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NM_006231.4:c.331-30G>A
p.? · POLE
León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
0%
complete
Final classification
VUS
PM2BP4
POLE
c.331-30G>A
p.?

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 germline mutations cause polyposis and predispose to colorectal cancer, typically via missense changes in the proofreading exonuclease domain. This intronic variant lies outside that domain, is predicted to have no effect on splicing (SpliceAI max delta 0.06), and is extremely rare in the population, so the finding remains of uncertain significance until functional or familial evidence becomes available.

Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.331-30G>A
GRCh38
chr12:132680076 C>T
GRCh37
chr12:133256662 C>T
VUS: the tally — one supporting pathogenic (PM2) plus one supporting benign (BP4, SpliceAI max delta 0.06) — matches no Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule.
Classification rationale
PM2 BP4 VUS
POLE c.331-30G>A

PM2 (Supporting): extremely low population frequency — gnomAD v4.1 AF 0.0034% with zero homozygotes in ~1.6 million alleles (flagged for human review: not literally absent, 54 carriers). BP4 (Supporting): SpliceAI max delta 0.06, below the <0.1 threshold, predicting no effect on splicing. Overall classification: VUS — one supporting pathogenic (PM2) plus one supporting benign (BP4) criterion matches no Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule.

PM2 + BP4 → 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_006231.4 · variants mapped to exon structure
POLE NM_006231.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 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 review Pathogenic
Met (supporting): gnomAD v4.1 allele frequency 0.0034% with zero homozygotes in ~1.6 million alleles, an extremely low frequency. Flagged for human review: the variant is not literally absent from gnomAD (54 carriers), so this relies on the extremely-low-frequency reading.
gnomAD v4.1 AF = 3.37335e-05 (0.00337%), 54/1,600,784 alleles, 0 homozygotes; grpmax FAF = 3.621e-05 (source: gnomad_v4)gnomAD v2.1 AF = 1.19612e-05 (0.00120%), 3/250,812 alleles, 0 homozygotes (source: gnomad_v2)Variant absent from gnomAD-Canada v1.0 (source: gnomad_canada)
BP4 supporting Benign
Met (supporting): SpliceAI max delta 0.06 is below the <0.1 BP4 threshold, predicting no impact on splicing.
SpliceAI max delta 0.06 < 0.1, the BP4 threshold for intronic variants (SVI Splicing Subgroup thresholds per Walker et al. 2023, PMID 37352859) -> BP4 (supporting)Generic in-silico calibration (generic_acmg_combination_rules): for intronic, synonymous, or non-canonical-splice-position variants use SpliceAI only; SpliceAI max delta < 0.1 -> BP4 (supporting); max delta 0.06 falls in this range, not the [0.1, 0.2] gray zoneACMG/AMP 2015 BP4 definition, PMID 25741868: 'Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing, etc.)' - governing definition; the generic calibration designates SpliceAI as the splice predictor for intronic variants
Assessed · not applied · 6 not met · 13 not assessed
Pathogenic
PVS1 Not met: intronic variant with no null-variant mechanism and SpliceAI max delta 0.06, below any splice-disruption evidence threshold.
PS2 Not assessed: no de novo observation, parental testing, or identity confirmation data exist for this variant.
PS3 Not assessed: no variant-specific functional studies (RNA, minigene, or enzyme-activity assays) were available.
PS4 Not assessed: insufficient case-level evidence was available to evaluate this criterion.
PM3 Not assessed: no proband or family genotype data exist to determine trans configuration with a pathogenic POLE variant.
PM6 Not assessed: no parental samples or family-history evidence of de novo occurrence was available.
PP1 Not assessed: no affected family members have been genotyped, so no segregation data exist for this variant.
PP3 Not met: SpliceAI max delta 0.06 is below the >0.2 PP3 threshold, predicting no splice impact.
PP4 Not assessed: insufficient evidence was available to evaluate this criterion.
PP5 Not assessed: the only ClinVar record is a 1-star single-submitter VUS, not a reputable-source pathogenic rating.
Benign
BA1 Not met: highest observed allele frequency 0.0046% (gnomAD v4.1 non-Finnish European) is ~1000-fold below the 5% BA1 threshold.
BS1 Not met: observed allele frequency (max 0.0046%) is orders of magnitude below any frequency expected for these rare POLE disorders.
BS2 Not met: zero homozygotes in ~1.85 million alleles, and the adult-onset POLE phenotype does not meet the early full-penetrance requirement.
BS3 Not assessed: no mRNA-level functional studies (patient RNA or minigene splicing assays) were available for this variant.
BS4 Not assessed: no family studies exist to document lack of segregation in affected members.
BP1 Not met: variant is intronic, and POLE's established disease mechanism is missense, not primarily truncating.
BP2 Not assessed: no cis/trans phase determination with a pathogenic POLE variant was available.
BP5 Not assessed: insufficient evidence was available to evaluate this criterion.
BP6 Not assessed: the only ClinVar record is a 1-star single-submitter VUS, providing no reputable-source benign rating.
N/A · 7 PS1 · PM1 · PM4 · PM5 · PP2 · 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= 3.37335e-05; MAF= 0.00337%, 54/1600784 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.62231e-05; MAF= 0.00462%, 54/1168248 alleles, homozygotes = 0); grpmax FAF= 3.621e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.19612e-05; MAF= 0.00120%, 3/250812 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.64359e-05; MAF= 0.00264%, 3/113482 alleles, homozygotes = 0); grpmax FAF= 7.03e-06.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0034% · 54 / 1,600,784
0 hom · FAF 0.0036%
European (non-Finnish)
54 / 1,168,248
0.0046%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0012% · 3 / 250,812
0 hom · FAF 0.0007%
European (non-Finnish)
3 / 113,482
0.0026%
+ 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 Uncertain significance (1 clinical laboratory). (ClinVarID = 2575150)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
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 ↗
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
Rule & framework references · cited for criterion definitions, not variant evidence
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.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC