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POLE
Final classification
VUS
PM2BP4
POLE
c.4275C>T
p.Gly1425=
synonymous · exon 33

POLE encodes the catalytic subunit of DNA polymerase epsilon, the enzyme that replicates the leading strand of DNA during cell division and participates in DNA repair. It contains a proofreading domain that corrects replication errors, keeping the accumulation of mutations in check. Germline mutations in POLE cause polyposis and predispose to colorectal cancer, and are also linked to a rare syndrome of facial dysmorphism, immunodeficiency, livedo, and short stature. Somatic mutations, particularly in the proofreading domain, occur in colorectal and endometrial cancers, where they drive an ultra-mutated tumor phenotype and are associated with better responses to immune checkpoint inhibitors.

This variant

POLE mutations cause polyposis, colorectal cancer predisposition, and, through proofreading-domain changes, an ultra-mutated tumor phenotype; this synonymous variant alters no amino acid and shows no splice impact, so it does not engage any known POLE disease mechanism. Its VUS classification reflects extreme rarity in population databases but no functional, segregation, or case-level evidence linking it to disease, leaving its clinical relevance unresolved.

Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.4275C>T
GRCh38
chr12:132643852 G>A
GRCh37
chr12:133220438 G>A
Basis VUS: only PM2 (Supporting) and BP4 (Supporting) are met, and one supporting pathogenic versus one supporting benign factor does not reach any combined classification threshold.
VUS: only PM2 (Supporting) and BP4 (Supporting) are met, and one supporting pathogenic versus one supporting benign factor does not reach any combined classification threshold.
Classification rationale
PM2 BP4 VUS
POLE c.4275C>T synonymous · exon 33

PM2 (Supporting): extremely rare in population databases (gnomAD v4.1 AF 1.86e-06, 0 homozygotes), below the 0.1% rarity threshold. BP4 (Supporting): SpliceAI max delta 0.037 predicts no splice impact, below the <0.1 benign-splice threshold. VUS: the single supporting pathogenic factor (PM2) conflicts with the single supporting benign factor (BP4), which does not reach any LP/LB or P/B combination.

PM2 + BP4 VUS
Gene diagram · NM_006231.4 · variants mapped to exon structure
POLE NM_006231.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 17 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
PM2 supporting Pathogenic
Met (Supporting): extremely rare in gnomAD v4.1 at AF 1.86e-06 (3/1,614,022 alleles), below the 0.1% rarity threshold.
gnomAD v4.1: 3/1,614,022 total alleles, AF 1.85871e-06 (0.000185871%), grpmax FAF 6.8e-07, and 0 homozygotes; the highest population AF is 2.54254e-06 in European non-Finnish individuals.gnomAD v2.1: 1/251,190 total alleles, AF 3.98105e-06 (0.000398105%), highest population AF 8.80483e-06 in European non-Finnish individuals, and 0 homozygotes.gnomAD-Canada v1.0: absent.
BP4 supporting Benign
Met (Supporting): SpliceAI max delta 0.037 is below the <0.1 benign-splice threshold.
SpliceAI evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04)'; underlying scores DS_AG=0.01, DS_AL=0.013, DS_DG=0.037, DS_DL=0.008, max_delta=0.037.Generic fallback rule (generic_acmg_classification_rules.md, cited as generic_acmg_combination_rules) specifies: for intronic/synonymous/non-canonical-splice-position variants, use SpliceAI only, and SpliceAI max delta < 0.1 triggers BP4 (supporting).Custom POLE literature-derived PP3/BP4 rule (Le\u00f3n-Castillo et al. 2020 supplementary Tables S2/S3, REVEL-class based) was checked but does not apply because it is scoped to exact missense variants present in those tables, and this variant is synonymous and absent from them.
Assessed · not applied · 7 not met · 10 not assessed
Pathogenic
PS2 Not assessed: no parental testing or de novo confirmation was available for this variant.
PS3 Not assessed: no functional assay data demonstrating an abnormal effect (e.g., polymerase activity or RNA studies) were available.
PS4 Not met: variant is reported only three times in COSMIC, below the required combined count of 10 with TCGA recurrence.
PM3 Not assessed: no phase-resolved biallelic or in-trans genotype evidence was available.
PM6 Not assessed: no de novo observation or parental testing was documented.
PP1 Not assessed: no segregation or pedigree data were available.
PP3 Not met: SpliceAI max delta 0.037 is below the >0.2 supporting-pathogenic splice threshold.
PP4 Not assessed: no proband phenotype or tumor characteristics were provided.
PP5 Not met: the ClinVar Likely benign label rests on two single-submitter submissions, with no expert-panel review.
Benign
BA1 Not met: gnomAD v4.1 AF 1.86e-06 is far below the stand-alone benign high-frequency threshold.
BS1 Not met: highest population AF 2.54e-06 (European non-Finnish) is below the benign frequency threshold.
BS2 Not met: no homozygotes are reported in gnomAD v2.1 or v4.1, so no benign homozygote evidence exists.
BS3 Not assessed: no functional data demonstrating normal protein function were available.
BS4 Not assessed: no unaffected relatives or segregation data were documented.
BP2 Not assessed: no phase-resolved observation with a pathogenic variant was available.
BP5 Not assessed: no alternate molecular cause or phenotype data were provided.
BP6 Not met: the ClinVar Likely benign label comes from two single-submitter laboratories, not an expert panel.
N/A · 9 PVS1 · PS1 · PM1 · 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= 1.85871e-06; MAF= 0.00019%, 3/1614022 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54254e-06; MAF= 0.00025%, 3/1179922 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.98105e-06; MAF= 0.00040%, 1/251190 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80483e-06; MAF= 0.00088%, 1/113574 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019% · 3 / 1,614,022
0 hom · FAF 6.8e-05%
European (non-Finnish)
3 / 1,179,922
0.00025%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,190
0 hom
European (non-Finnish)
1 / 113,574
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, 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 (2 clinical laboratories). (ClinVarID = 1127492)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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; COSV57674767, n = 3 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
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