NM_006231.4:c.3459+12G>T

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133233923 C>A · GRCh38: chr12:132657337 C>A

Gene: POLE Transcript: NM_006231.4

Final call

VUS

PM2 supporting BP7 supporting benign

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.?

gnomAD AF

1.2390852081725104e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

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

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).

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).

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.

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.

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).

Final determination: Under ACMG/AMP 2015 combination rules, a single supporting pathogenic criterion with a single supporting benign criterion does not meet any classified category threshold and defaults to VUS (Uncertain Significance).

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	Intronic variant at c.3459+12, 12 bases downstream of exon 28. Not a nonsense, frameshift, or canonical ±1,2 splice site variant. PVS1 decision tree classifies this as 'other' and does not apply the generic null-variant framework.	pvs1_generic_framework
PS1	N/A	Intronic variant with no protein change; no amino acid residue to compare against known pathogenic missense variants at the same position.
PS2	Not met	No de novo evidence identified for this variant. The only literature source (PMID:28492532) is a methods paper that does not report any patient-level data for this variant.
PS3	Not met	No functional assay data exists for this intronic variant. The León-Castillo et al. 2020 framework and supplementary tables are exclusively missense-focused. SpliceAI predicts no splicing effect (delta=0.0), indicating this variant is unlikely to be functional.	spliceai vcep_path_250_323
PS4	Not met	Variant is absent from COSMIC and not present in the León-Castillo et al. 2020 recurrent variant table (Supplementary Table S1, missense-only). No germline case-control enrichment data available. Custom PS4_Supporting rule requires exact missense variant recurrence in both COSMIC and TCGA EC cohorts with combined count >=10.	vcep_path_250_323_s002
PS5	N/A	Variant does not alter an amino acid residue; cannot assess whether a different pathogenic missense change has been described at the same codon.
PM1	N/A	Custom León-Castillo 2020 PM1 applies only to missense variants in the exonuclease domain. This is an intronic variant (c.3459+12G>T) that does not reside in a protein functional domain. No hotspot data (cancerhotspots.org negative).	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	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_v2 gnomad_v4
PM5	N/A	Intronic variant with no protein residue; unable to perform same-residue missense comparator search. PM5 candidate harvesting confirmed not applicable (eligible_for_classic_pm5_search=false).	pm5_candidates
PM6	Not assessed	No de novo data available in the literature or ClinVar submissions for this variant. Cannot assess PM6 without variant-specific de novo confirmation.
PP1	Not assessed	No segregation data available for this variant. Cannot assess co-segregation with disease in affected family members.
PP2	N/A	PP2 applies to missense variants in genes with low rate of benign missense variation. This variant is intronic (c.3459+12G>T), not missense.
PP3	Not met	No computational evidence supports a deleterious effect. SpliceAI delta=0.0 predicts no splicing impact. REVEL and BayesDel unavailable for intronic variants. The León-Castillo custom PP3 rule applies only to missense variants present in Supplementary Tables S2/S3.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not assessed	No patient phenotype data provided for this case. Cannot assess whether the variant's phenotype is highly specific for a disease.
PP5	Not met	ClinVar classification is Likely Benign, not Pathogenic. Review status is 1-star (criteria provided, single submitter), which is below the 3-star expert panel threshold required for PP5. Additionally, PP5 requires a pathogenic assertion — the only ClinVar submission asserts Likely Benign.	clinvar
BA1	Not met	Allele frequency is 1.24e-6 (0.00012%) in gnomAD v4.1, well below the 1% BA1 threshold. Absent from gnomAD v2.1.	gnomad_v2 gnomad_v4
BS1	Not met	Allele frequency is 1.24e-6 (0.00012%) in gnomAD v4.1, well below the 0.3% BS1 threshold.	gnomad_v2 gnomad_v4
BS2	Not met	No homozygotes observed in gnomAD v4.1 or v2.1. No evidence of homozygous or biallelic occurrence in controls.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established functional studies demonstrate no damaging effect for this specific variant. SpliceAI prediction is computational, not a functional assay.	spliceai
BS4	Not assessed	No segregation data available. Cannot assess lack of segregation in affected family members.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the primary disease mechanism. This variant is intronic (c.3459+12G>T), not missense.
BP2	Not assessed	No data on observation in trans with a known pathogenic variant. Cannot assess BP2.
BP3	N/A	Skipped per instructions — trivially not applicable.
BP4	Not met	Only one line of computational evidence (SpliceAI delta=0.0) is available. BP4 requires multiple lines of computational evidence suggesting no impact. REVEL and BayesDel are unavailable for intronic variants. The León-Castillo custom BP4 rule applies only to missense variants in Tables S2/S3.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
BP5	Not assessed	No data on alternate molecular basis for disease. Cannot assess whether this variant was found in a case with a clear alternative explanation.
BP6	Not met	ClinVar classification is Likely Benign with 1-star review status (criteria provided, single submitter). BP6 requires a 3-star expert panel reputable source classification as benign. Single submitter does not meet the threshold.	clinvar
BP7	Met	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

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