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 BP6 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

NM_006231.4:c.6748-18G>A is an intronic variant in POLE located 18 bases upstream of exon 48. This variant has been observed at very 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%) with no homozygotes.

The variant meets PM2 (Supporting) due to its very low population frequency, below the 0.1% threshold.

SpliceAI predicts no impact on splicing (max delta score = 0.00), and no other computational tools predict a deleterious effect. PP3 is not met and BP4 does not reach the 'multiple lines' threshold.

This variant has been reported in ClinVar as Likely benign by Labcorp Genetics (formerly Invitae), meeting BP6 (Supporting).

The variant is not located in a known POLE mutational hotspot or functional domain. The custom POLE framework (León-Castillo et al. 2020) applies exclusively to missense variants and does not provide applicable PM1, PS4, PP3, or BP4 rules for this intronic variant.

No functional studies, segregation data, de novo observations, or case-control data are available. PVS1 is not applicable as the variant does not meet null-variant criteria. PS1, PM5, PP2, BP1, and BP7 are not applicable due to the intronic nature of the variant.

The evidence profile consists of one pathogenic supporting criterion (PM2) and one benign supporting criterion (BP6), resulting in a variant of uncertain significance (VUS) under the custom POLE framework using generic ACMG/AMP 2015 combination rules.

Final determination: No pathogenic, likely pathogenic, benign, or likely benign combination rule in the León-Castillo et al. 2020 custom POLE framework (which adopts ACMG/AMP 2015 thresholds) is satisfied by one pathogenic supporting criterion (PM2) and one benign supporting criterion (BP6); conflicting evidence defaults to VUS per ACMG/AMP 2015.

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	NM_006231.4:c.6748-18G>A is an intronic variant located 18 bases upstream of exon 48. It does not fall into the default generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. The ClinGen SVI PVS1 framework is not applicable.	pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	Intronic variant with unknown protein consequence (NP_006222.2:p.?). No amino acid change to compare against known pathogenic variants at the same position.
PS2	Not assessed	No de novo data available for this variant. No publications or databases report de novo occurrence.
PS3	Not assessed	No well-established functional studies available for this intronic variant. No publications report variant-specific functional assays.
PS4	Not met	No evidence of increased prevalence in affected individuals. The custom POLE PS4 framework (León-Castillo et al. 2020) applies exclusively to exonuclease-domain missense variants and is not applicable to this intronic variant. No germline case-control data or variant-specific observations in affected cohorts are available.	clinvar PMID:28492532
PS5	Not assessed	No known pathogenic variant at the exact same nucleotide position (c.6748-18) with a different nucleotide change has been identified.
PM1	Not met	This intronic variant at position c.6748-18 is not located in a known mutational hotspot or critical functional domain. The custom POLE PM1 framework (León-Castillo et al. 2020) applies exclusively to exonuclease-domain missense variants and is not applicable here. The variant is not among the established hotspot substitutions (P286R, V411L, S297F, A456P, S459F) or any other POLE-score-classified missense variants.	vcep_path_250_323
PM2	Met	This variant is present in gnomAD at very low frequency: v2.1 exomes AF=0.0032% (8/249,726 alleles, 0 homozygotes) and v4.1 exomes AF=0.00082% (13/1,594,924 alleles, 0 homozygotes). Both are well below the 0.1% threshold for PM2. The variant is absent from gnomAD-Canada and absent from most subpopulations; the highest subpopulation frequency is in the Remaining individuals population at 0.033% (v2.1). The very low allele frequency in population databases is consistent with PM2 at Supporting strength.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	Intronic variant with no defined protein residue. PM5 requires a known pathogenic missense change at the same amino acid residue; this variant has no protein consequence (p.?) and therefore same-residue comparison is not semantically meaningful. Confirmed by pm5_candidates.json: unable to parse missense residue context.	pm5_candidates
PM6	Not assessed	No de novo data available. No publications or databases report de novo occurrence of this variant.
PP1	Not assessed	No co-segregation data available. No publications report family studies or segregation analysis 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 (c.6748-18G>A), not a missense change.
PP3	Not met	SpliceAI predicts no splicing impact (max delta score = 0.00) for this intronic variant, indicating no predicted effect on pre-mRNA splicing. REVEL and BayesDel scores are not available (not applicable for intronic variants). The custom POLE PP3 framework (León-Castillo et al. 2020) applies exclusively to missense variants in Supplementary Tables S2/S3 and is not applicable here. No computational evidence supports a deleterious effect.	spliceai
PP4	Not assessed	No patient phenotype data available for comparison to the POLE-associated disease spectrum. The variant's phenotype specificity cannot be evaluated without clinical context.
PP5	Not met	ClinVar reports this variant as Likely benign (VariationID 1540941, single submitter: Labcorp Genetics/Invitae, review status: criteria provided, single submitter). No reputable source has reported this variant as pathogenic. PP5 requires a reputable source to have classified the variant as pathogenic, which is not the case here.	clinvar
BA1	Not met	The gnomAD allele frequency (v2.1 AF=0.0032%, v4.1 AF=0.00082%) is far below the BA1 threshold of >1%. This variant is not common enough in population databases to qualify as a stand-alone benign criterion.	gnomad_v2 gnomad_v4
BS1	Not met	The gnomAD allele frequency (v2.1 AF=0.0032%) is below the BS1 threshold of >0.3%. The variant is too rare in population databases to meet BS1.	gnomad_v2 gnomad_v4
BS2	Not assessed	The variant is observed in gnomAD (8 alleles v2.1, 13 alleles v4.1, no homozygotes), but the phenotype status of carriers is unknown. BS2 requires observation in healthy adults with full penetrance expected at an early age; without individual-level phenotype data, this cannot be applied.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established functional studies are available for this intronic variant. SpliceAI prediction of no splicing impact (max delta=0.00) is an in silico prediction, not a well-established functional assay. BS3 requires experimental evidence demonstrating no deleterious effect in a validated functional assay.	spliceai
BS4	Not assessed	No segregation data available. BS4 requires observation of non-segregation with disease in affected families, which has not been reported for this variant.
BP1	N/A	BP1 applies to missense variants in genes where a truncating mechanism is the primary cause of disease. This is an intronic variant, not a missense change.
BP2	Not assessed	No data on observation in trans with a known pathogenic variant. Phase information and co-occurrence data are not available.
BP4	Not met	SpliceAI predicts no splicing impact (max delta score = 0.00). However, BP4 requires multiple lines of computational evidence suggesting no impact. Only one computational tool (SpliceAI) is applicable to this intronic variant; REVEL, BayesDel, and HCI prior are not available for non-coding variants. The custom POLE BP4 framework applies only to missense variants. A single in silico prediction does not satisfy the 'multiple lines' requirement.	spliceai
BP5	Not assessed	No data on an alternate molecular basis for disease in a case carrying this variant. BP5 requires observation in a case with an alternative confirmed genetic cause.
BP6	Met	This variant has been reported in ClinVar as Likely benign by Labcorp Genetics (formerly Invitae), a reputable clinical diagnostic laboratory, with criteria provided (SCV002332903, review status: criteria provided, single submitter). Per ACMG/AMP BP6, a reputable source reporting a variant as benign when the underlying evidence is not independently available supports a benign interpretation at Supporting strength.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splicing impact. This is an intronic variant (c.6748-18G>A), not a synonymous substitution.

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