0.004%
Admixed American
1 / 59,976
0.0017%
Remaining individuals
1 / 62,488
0.0016%
+ 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
0.0078% · 22 / 282,130
0 hom · FAF 0.011%
European (non-Finnish)
20 / 128,560
0.016%
Remaining individuals
1 / 7,198
0.014%
Admixed American
1 / 35,412
0.0028%
+ 5 not observed (African/African American, 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 Uncertain significance (8 clinical laboratories) and as Likely benign (4 clinical laboratories) and as likely benign (1 clinical laboratory) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 141191)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.358. BayesDel score = 0.0425822.
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; COSV57335904, n = 6 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
21368914 ↗ Clinical utility gene card for: familial adenomatous polyposis (FAP) and attenua CLINVAR
23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and CLINVAR
25148578 ↗ Beyond BRAF(V600): clinical mutation panel testing by next-generation sequencing in advanced melanoma. CLINVAR
25186627 ↗ Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. CLINVAR
25256751 ↗ Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery. CLINVAR
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting CLINVAR
25452455 ↗ Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Cl CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint co CLINVAR