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POLE
Final classification
VUS
POLE c.3386A>G · p.Asp1129Gly
POLE

NM_006231.4:c.3386A>G (p.Asp1129Gly) in POLE is a rare missense variant with an allele frequency of 0.00025% in gnomAD v4.1 (4/1,613,948 alleles, 0 homozygotes), meeting PM2 at supporting strength.

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.3386A>G
Consequence
N/A
GRCh38
chr12:132657422 T>C
GRCh37
chr12:133234008 T>C
Basis Only one supporting-level pathogenic criterion (PM2_supporting) is met; no benign criteria are met. None of the ACMG/AMP 2015 pathogenic, likely pathogenic, benign, or likely benign combination rules are satisfied. Per the León-Castillo et al. 2020 custom POLE framework (which uses standard ACMG/AMP 2015 final classification thresholds), the evidence defaults to Variant of Uncertain Significance.
Only one supporting-level pathogenic criterion (PM2_supporting) is met; no benign criteria are met. None of the ACMG/AMP 2015 pathogenic, likely pathogenic, benign, or likely benign combination rules are satisfied. Per the León-Castillo et al. 2020 custom POLE framework (which uses standard ACMG/AMP 2015 final classification thresholds), the evidence defaults to Variant of Uncertain Significance.
Classification rationale
PM2 VUS
POLE c.3386A>G

NM_006231.4:c.3386A>G (p.Asp1129Gly) in POLE is a rare missense variant with an allele frequency of 0.00025% in gnomAD v4.1 (4/1,613,948 alleles, 0 homozygotes), meeting PM2 at supporting strength.1 This variant is absent from gnomAD v2.1 and has a grpmax filtering allele frequency of 7.9e-07, consistent with a rare variant.2 The variant has been reported as Uncertain significance in ClinVar (VariationID 934060) by a single clinical laboratory (Labcorp Genetics, SCV001373503).3 This variant has previously been reported in somatic cancers (COSMIC COSV57675934, n=1). SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).4 The variant is absent from the León-Castillo et al. 2020 supplementary tables of recurrent POLE endometrial carcinoma variants and does not map to any of the five established exonuclease-domain hotspot positions (P286R, V411L, S297F, A456P, S459F).5 In silico predictions are conflicting: REVEL score of 0.797 is in the deleterious range but BayesDel score of 0.157532 is in the benign range, and HCI prior is not available, precluding application of PP3 or BP4.6 OncoKB did not identify variant-specific reviewed functional evidence for p.Asp1129Gly.7 Overall, only one supporting-level pathogenic criterion (PM2) is met. No benign criteria are met. The evidence is insufficient for a classification beyond Variant of Uncertain Significance under the custom POLE framework (León-Castillo et al. 2020).8

PM2 VUS
5 vcep_path_250_323_s002vcep_path_250_323
6 revelbayesdel
8 vcep_path_250_323
Gene diagram · NM_006231.4 · variants mapped to exon structure
POLE NM_006231.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 22 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (AF=2.48e-06, 4/1,613,948 alleles, no homozygotes). The allele frequency of 0.00025% is well below the 0.1% PM2 threshold. grpmax FAF is 7.9e-07.
gnomAD v2.1: absent.gnomAD v4.1: AF=2.48e-06 (0.00025%)4/1
Assessed · not applied
Pathogenic
PS1 No evidence was identified for a different nucleotide change at codon 1129 resulting in the same amino acid substitution (p.Asp1129Gly) with an established pathogenic classification.
PS2 No de novo data are available for this variant.
PS3 No variant-specific functional studies were identified for p.Asp1129Gly.
PS4 The León-Castillo custom POLE framework limits PS4_Supporting to four specific hotspot variants (p.P286R, p.V411L, p.A456P, p.S297F).
PM1 p.Asp1129 is located at position 1129, well outside the POLE exonuclease domain (residues 268–471).
PM5 No comparator variant at codon 1129 with a different missense change and an established pathogenic classification was identified.
PM6 No de novo data are available for this variant.
PP1 No cosegregation data are available for this variant.
PP2 PP2 requires a missense variant in a gene where missense variants are a common disease mechanism and benign missense variation is rare.
PP3 The variant is absent from Supplementary Tables S2 and S3, so the custom POLE PP3 rule does not apply.
PP4 No phenotype or family history data specific to the proband are available.
PP5 ClinVar reports this variant as Uncertain significance with a review status of criteria provided, single submitter (1-star).
Benign
BA1 The allele frequency in gnomAD v4.1 is 0.00025% (AF=2.48e-06), far below the 1% BA1 threshold.
BS1 The allele frequency of 0.00025% is well below the 0.3% BS1 threshold.
BS2 No homozygotes have been observed in gnomAD v2.1 or v4.1.
BS3 No well-established functional studies demonstrating no deleterious effect were identified for this variant.
BS4 No cosegregation data are available to assess lack of segregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene where only truncating variants are known to cause disease.
BP2 No data on observations in trans with a pathogenic variant are available.
BP4 BP4 requires multiple lines of in silico evidence predicting no impact.
BP5 No information about an alternative molecular cause of disease in the proband is available.
BP6 ClinVar reports this variant as Uncertain significance, not benign.
N/A · 3 PVS1 · 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= 2.47839e-06; MAF= 0.00025%, 4/1613948 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.38995e-06; MAF= 0.00034%, 4/1179960 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
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
0.00025% · 4 / 1,613,948
0 hom · FAF 7.9e-05%
European (non-Finnish)
4 / 1,179,960
0.00034%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 Uncertain significance (1 clinical laboratory). (ClinVarID = 934060)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.797. BayesDel score = 0.157532.
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. POLE, the catalytic subunit of DNA polymerase epsilon, is an enzyme involved in DNA replication and repair. Select POLE mutations lead to ultra-high m
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; COSV57675934, 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