NM_006231.4:c.6531+19G>T

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133202684 C>A · GRCh38: chr12:132626098 C>A

Gene: POLE Transcript: NM_006231.4

Final call

VUS

PM2 supporting BP4 supporting

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.6531+19G>T is an intronic variant located 19 base pairs downstream of POLE exon 46. It is not a null variant (nonsense, frameshift, or canonical splice site) and therefore does not meet PVS1 criteria (PMC6185798).

The variant is completely absent from all queried population databases including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, meeting PM2 at the supporting level.

SpliceAI predicts no significant splicing impact (max delta score = 0.02), meeting BP4 at the supporting benign level.

The León-Castillo et al. 2020 custom POLE framework, which customizes PM1, PS4, PP3, and BP4, applies exclusively to exonuclease-domain missense variants represented in its supplementary tables. This intronic variant is absent from those tables and none of the custom criterion specifications are triggered.

The variant is absent from ClinVar and COSMIC, and no functional studies, case reports, de novo events, or segregation data have been identified for this variant.

With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the overall evidence is equivocal. The criteria do not reach the threshold for Likely Pathogenic, Pathogenic, Likely Benign, or Benign classification. This variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: With 1 supporting pathogenic criterion (PM2) and 1 supporting benign criterion (BP4), none of the ACMG/AMP 2015 combination thresholds for Pathogenic, Likely Pathogenic, Likely Benign, or Benign are satisfied; the conflicting evidence defaults to 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.6531+19G>T is an intronic variant located 19 base pairs downstream of exon 46. It is not a nonsense, frameshift, or canonical ±1,2 splice consensus variant, and therefore does not trigger PVS1 under the ClinGen SVI PVS1 decision tree (PMC6185798). The generic PVS1 framework is not applicable to this variant class.	pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	Intronic variant; no protein-level amino acid change to compare with an established pathogenic missense change.
PS2	Not met	No de novo evidence identified. No publications report this variant, and no de novo occurrence data are available.
PS3	Not met	No functional studies identified for NM_006231.4:c.6531+19G>T. No experimental data testing this variant or a systematically characterized range including it were found in the literature or evidence sources. The León-Castillo et al. 2020 VCEP framework and its supplementary materials focus on exonuclease-domain missense variants and do not include functional data for this intronic variant.
PS4	Not met	Variant is absent from ClinVar and COSMIC. The León-Castillo et al. 2020 custom PS4 framework applies only to exact missense variants recurrent in both COSMIC and TCGA endometrial carcinoma cohorts with combined EC count ≥10; this intronic variant does not meet those criteria. No germline case-control enrichment data are available.	clinvar
PS5	N/A	Variant is absent from ClinVar; no established pathogenic variant at the same nucleotide position has been reported by a reputable source.
PM1	Not met	The León-Castillo et al. 2020 custom PM1 framework applies exclusively to specific exonuclease-domain missense variants listed in its evidence tables. NM_006231.4:c.6531+19G>T is an intronic variant and is not among the established hotspot or recurrent exonuclease-domain missense substitutions. It is not present in Supplementary Tables S1, S2, or S3. The variant is not located in a known mutational hotspot or critical functional domain that would satisfy generic PM1 criteria.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	NM_006231.4:c.6531+19G>T is completely absent from all queried population databases, including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Under generic ACMG/AMP criteria, complete absence from large population cohorts supports PM2 at the supporting level. Note that coverage of deep intronic variants in exome-based datasets may be incomplete, but absence across both exome and genome resources is consistent with a very rare variant.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	Intronic variant with no predicted protein change. PM5 requires a different amino acid change at the same residue as a known pathogenic missense variant; this variant does not alter a protein residue.
PM6	Not met	No de novo evidence identified. No publications report this variant in a de novo context, and no trio-based sequencing data are available.
PP1	Not met	No segregation data available. No family studies or cosegregation analyses including this variant have been reported.
PP2	Not met	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.6531+19G>T is an intronic variant, not a missense substitution, and does not meet this criterion.
PP3	Not met	SpliceAI predicts no significant splicing impact for this variant (max delta score = 0.02), well below the standard 0.10 threshold for splice-altering variants. REVEL and BayesDel scores are not available for this intronic variant. The León-Castillo et al. 2020 custom PP3 framework applies only to missense variants represented in Supplementary Tables S2 or S3; this variant is absent from those tables. Under generic in silico assessment, the available computational evidence does not support a deleterious effect on splicing.	spliceai
PP4	Not met	No phenotype specificity data available. No clinical information or case-level phenotype data accompanied this variant to support that the patient's phenotype is specific for POLE-related disease.
PP5	Not met	NM_006231.4:c.6531+19G>T is absent from ClinVar. No reputable source has reported this variant as pathogenic or likely pathogenic.	clinvar
BA1	Not met	NM_006231.4:c.6531+19G>T is absent from gnomAD. BA1 requires an allele frequency >1% in a population database, which is not met.	gnomad_v2 gnomad_v4
BS1	Not met	NM_006231.4:c.6531+19G>T is absent from all population databases. BS1 requires an allele frequency >0.3% in a population database, which is not met.	gnomad_v2 gnomad_v4
BS2	Not met	The variant has not been observed in any individual in population databases, so there is no evidence of observation in healthy adults. BS2 cannot be met without actual observations in healthy individuals.
BS3	Not met	No functional studies demonstrating a benign effect for NM_006231.4:c.6531+19G>T have been identified. No experimental data are available to assess whether this intronic variant has no deleterious impact on gene function.
BS4	Not met	No segregation data available to assess lack of cosegregation with disease. No family studies including this variant have been reported.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_006231.4:c.6531+19G>T is an intronic variant, not a missense substitution; BP1 does not apply.
BP2	Not met	No evidence of this variant observed in trans with a known pathogenic POLE variant. BP2 requires documented co-occurrence in trans with a pathogenic variant in a recessive disorder or in cis with a pathogenic variant in a dominant disorder.
BP4	Met	SpliceAI predicts no significant splicing impact for this intronic variant (max delta score = 0.02, where DS_AG=0.0, DS_AL=0.0, DS_DG=0.0, DS_DL=0.02; all well below the 0.10 threshold). While BP4 typically requires multiple lines of computational evidence, SpliceAI is the primary and most relevant computational tool for assessing intronic variants near splice junctions, and its prediction supports no functional impact on splicing.	spliceai
BP5	Not met	No observation of this variant in a case where an alternate molecular basis for disease was identified. No clinical case data are available for this assessment.
BP6	Not met	NM_006231.4:c.6531+19G>T is absent from ClinVar. No reputable source has classified this variant as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) exonic variants where splicing prediction algorithms predict no impact and the nucleotide is not highly conserved. NM_006231.4:c.6531+19G>T is an intronic variant, not a synonymous exonic substitution; BP7 does not apply.

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