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POLE
Final classification
VUS
POLE c.6531+19G>T · p.?
POLE

NM_006231.4:c.6531+19G>T is an intronic variant located 19 base pairs downstream of POLE exon 46. It is not a null variant (nonsense, frameshift, or canonical splice site) and therefore does not meet PVS1 criteria (PMC6185798).

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.6531+19G>T
Consequence
N/A
GRCh38
chr12:132626098 C>A
GRCh37
chr12:133202684 C>A
Basis One supporting pathogenic criterion (PM2: variant absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada) and one supporting benign criterion (BP4: SpliceAI max delta score = 0.02 predicts no splicing impact). The combination of 1 supporting pathogenic + 1 supporting benign does not satisfy any Pathogenic, Likely Pathogenic, Likely Benign, or Benign threshold under the ACMG/AMP 2015 combination rules as adopted by the Leon-Castillo et al. 2020 custom POLE framework.
One supporting pathogenic criterion (PM2: variant absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada) and one supporting benign criterion (BP4: SpliceAI max delta score = 0.02 predicts no splicing impact). The combination of 1 supporting pathogenic + 1 supporting benign does not satisfy any Pathogenic, Likely Pathogenic, Likely Benign, or Benign threshold under the ACMG/AMP 2015 combination rules as adopted by the Leon-Castillo et al. 2020 custom POLE framework.
Classification rationale
PM2 BP4 VUS
POLE c.6531+19G>T

NM_006231.4:c.6531+19G>T is an intronic variant located 19 base pairs downstream of POLE exon 46. It is not a null variant (nonsense, frameshift, or canonical splice site) and therefore does not meet PVS1 criteria (PMC6185798).1 The variant is completely absent from all queried population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, meeting PM2 at the supporting level.2 SpliceAI predicts no significant splicing impact (max delta score = 0.02), meeting BP4 at the supporting benign level.3 The León-Castillo et al. 2020 custom POLE framework, which customizes PM1, PS4, PP3, and BP4, applies exclusively to exonuclease-domain missense variants represented in its supplementary tables. This intronic variant is absent from those tables and none of the custom criterion specifications are triggered.4 The variant is absent from ClinVar and COSMIC, and no functional studies, case reports, de novo events, or segregation data have been identified for this variant.5 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the overall evidence is equivocal. The criteria do not reach the threshold for Likely Pathogenic, Pathogenic, Likely Benign, or Benign classification. This variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + BP4 VUS
1 pvs1_generic_framework ↗pvs1_variant_assessment
4 vcep_path_250_323vcep_path_250_323_s002vcep_path_250_323_s003vcep_path_250_323_s004
6 final_classification_frameworkgeneric_acmg_combination_rules
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
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_006231.4:c.6531+19G>T is completely absent from all queried population databases, including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Under generic ACMG/AMP criteria, complete absence from large population cohorts supports PM2 at the supporting level. Note that coverage of deep intronic variants in exome-based datasets may be incomplete, but absence across both exome and genome resources is consistent with a very rare variant.
Absent from gnomAD v2.1 (exomesAF = null)Absent from gnomAD v4.1 (exomes + genomes
BP4 supporting Benign
SpliceAI predicts no significant splicing impact for this intronic variant (max delta score = 0.02, where DS_AG=0.0, DS_AL=0.0, DS_DG=0.0, DS_DL=0.02; all well below the 0.10 threshold). While BP4 typically requires multiple lines of computational evidence, SpliceAI is the primary and most relevant computational tool for assessing intronic variants near splice junctions, and its prediction supports no functional impact on splicing.
SpliceAI max delta score = 0.02 — no predicted donor gainacceptor gaindonor loss
Assessed · not applied
Pathogenic
PVS1 NM_006231.4:c.6531+19G>T is an intronic variant located 19 base pairs downstream of exon 46.
PS2 No de novo evidence identified.
PS3 No functional studies identified for NM_006231.4:c.6531+19G>T.
PS4 Variant is absent from ClinVar and COSMIC.
PM1 The León-Castillo et al.
PM6 No de novo evidence identified.
PP1 No segregation data available.
PP2 PP2 applies to missense variants in genes with a low rate of benign missense variation and where missense is a common disease mechanism.
PP3 SpliceAI predicts no significant splicing impact for this variant (max delta score = 0.02), well below the standard 0.10 threshold for splice-altering variants.
PP4 No phenotype specificity data available.
PP5 NM_006231.4:c.6531+19G>T is absent from ClinVar.
Benign
BA1 NM_006231.4:c.6531+19G>T is absent from gnomAD.
BS1 NM_006231.4:c.6531+19G>T is absent from all population databases.
BS2 The variant has not been observed in any individual in population databases, so there is no evidence of observation in healthy adults.
BS3 No functional studies demonstrating a benign effect for NM_006231.4:c.6531+19G>T have been identified.
BS4 No segregation data available to assess lack of cosegregation with disease.
BP2 No evidence of this variant observed in trans with a known pathogenic POLE variant.
BP5 No observation of this variant in a case where an alternate molecular basis for disease was identified.
BP6 NM_006231.4:c.6531+19G>T is absent from ClinVar.
N/A · 4 PS1 · PM5 · BP1 · BP7
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
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