Variant classification summary

NM_006231.4:c.1474-9C>T

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133249434 G>A · GRCh38: chr12:132672848 G>A

Gene: POLE Transcript: NM_006231.4

Final call

Likely Benign

PM2 supporting BP4 supporting BP6 supporting

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.?

gnomAD AF

6.204212908733547e-07 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006231.4:c.1474-9C>T is an intronic substitution in POLE located 9 bases upstream of exon 14. SpliceAI predicts no significant splicing impact (max delta score = 0.01), indicating the variant is unlikely to alter normal splicing.

2

This variant is extremely rare in population databases, with an allele frequency of 4.10e-06 in gnomAD v2.1 (1/244,126 alleles) and 6.20e-07 in gnomAD v4.1 (1/1,611,808 alleles), both meeting the PM2_Supporting threshold for absence from population databases.

3

ClinVar classifies this variant as Likely benign (VariationID 2897960, Labcorp Genetics, criteria provided, single submitter), supporting benign interpretation under BP6_Supporting.

4

SpliceAI predicts no significant splice impact (max delta score = 0.01), consistent with a neutral computational assessment under BP4_Supporting.

5

No pathogenic evidence criteria are met. The custom León-Castillo PM1 and PS4 rules are missense-specific and do not apply to this intronic substitution. The variant is absent from COSMIC and the León-Castillo supplementary tables. No de novo observations, functional studies, or segregation data are available.

6

Applying the custom León-Castillo framework with generic ACMG/AMP 2015 fallback: the variant accrues one pathogenic supporting criterion (PM2_Supporting) and two benign supporting criteria (BP4_Supporting, BP6_Supporting). Under the likely_benign combination rules of the framework, two supporting benign criteria are sufficient for a classification of Likely benign. This classification is consistent with the existing ClinVar classification.

Final determination: >=2 Supporting benign criteria (BP4_Supporting + BP6_Supporting) is sufficient for Likely Benign under the León-Castillo custom POLE framework, which mirrors the generic ACMG/AMP 2015 likely_benign combination rule (2 BP -> Likely Benign).

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	This intronic variant (c.1474-9C>T) does not fall into the PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. SpliceAI predicts no significant splicing effect (max delta 0.01). The generic PVS1 framework (PMC6185798) does not apply to this variant class.	spliceai pvs1_variant_assessment pvs1_gene_context
PS1	N/A	PS1 requires a known pathogenic variant with the same amino acid change as the variant under assessment. NM_006231.4:c.1474-9C>T is an intronic substitution with unknown protein consequence (p.?); no amino acid change is defined.
PS2	Not met	No de novo observation of NM_006231.4:c.1474-9C>T has been reported in the literature or clinical databases. PS2 requires a confirmed de novo occurrence with maternity and paternity confirmed.
PS3	Not assessed	No functional studies (e.g., RNA splicing assays, minigene constructs, polymerase activity assays) have been identified that evaluate the functional impact of NM_006231.4:c.1474-9C>T. SpliceAI predicts no splicing effect, but direct experimental validation is absent.	spliceai
PS4	Not met	The custom León-Castillo PS4 rule applies only to missense variants recurrent in COSMIC and TCGA endometrial carcinoma cohorts with combined EC count ≥10. NM_006231.4:c.1474-9C>T is an intronic substitution, not assessed in the León-Castillo supplementary tables, and is absent from COSMIC. No germline case-control studies have been identified that report this variant in affected versus unaffected individuals.	vcep_path_250_323_s002
PS5	Not met	ClinVar classifies this variant as Likely benign (VariationID 2897960, 1 clinical laboratory submitter: Labcorp Genetics). PS5 requires a reputable source to have independently classified the variant as pathogenic; the current ClinVar classification contradicts this. The ClinVar submission cites PMID:28492532 (Sherloc methods paper), which does not contain variant-specific evidence for NM_006231.4:c.1474-9C>T.	clinvar
PM1	Not met	The custom León-Castillo PM1 rules apply only to specific missense variants in the exonuclease domain (five established hotspots at PM1_Strong, specific recurrent variants at PM1_Moderate, and specific uncertain-tier variants at PM1_Supporting). NM_006231.4:c.1474-9C>T is an intronic substitution, not a missense variant, and does not appear in the León-Castillo supplementary tables. Although the variant is located in intron 13 adjacent to exon 14 (which encodes part of the exonuclease domain), SpliceAI predicts no significant splicing impact (max delta 0.01), so there is no evidence this substitution disrupts a critical functional domain.	spliceai vcep_path_250_323_s002
PM2	Met	This variant is present at extremely low allele frequency in population databases: gnomAD v2.1 AF = 4.10e-06 (1/244,126 alleles, 0 homozygotes) and gnomAD v4.1 AF = 6.20e-07 (1/1,611,808 alleles, 0 homozygotes). Both frequencies are well below the 0.1% PM2 threshold. The variant is absent from gnomAD-Canada v1.0.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a known pathogenic missense change at the same amino acid residue as the variant under assessment. NM_006231.4:c.1474-9C>T is an intronic substitution with unknown protein consequence (p.?); no amino acid residue can be assigned.
PM6	Not met	No de novo observation of NM_006231.4:c.1474-9C>T has been reported in the literature or clinical databases. PM6 requires a de novo observation without confirmation of maternity and paternity; no such report exists for this variant.
PP1	Not assessed	No co-segregation data are available for NM_006231.4:c.1474-9C>T. PP1 requires evidence of co-segregation with disease in multiple affected family members.
PP2	N/A	PP2 applies to missense variants in genes where missense variants are a common mechanism of disease and benign missense variation is low. NM_006231.4:c.1474-9C>T is an intronic substitution, not a missense variant.
PP3	Not met	The custom León-Castillo PP3 rule applies only to missense variants present in Supplementary Tables S2 or S3 with REVEL class 'likely disease causing' and ≤1 benign in silico result. NM_006231.4:c.1474-9C>T is an intronic substitution not found in these tables. Under generic in silico assessment: SpliceAI predicts no significant splicing effect (max delta 0.01); REVEL, BayesDel, and HCI prior scores are not available for this intronic variant. No computational evidence supports a pathogenic effect.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not assessed	No phenotype or clinical data specifically associated with NM_006231.4:c.1474-9C>T have been identified. PP4 requires that the variant is found in a patient whose phenotype or family history is highly specific for the gene/disease.
PP5	Not met	ClinVar classifies this variant as Likely benign (VariationID 2897960, Labcorp Genetics, criteria provided, single submitter). PP5 requires a reputable source to have independently classified the variant as pathogenic. The ClinVar submission cites PMID:28492532 (Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria), which is a general methodology paper and does not contain variant-specific evidence for NM_006231.4:c.1474-9C>T. No full-text is available for this PMID, but its title and known content confirm it is a framework paper, not a case report.	clinvar
BA1	Not met	The allele frequency in gnomAD v2.1 (AF = 4.10e-06, 0.0004%) and v4.1 (AF = 6.20e-07, 0.00006%) is far below the 1% BA1 threshold. This criterion is not met.	gnomad_v2 gnomad_v4
BS1	Not met	The allele frequency in gnomAD v2.1 (AF = 4.10e-06, 0.0004%) is far below the 0.3% BS1 threshold. The highest subpopulation frequency is in East Asians at 0.0056% (v2.1), also well below the threshold.	gnomad_v2 gnomad_v4
BS2	Not met	The variant is not observed in a homozygous state in gnomAD (0 homozygotes in both v2.1 and v4.1). No systematic evidence of observation in healthy adults independent of population databases has been identified. BS2 requires observation in a healthy adult individual for a recessive disorder, or observation in trans with a pathogenic variant, or homozygous observation in a dominant disorder with full penetrance expected early in life.	gnomad_v2 gnomad_v4
BS3	Not assessed	No functional studies (e.g., RNA splicing assays, minigene constructs, enzymatic activity assays) assessing the impact of NM_006231.4:c.1474-9C>T have been identified. BS3 requires well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing.	spliceai
BS4	Not assessed	No segregation data are available for NM_006231.4:c.1474-9C>T. BS4 requires lack of co-segregation with disease in affected family members.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the primary known disease mechanism. NM_006231.4:c.1474-9C>T is an intronic substitution, not a missense variant.
BP2	Not assessed	No observations of NM_006231.4:c.1474-9C>T in trans with a known pathogenic POLE variant have been reported. BP2 requires observation in trans with a pathogenic variant in a gene associated with a recessive disorder, or observation in cis with a pathogenic variant in any inheritance pattern.
BP3	N/A	BP3 applies to in-frame insertions or deletions in repetitive regions without known function. This is a single-nucleotide intronic substitution, not an in-frame indel.
BP4	Met	SpliceAI predicts no significant splice impact for this intronic substitution (max delta score = 0.01), suggesting the variant is unlikely to disrupt normal splicing of POLE. The custom León-Castillo BP4 rule applies only to missense variants in Supplementary Tables S2/S3 and is not triggered here; under generic BP4 assessment, computational evidence supports a neutral effect.	spliceai
BP5	Not assessed	No observations of NM_006231.4:c.1474-9C>T in cases with an alternate molecular cause for disease have been identified. BP5 requires that the variant is found in a case with an alternate molecular basis for disease.
BP6	Met	This variant has been classified as Likely benign by a clinical diagnostic laboratory (Labcorp Genetics, formerly Invitae; ClinVar SCV004525736, VariationID 2897960) with criteria provided. The submitter is a reputable clinical testing laboratory.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) coding variants with no predicted splice impact. NM_006231.4:c.1474-9C>T is an intronic substitution located 9 bases upstream of exon 14, not a synonymous coding variant.
PM3	N/A	PM3 applies to variants detected in trans with a pathogenic variant in recessive disorders. POLE is associated with autosomal dominant polymerase proofreading-associated polyposis (PPAP), and recessive inheritance is not established.
PM4	N/A	PM4 applies to protein-length altering in-frame insertions, deletions, or stop-loss variants. NM_006231.4:c.1474-9C>T is an intronic single-nucleotide substitution that does not alter protein length through these mechanisms.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.