Variant classification summary

NM_006231.4:c.6330+19G>A

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133208882 C>T · GRCh38: chr12:132632296 C>T

Gene: POLE Transcript: NM_006231.4

Final call

Benign

BA1 stand-alone benign BP4 supporting benign BP6 supporting benign

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.?

gnomAD AF

0.0021853130470310855 (v4.1)

ClinVar

Benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006231.4:c.6330+19G>A is classified as Benign.

2

BA1 is met: the variant has a grpmax filtering allele frequency of 4.01% (gnomAD v2.1) and 4.05% (gnomAD v4.1), exceeding the 1% stand-alone benign threshold. The variant is observed in 1169/280568 alleles (16 homozygotes) in gnomAD v2.1 and 3498/1600686 alleles (54 homozygotes) in gnomAD v4.1, with highest frequency in the African/African American population (4.23% v2.1, 4.17% v4.1).

3

BP4 (supporting benign) is met: SpliceAI predicts no splicing impact (max delta = 0.00).

4

BP6 (supporting benign) is met: ClinVar reports this variant as Benign from 6 independent clinical laboratories.

5

All pathogenic criteria were assessed and are either not met, not applicable, or not supported by the available evidence. PVS1 is not applicable (deep intronic, not a null variant). PM1 is not applicable (not an exonuclease-domain missense hotspot). PM2 is not met (allele frequency exceeds 0.1%). PP3 is not met (SpliceAI delta = 0, no REVEL score available).

6

BA1 alone satisfies the Benign classification rule under both the León-Castillo custom POLE framework and generic ACMG/AMP 2015 combination rules.

Final determination: BA1 alone satisfies the Benign classification rule under both the León-Castillo custom POLE framework and generic ACMG/AMP 2015 combination rules.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is a deep intronic variant (c.6330+19G>A in intron 45). It does not fall into any null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus). SpliceAI max delta score is 0.00, confirming no predicted impact on splicing. The generic PVS1 framework is not applicable.	pvs1_generic_framework pvs1_variant_assessment spliceai
PS1	N/A	PS1 applies when a different nucleotide change at the same position has been previously established as pathogenic. No known pathogenic variant exists at the c.6330+19 nucleotide position. This is an intronic substitution with no ClinVar or literature evidence of a pathogenic substitution at this exact position.	clinvar
PS2	N/A	No de novo data available for this variant. PS2 requires a confirmed de novo observation in a patient with the disease and no family history.
PS3	Not met	No functional studies have been performed on this intronic variant. No publications report in vitro or in vivo functional data for NM_006231.4:c.6330+19G>A.
PS4	N/A	The custom POLE framework PS4 rule is restricted to exact missense variants recurrent in both COSMIC and TCGA endometrial carcinoma cohorts with combined EC count ≥10 in the established pathogenic set highlighted by León-Castillo et al. 2020. NM_006231.4:c.6330+19G>A is an intronic variant, not a missense change, and is absent from the VCEP POLE supplementary tables. The generic PS4 (case-control or increased prevalence in affected individuals) also lacks supporting data.	vcep_path_250_323 vcep_path_250_323_s002
PS5	N/A	PS5 requires a reputable source (e.g., ClinGen expert panel) to have classified this variant as pathogenic, with evidence not independently verified. ClinVar classifies this variant as Benign, not Pathogenic. No expert panel has classified it as pathogenic.	clinvar
PM1	N/A	The custom POLE framework PM1 rules apply only to specific exonuclease-domain missense hotspot variants (P286R, V411L, S297F, A456P, S459F for PM1_Strong; F367S, L424I, M295R, P436R, M444K, D368Y for PM1_Moderate; A465V, L424V, T278M, A428T for PM1_Supporting). NM_006231.4:c.6330+19G>A is a deep intronic variant with no protein consequence and is not in a known functional domain hotspot. Generic PM1 (mutational hot spot) also does not apply as there is no pathogenic variation clustered at this intronic position.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Not met	PM2 requires absence from population databases or presence at extremely low frequency (<0.1%). This variant is common in gnomAD: v2.1 overall AF=0.4166% (1169/280568 alleles, 16 homozygotes); v4.1 overall AF=0.2185% (3498/1600686 alleles, 54 homozygotes). Both exceed the 0.1% threshold for PM2.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a different pathogenic missense change at the same amino acid residue. This is an intronic variant with no protein consequence (NP_006222.2:p.?). No same-residue comparator is possible. pm5_candidates.json confirms eligible_for_classic_pm5_search=false.	pm5_candidates
PM6	N/A	No de novo observation reported for this variant. PM6 requires a confirmed de novo event with confirmed maternity and paternity.
PP1	Not met	No segregation data are available for this variant. PP1 requires cosegregation of the variant with disease in multiple affected family members.
PP2	N/A	PP2 applies to missense variants in a gene with a low rate of benign missense variation and where missense is a common pathogenic mechanism. NM_006231.4:c.6330+19G>A is an intronic variant, not a missense change.
PP3	Not met	SpliceAI predicts no splicing impact (max delta score = 0.00). REVEL and BayesDel scores are not available for this intronic variant. The custom POLE PP3 framework requires the variant to appear in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' — this variant is absent from those tables. No computational evidence supports pathogenicity.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not met	No patient phenotype data specific to this variant are available. PP4 requires the patient's phenotype or family history to be highly specific for the disease associated with the gene.
PP5	Not met	PP5 requires a reputable source to have classified the variant as pathogenic. ClinVar classifies this variant as Benign (6 clinical laboratories, variation ID 380224). No source classifies it as pathogenic.	clinvar
BA1	Met	This variant is present at high frequency in gnomAD population databases. In gnomAD v2.1: overall AF=0.4166% (1169/280568 alleles), African/African American subpopulation AF=4.23% (1052/24896 alleles), grpmax FAF=4.01%, with 16 homozygotes observed. In gnomAD v4.1: overall AF=0.2185% (3498/1600686 alleles), African/African American subpopulation AF=4.17% (3108/74566 alleles), grpmax FAF=4.05%, with 54 homozygotes observed. The grpmax filtering allele frequency exceeds the BA1 threshold of >1% in both datasets, and the observation of multiple homozygotes confirms this is a common population polymorphism incompatible with a Mendelian disease-causing role.	gnomad_v2 gnomad_v4
BS1	N/A	BA1 (stand-alone benign) has been met at a higher strength level based on grpmax filtering allele frequency >1%. BS1 (>0.3% overall) is superseded by BA1.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 requires observation of the variant in a healthy adult individual in the homozygous state, or in trans with a pathogenic variant, with full penetrance expected at an early age for a dominant disorder. While multiple homozygotes in gnomAD are strong evidence captured by BA1, no published case reports document the specific clinical phenotype of homozygous carriers or trans configurations. BA1 already captures the population-level evidence.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established functional studies have demonstrated no deleterious effect of this variant. BS3 requires a well-established assay showing no damaging effect on protein function or splicing.
BS4	Not met	No segregation data are available demonstrating lack of cosegregation with disease. BS4 requires observation of the variant in multiple family members without the disease phenotype.
BP1	N/A	BP1 applies to missense variants in genes where a truncating (loss-of-function) mechanism is the primary cause of disease. NM_006231.4:c.6330+19G>A is a deep intronic variant, not a missense change.
BP2	N/A	BP2 requires observation of the variant in trans with a known pathogenic variant in a gene for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder. No such observations have been reported.
BP4	Met	SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00), indicating that the c.6330+19G>A substitution does not create or disrupt a splice site. In the absence of applicable missense prediction tools (REVEL and BayesDel not available for intronic variants), SpliceAI provides the primary computational evidence for this variant class, and its prediction of no splicing effect supports a benign interpretation.	spliceai
BP5	N/A	BP5 requires observation of the variant in a case with an alternate molecular basis for disease. No such case data are available for NM_006231.4:c.6330+19G>A.
BP6	Met	ClinVar reports this variant as Benign (6 clinical laboratories: GeneDx, PreventionGenetics, ARUP Laboratories, KCCC/NGS Laboratory, Labcorp/Invitae, and Center for Genomic Medicine Rigshospitalet). Although review status is 'criteria provided, single submitter' and no expert panel review is recorded, the unanimous classification as Benign across multiple independent clinical laboratories provides supporting evidence for a benign interpretation.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact. NM_006231.4:c.6330+19G>A is a deep intronic variant, not a synonymous coding variant.

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