NM_006231.4:c.4952+13C>A

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133219079 G>T · GRCh38: chr12:132642493 G>T

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

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.4:c.4952+13C>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).

SpliceAI predicts no splice impact with a maximum delta score of 0.01, supporting a benign computational interpretation (BP7_Supporting).

The variant is an intronic substitution at position +13 of intron 37, outside the canonical splice consensus. PVS1 is not applicable; no null variant mechanism is supported.

The variant is absent from ClinVar with no published literature describing this exact variant. No functional, segregation, case-control, or de novo data are available.

The León-Castillo et al. 2020 custom POLE framework (local gene-specific framework) covers PM1, PS4, PP3, and BP4 for exonuclease-domain missense variants only. This intronic variant falls outside the framework's scope, and none of the four customized criteria are met under the framework's rules.

Overall evidence is insufficient for classification. PM2_Supporting and BP7_Supporting provide offsetting weak pathogenic and benign signals. This variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: No ACMG/AMP 2015 combination rule is satisfied: one pathogenic supporting criterion (PM2) and one benign supporting criterion (BP7) are insufficient to meet any defined classification threshold, defaulting to Variant of Uncertain Significance (VUS).

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	Not met	NM_006231.4:c.4952+13C>A is an intronic substitution at position +13 of intron 37, outside the canonical splice consensus (±1,2). PVS1 variant assessment confirms this variant does not fall into any PVS1 null-variant bucket (nonsense, frameshift, or canonical splice). SpliceAI predicts no significant splice impact (max delta score = 0.01). PVS1 is not applicable for this variant under generic ClinGen SVI PVS1 framework (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment spliceai
PS1	Not met	No known pathogenic variant has been reported at this exact nucleotide position (c.4952+13). This variant is absent from ClinVar and no literature exists reporting a different pathogenic change at the same nucleotide.	clinvar
PS2	N/A	No de novo data available. De novo confirmation requires parental testing results for this variant, which have not been reported in any source.
PS3	Not met	No functional data exists for NM_006231.4:c.4952+13C>A. No variant-specific or systematically characterized range functional studies were identified. The variant is intronic (+13) and not expected to alter protein function; no experimental functional assays have been performed for this variant.
PS4	Not met	The León-Castillo custom POLE framework restricts PS4 to specific exonuclease-domain hotspot missense variants with ≥10 combined COSMIC+TCGA cases. This variant is an intronic substitution, not a missense variant, and is absent from all León-Castillo supplementary tables. No case-control or cohort enrichment data exists. Falls outside custom framework scope; under generic ACMG, no evidence for enrichment in affected individuals.	vcep_path_250_323 vcep_path_250_323_s002
PS5	N/A	Variant is intronic with no protein consequence (NP_006222.2:p.?). Criterion is not applicable as there is no amino acid residue to assess for a different pathogenic missense change.
PM1	Not met	The León-Castillo custom POLE framework defines PM1 exclusively for specific exonuclease-domain missense variants. This variant is an intronic substitution at position +13 of intron 37, which is outside the exonuclease domain and does not affect any known functional domain or mutational hotspot. The variant does not correspond to any of the five established hotspot residues (P286, V411, S297, A456, S459) or the extended moderate/supporting PM1 list in the custom framework.	vcep_path_250_323 vcep_path_250_323_s002 vcep_path_250_323_s001
PM2	Met	NM_006231.4:c.4952+13C>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1, and gnomAD-Canada v1.0. Under generic ACMG/AMP guidelines, complete absence from large population databases supports PM2 at supporting strength (allele frequency <0.1%).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	Variant is intronic (c.4952+13C>A) with no protein consequence (NP_006222.2:p.?). Unable to parse missense residue context for same-residue comparator search. PM5 candidate harvesting was automatically skipped as classic same-residue semantics cannot be safely confirmed.	pm5_candidates
PM6	Not assessed	No de novo report for NM_006231.4:c.4952+13C>A was identified in any source. PM6 requires a confirmed de novo observation (with maternity and paternity confirmed) for this specific variant.
PP1	Not met	No segregation data available. Cosegregation with disease in multiple affected family members has not been reported for this variant.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation and where missense is a common disease mechanism. NM_006231.4:c.4952+13C>A is an intronic substitution, not a missense variant.
PP3	Not met	The León-Castillo custom POLE framework restricts PP3 to exact missense variants appearing in Supplementary Tables S2 or S3 with REVEL class 'likely disease causing' and ≤1 benign in silico result. This variant is intronic, not missense, and is absent from both supplementary tables. Under generic ACMG, multiple lines of computational evidence supporting a deleterious effect are required. SpliceAI predicts no splice impact (max delta 0.01). REVEL and BayesDel scores are not applicable for this intronic variant. No computational tools support pathogenicity.	vcep_path_250_323_s003 vcep_path_250_323_s004 spliceai
PP4	Not met	No patient phenotype data is available to assess whether the variant's phenotype is highly specific for a disease. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not met	NM_006231.4:c.4952+13C>A is absent from ClinVar. No 3-star expert panel classification exists for this variant. PP5 requires a reputable source (3-star ClinVar expert panel) classifying the variant as pathogenic.	clinvar
BA1	Not met	NM_006231.4:c.4952+13C>A is absent from all gnomAD databases (allele frequency = 0%). BA1 requires an allele frequency >1% in population databases. This variant is too rare to meet BA1.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	NM_006231.4:c.4952+13C>A is absent from all gnomAD databases (allele frequency = 0%). BS1 requires an allele frequency >0.3% in population databases. The variant is too rare to meet BS1.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No observation of this variant in a homozygous state or in trans with a pathogenic variant in healthy controls. No data available to assess BS2.
BS3	Not met	No functional studies, either in vivo or in vitro, have been performed for NM_006231.4:c.4952+13C>A demonstrating no damaging effect on protein function or splicing. BS3 requires well-established functional studies showing no deleterious effect.
BS4	Not met	No segregation data available to demonstrate lack of cosegregation with disease in affected family members. BS4 requires observation of the variant in healthy family members failing to segregate with disease.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_006231.4:c.4952+13C>A is an intronic substitution, not a missense variant.
BP2	Not met	No data available on whether this variant has been observed in trans with a pathogenic variant or in cis with a pathogenic variant. BP2 requires specific phase information that is not available.
BP4	Not met	The León-Castillo custom POLE framework restricts BP4 to exact missense variants in Tables S2/S3 with REVEL 'Likely benign' and ≥4 benign in silico results. This intronic variant is absent from those tables. Under generic ACMG, BP4 requires multiple lines of computational evidence suggesting no impact. The only applicable tool (SpliceAI) shows no splice effect (max delta 0.01), but a single tool does not constitute multiple independent lines of computational evidence required for BP4.	vcep_path_250_323_s003 vcep_path_250_323_s004 spliceai
BP5	Not met	No observation of this variant in a case with an alternate molecular basis for disease. BP5 requires the variant to be found in a patient with an alternate established cause of their phenotype.
BP6	Not met	NM_006231.4:c.4952+13C>A is absent from ClinVar. No 3-star expert panel classification exists for this variant. BP6 requires a reputable source (3-star ClinVar expert panel) classifying the variant as benign.	clinvar
BP7	Met	NM_006231.4:c.4952+13C>A is an intronic variant at position +13 of intron 37. SpliceAI predicts no splice impact (max delta score = 0.01, well below the 0.2 threshold for any splice-altering effect). All four delta scores (acceptor gain, acceptor loss, donor gain, donor loss) are ≤0.01. While BP7 was originally defined for synonymous variants, extended ACMG/AMP interpretations support its application to intronic variants at non-conserved positions where splicing algorithms predict no impact on native splicing or creation of a novel splice site.	spliceai

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