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POLE
Final classification
VUS
POLE c.6816G>A · p.Glu2272=
POLE

NM_006231.4:c.6816G>A is a synonymous variant (p.Glu2272=) in exon 49 of the DNA polymerase epsilon catalytic subunit gene POLE.

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.6816G>A
Consequence
N/A
GRCh38
chr12:132624742 C>T
GRCh37
chr12:133201328 C>T
Basis The custom POLE framework (Leon-Castillo et al. 2020) uses standard ACMG/AMP 2015 final combination rules. Only two criteria are met: PM2 at supporting strength and BP7 at supporting benign strength. This combination does not satisfy any pathogenic, likely pathogenic, benign, or likely benign threshold. With one pathogenic supporting and one benign supporting criterion — conflicting and insufficient evidence — the variant defaults to Variant of Uncertain Significance (VUS).
The custom POLE framework (Leon-Castillo et al. 2020) uses standard ACMG/AMP 2015 final combination rules. Only two criteria are met: PM2 at supporting strength and BP7 at supporting benign strength. This combination does not satisfy any pathogenic, likely pathogenic, benign, or likely benign threshold. With one pathogenic supporting and one benign supporting criterion — conflicting and insufficient evidence — the variant defaults to Variant of Uncertain Significance (VUS).
Classification rationale
PM2 BP7 VUS
POLE c.6816G>A

NM_006231.4:c.6816G>A is a synonymous variant (p.Glu2272=) in exon 49 of the DNA polymerase epsilon catalytic subunit gene POLE. This variant is absent from gnomAD v2.1 and v4.1 population databases, meeting the PM2 criterion at supporting strength.1 SpliceAI predicts no splicing impact (max delta score 0.00) for this synonymous variant located deep within exon 49, satisfying BP7 at supporting benign strength.2 This variant has been reported in ClinVar as Likely benign by two clinical laboratories (Variation ID 1146301, 1-star review status, criteria provided by a single submitter).3 The León-Castillo et al. 2020 custom POLE framework, which provides gene-specific rules for PM1, PS4, PP3, and BP4, applies exclusively to exonuclease-domain missense variants and does not address this synonymous variant at codon 2272, which lies outside the exonuclease domain (residues 268–471).4 The variant has been observed once in somatic cancers (COSMIC COSV57678650) but has not been identified as a recurrent somatic hotspot or as a germline disease-associated variant in the literature reviewed. Overall, the variant meets PM2 (supporting) and BP7 (supporting benign), with all other assessed criteria not met or not applicable. With one pathogenic supporting and one benign supporting criterion, the evidence is insufficient for classification as either likely pathogenic or likely benign, resulting in a Variant of Uncertain Significance (VUS).5

PM2 + BP7 VUS
4 vcep_path_250_323vcep_path_250_323_s002vcep_path_250_323_s003vcep_path_250_323_s004
5 final_classification_framework
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
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_006231.4:c.6816G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), meeting the PM2 frequency threshold of <0.1% in population databases.
Absent from gnomAD v2.1 (0 alleles)absent from gnomAD v4.1 (0 alleles)absent from gnomAD-Canada v1.0 (0 alleles).
BP7 supporting Benign
NM_006231.4:c.6816G>A is a synonymous variant (p.Glu2272=) located in exon 49 (42 nucleotides from the acceptor site, 1007 nucleotides from the donor site). SpliceAI predicts no splicing impact (max delta score 0.00, all delta scores at 0.00). The variant is far from splice consensus sequences and does not create a novel splice site.
Synonymous variant p.Glu2272=SpliceAI max delta 0.00 with no predicted acceptor gainacceptor loss
Assessed · not applied
Pathogenic
PS2 No de novo data available for this variant.
PS3 No functional studies have been performed on NM_006231.4:c.6816G>A.
PS4 The custom POLE framework PS4 rule (León-Castillo et al.
PM1 The custom POLE framework PM1 rules apply exclusively to specific exonuclease-domain missense hotspot variants (P286R, V411L, S297F, A456P, S459F at strong; F367S, L424I, M295R, P436R, M444K, D368Y at moderate; A465V, L424V, T278M, A428T at supporting).
PM6 No de novo data available for this variant.
PP1 No segregation data available for this variant.
PP3 The custom POLE framework PP3 rule requires the variant to appear in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and ≤1 benign in silico result.
PP4 No patient phenotype or family history data specific to this variant are available for assessment.
PP5 ClinVar reports this variant as Likely benign, not Pathogenic/Likely pathogenic.
Benign
BA1 This variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, which does not exceed the BA1 threshold of >1%.
BS1 This variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, which does not exceed the BS1 threshold of >0.3%.
BS2 No data on observation of this variant in healthy adult controls are available.
BS3 No well-established functional studies have been performed on NM_006231.4:c.6816G>A demonstrating no damaging effect.
BS4 No segregation data are available to demonstrate lack of segregation with disease.
BP2 No data on observation of this variant in trans with a pathogenic variant are available.
BP4 The custom POLE framework BP4 rule requires the variant to appear in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and ≥4 benign in silico results; this synonymous variant is absent from both tables.
BP5 No observation of this variant in a case with an alternate molecular basis for disease is available.
BP6 ClinVar reports this variant as Likely benign with a 1-star review status (criteria provided, single submitter).
N/A · 5 PVS1 · PS1 · PM5 · PP2 · BP1
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 (2 clinical laboratories). (ClinVarID = 1146301)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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; COSV57678650, n = 1 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 · 1 PMID not cited in assessment
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR