Variant classification summary

NM_006231.4:c.6748-18G>A

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133201414 C>T · GRCh38: chr12:132624828 C>T

Gene: POLE Transcript: NM_006231.4

Final call

VUS

PM2 supporting

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.?

gnomAD AF

8.150858598905027e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006231.4:c.6748-18G>A is an intronic variant in POLE (intron 48) that is present at extremely low frequency in population databases (gnomAD v2.1: 8/249,726 alleles, AF=0.0032%; gnomAD v4.1: 13/1,594,924 alleles, AF=0.00082%), meeting PM2 at supporting strength.

2

SpliceAI predicts no splice impact (max delta score 0.0), and this variant does not involve canonical splice consensus sequences. No functional studies or computational tools support a deleterious effect.

3

This variant has been reported in ClinVar as Likely benign by a single clinical laboratory (Invitae, SCV002332903, VCV001540941). The cited publication (PMID:28492532) is a methodology paper describing the Sherloc classification framework and does not provide variant-specific evidence.

4

The custom León-Castillo et al. 2020 POLE framework (PM1, PS4, PP3, BP4) applies only to missense variants in the exonuclease domain; this intronic variant is outside the scope of the custom rules, which rely on specific variant-level evidence from the paper's supplementary tables where this variant is absent.

5

Overall, only one criterion is met (PM2_Supporting), which is insufficient to reach a classification under ACMG/AMP 2015 combination rules. The variant remains a Variant of Uncertain Significance (VUS) by default, though the available evidence leans benign (ClinVar Likely benign, SpliceAI no impact).

Final determination: Under generic ACMG/AMP 2015 combination rules (PMID:25741868), a single PM2 supporting criterion satisfies no pathogenic, likely pathogenic, benign, or likely benign combination; all other combinations default to 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 (c.6748-18G>A, intron 48); not a null variant (nonsense, frameshift, or canonical ±1,2 splice consensus). PVS1 framework not applicable.
PS1	N/A	No known pathogenic variant has been established at this same nucleotide position to support PS1.
PS2	Not assessed	No de novo data available for this variant.
PS3	Not assessed	No functional data available for this intronic variant. SpliceAI predicts no splice impact (max delta 0.0), but this is insufficient alone as well-established functional evidence in either direction.	spliceai
PS4	N/A	Custom León-Castillo PS4 rule applies only to specific recurrent missense variants in endometrial carcinoma cohorts (Table S1) with combined EC count ≥10. This is an intronic variant absent from the supplementary tables; no germline case-control data available.
PS5	Not assessed	No data available to assess this criterion.
PM1	N/A	Custom León-Castillo PM1 rules apply only to specific missense variants in the POLE exonuclease domain. This is an intronic variant (c.6748-18G>A, intron 48) outside the exonuclease domain and outside the scope of the custom framework.
PM2	Met	This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.2e-05 (8/249,726 alleles), gnomAD v4.1 AF=8.2e-06 (13/1,594,924 alleles), both well below the 0.1% PM2 threshold. No homozygotes observed.	gnomad_v2 gnomad_v4
PM5	N/A	Intronic variant; cannot establish same-residue missense comparator. PM5 candidate harvesting returned no eligible comparators.
PM6	Not assessed	No de novo data available for this variant.
PP1	Not assessed	No segregation data available for this variant.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation. This is an intronic variant.
PP3	Not met	SpliceAI predicts no splice impact (max delta 0.0). REVEL and BayesDel scores are not available for this intronic variant. The variant is absent from León-Castillo supplementary Tables S2 and S3. No multiple lines of computational evidence support a deleterious effect.	spliceai
PP4	Not assessed	No phenotype or family history data specific to this variant are available.
PP5	N/A	ClinVar reports this variant as Likely benign (single submitter, criteria provided). PP5 requires a reputable source reporting the variant as pathogenic; the available classification is benign-leaning.	clinvar
BA1	Not met	Highest population allele frequency is 0.0327% (gnomAD v2.1, OTH subpopulation), far below the 1% BA1 threshold. This variant is not a common polymorphism.	gnomad_v2 gnomad_v4
BS1	Not met	Global allele frequency is 0.0032% (gnomAD v2.1, 8/249,726 alleles), below the 0.3% BS1 threshold. This variant is not sufficiently common to support a benign interpretation via BS1.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available on observation of this variant in healthy adults with expected full-penetrance early-onset disease, either in trans with a pathogenic variant or in homozygous state.
BS3	Not assessed	No well-established functional studies demonstrate no damaging effect for this specific variant. SpliceAI max delta 0.0 alone is insufficient to meet BS3.	spliceai
BS4	Not assessed	No segregation data available to assess lack of cosegregation with disease.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. This is an intronic variant.
BP2	Not assessed	No data available on observation of this variant in trans with a known pathogenic variant in a recessive disorder, or in cis with a pathogenic variant in any inheritance pattern.
BP3	N/A	Not an in-frame deletion/insertion in a repetitive region.
BP4	Not met	SpliceAI predicts no splice impact (max delta 0.0), but multiple lines of computational evidence are not available for this intronic variant. REVEL and BayesDel are not applicable. The variant is absent from León-Castillo Tables S2/S3. Insufficient computational evidence to meet BP4.	spliceai
BP5	Not assessed	No data available on an alternative molecular basis for disease in cases carrying this variant.
BP6	Not assessed	No data available from a reputable source classifying this variant as benign.
BP7	N/A	BP7 applies to synonymous (silent) coding variants with no predicted splice impact. This is an intronic variant, not a synonymous coding variant.

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