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POLE
Final classification
VUS
POLE c.3459+12G>T · p.?
POLE

NM_006231.4:c.3459+12G>T is a rare intronic variant in POLE located 12 bases downstream of exon 28.

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.3459+12G>T
Consequence
N/A
GRCh38
chr12:132657337 C>A
GRCh37
chr12:133233923 C>A
Basis Only two criteria met: PM2 at supporting strength (extremely rare in gnomAD, AF=1.24e-6) and BP7 at supporting benign strength (intronic +12, SpliceAI delta=0.0). No other pathogenic or benign criteria met. This constitutes conflicting evidence (1 supporting pathogenic + 1 supporting benign) and does not satisfy the threshold for any classified category under the standard ACMG/AMP 2015 combination rules used by the local POLE framework. Falls to VUS.
Only two criteria met: PM2 at supporting strength (extremely rare in gnomAD, AF=1.24e-6) and BP7 at supporting benign strength (intronic +12, SpliceAI delta=0.0). No other pathogenic or benign criteria met. This constitutes conflicting evidence (1 supporting pathogenic + 1 supporting benign) and does not satisfy the threshold for any classified category under the standard ACMG/AMP 2015 combination rules used by the local POLE framework. Falls to VUS.
Classification rationale
PM2 BP7 VUS
POLE c.3459+12G>T

NM_006231.4:c.3459+12G>T is a rare intronic variant in POLE located 12 bases downstream of exon 28.1 This variant is extremely rare in population databases, present at an allele frequency of 1.24e-6 (2/1,614,094 alleles) in gnomAD v4.1 and absent from gnomAD v2.1 (PM2_Supporting).2 SpliceAI predicts no splicing impact (max delta=0.0), and the variant lies outside the canonical splice consensus at the +12 intronic position (BP7_Supporting).3 This variant has been reported in ClinVar as Likely Benign by a single clinical laboratory (VariationID 1580883, 1-star review status), though the 1-star rating is insufficient for PP5 or BP6 application.4 No functional data, segregation data, de novo reports, or case-control evidence are available for this variant. The León-Castillo et al. 2020 custom POLE framework is exclusively missense-focused and does not provide applicable rules for this intronic variant.5 The variant has not been reported in somatic cancers (COSMIC) and is not a known hotspot (cancerhotspots.org negative). With PM2_Supporting (pathogenic) and BP7_Supporting (benign), the evidence is conflicting and insufficient to reach a likely benign or likely pathogenic classification. This variant is classified as a Variant of Uncertain Significance (VUS).

PM2 + BP7 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
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Extremely low allele frequency in population databases. Present at AF=1.24e-6 (2/1,614,094 alleles) in gnomAD v4.1 and absent from gnomAD v2.1. Well below the 0.1% PM2 threshold. No homozygotes observed.
gnomAD v4.1: AF=1.24e-6 (2/1614094 alleles
BP7 supporting review Benign
Intronic variant at c.3459+12, 12 bases downstream of exon 28, outside the canonical splice site consensus region. SpliceAI predicts no splicing impact (max delta=0.0, no cryptic splice site creation). Per ClinGen SVI guidance, BP7 can be applied to intronic variants beyond the +7 position when splicing prediction tools show no effect.
SpliceAI max delta = 0.0no acceptor gain/lossno donor gain/loss
Assessed · not applied
Pathogenic
PS2 No de novo evidence identified for this variant.
PS3 No functional assay data exists for this intronic variant.
PS4 Variant is absent from COSMIC and not present in the León-Castillo et al.
PM6 No de novo data available in the literature or ClinVar submissions for this variant.
PP1 No segregation data available for this variant.
PP3 No computational evidence supports a deleterious effect.
PP4 No patient phenotype data provided for this case.
PP5 ClinVar classification is Likely Benign, not Pathogenic.
Benign
BA1 Allele frequency is 1.24e-6 (0.00012%) in gnomAD v4.1, well below the 1% BA1 threshold.
BS1 Allele frequency is 1.24e-6 (0.00012%) in gnomAD v4.1, well below the 0.3% BS1 threshold.
BS2 No homozygotes observed in gnomAD v4.1 or v2.1.
BS3 No well-established functional studies demonstrate no damaging effect for this specific variant.
BS4 No segregation data available.
BP2 No data on observation in trans with a known pathogenic variant.
BP4 Only one line of computational evidence (SpliceAI delta=0.0) is available.
BP5 No data on alternate molecular basis for disease.
BP6 ClinVar classification is Likely Benign with 1-star review status (criteria provided, single submitter).
N/A · 7 PVS1 · PS1 · PM1 · PM5 · PP2 · BP1 · BP3
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= 1.23909e-06; MAF= 0.00012%, 2/1614094 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69492e-06; MAF= 0.00017%, 2/1179994 alleles, homozygotes = 0); grpmax FAF= 2.8e-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
0.00012% · 2 / 1,614,094
0 hom · FAF 2.8e-05%
European (non-Finnish)
2 / 1,179,994
0.00017%
+ 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 Likely benign (1 clinical laboratory). (ClinVarID = 1580883)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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 ↗
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Triaged references · 1 PMID not cited in assessment
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR