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NM_006231.4:c.2964G>T
p.Ser988= · POLE
León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
0%
complete
Final classification
VUS
PM2BP7
POLE
c.2964G>T
p.Ser988=
missense

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 variants predispose to polyposis and colorectal cancer, mostly through missense changes in the proofreading (exonuclease) domain. This variant is a synonymous change (p.Ser988=) in exon 25, outside that domain, with no predicted splice impact. Its VUS classification reflects that it does not match the gene's established disease mechanism, while population-frequency and functional evidence needed for a benign call are lacking.

Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.2964G>T
GRCh38
chr12:132661065 C>A
GRCh37
chr12:133237651 C>A
VUS: only two supporting criteria are met — PM2 (absent from all population databases) and BP7 (synonymous, no splice impact) — which conflict and satisfy no enumerated combination.
Classification rationale
PM2 BP7 VUS
POLE c.2964G>T missense

PM2 (Supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada — no carriers in large control populations. BP7 (Supporting): synonymous p.Ser988= with SpliceAI max delta 0.01, predicting no splice impact. Overall: VUS — the conflicting PM2 and BP7 supporting evidence satisfies no enumerated Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination.

PM2 + BP7 → 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 · 18 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): absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying the 'absent in controls' population criterion.
gnomAD v2.1 (exome): variant absent (search_status=absent).gnomAD v4.1 (exome): variant absent (search_status=absent).gnomAD-Canada v1.0 (HostSeq genomes): variant absent (search_status=absent).
BP7 supporting Benign
Met (supporting): synonymous p.Ser988= with SpliceAI max delta 0.01, far below the 0.2 impact threshold, predicting no splice effect.
spliceai: SpliceAI max delta score 0.01 (DS_AG 0.01, DS_AL 0.0, DS_DG 0.0, DS_DL 0.0) for NM_006231.4:c.2964G>T (SpliceAI Lookup, Broad Institute, distance=500, basic mode); below the 0.2 high-impact delta threshold (Jaganathan et al. 2019, PMID 30661751), predicting no splice impact and no new splice-site creation.pvs1_variant_assessment: consequence_class='synonymous', protein NP_006222.2:p.(Ser988=), canonical_splice_consensus=false.generic_acmg_combination_rules: BP7 criterion from Richards et al. 2015 (PMID 25741868) - synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site.
Assessed · not applied · 8 not met · 10 not assessed
Pathogenic
PS2 Not assessed: no de novo occurrence with confirmed parental testing is documented in ClinVar or the literature.
PS3 Not assessed: no functional assay of this variant exists; the only related data is an in silico SpliceAI prediction (max delta 0.01), not a functional study.
PS4 Not met: the gene-specific rule applies only to recurrent missense variants (none at residue 988), and no case-control study exists for this variant.
PM3 Not assessed: no proband genotype or phase data exist to evaluate a trans configuration with a pathogenic variant.
PM6 Not assessed: no de novo occurrence, with or without parentage confirmation, is documented for this variant.
PP1 Not assessed: no segregation study or family testing data exists — zero informative meioses are documented.
PP3 Not met: SpliceAI predicts no splice impact (max delta 0.01), the only predictor available, so no computational evidence supports a deleterious effect.
PP4 Not assessed: no proband phenotype or family-history data for a carrier of this variant is available.
PP5 Not met: no ClinVar expert-panel (3-star) pathogenic classification exists; the only submission is a 1-star laboratory 'Likely benign'.
Benign
BA1 Not met: the variant is absent (frequency 0) from gnomAD v2.1, v4.1, and gnomAD-Canada, so no population threshold is exceeded.
BS1 Not met: observed frequency is 0 in all three population databases, the opposite of a frequency greater than expected.
BS2 Not met: no healthy adult carriers or homozygotes are observed; the variant is absent from all three population databases.
BS3 Not assessed: no functional studies of this variant exist; in silico and population data cannot substitute for them.
BS4 Not assessed: no affected family member has been tested and reported as not carrying the variant.
BP2 Not assessed: no genotype data exists to establish a trans or cis configuration with a pathogenic variant.
BP4 Not met: the only 'no impact' prediction (SpliceAI max delta 0.01) is already counted under BP7; no independent benign computational line exists.
BP5 Not assessed: no reported carrier with an alternate molecular basis exists, so an alternate diagnosis can be neither established nor excluded.
BP6 Not met: the 'Likely benign' label is a 1-star laboratory submission, not an expert-panel classification, so BP6 does not apply.
N/A · 8 PVS1 · PS1 · PM1 · PM4 · PM5 · PP2 · BP1 · BP3
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 (1 clinical laboratory). (ClinVarID = 1798204)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
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 not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
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
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.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots