NM_006231.4:c.6531+4C>T

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133202699 G>A · GRCh38: chr12:132626113 G>A

Gene: POLE Transcript: NM_006231.4

Final call

VUS

BP6 supporting benign

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.?

gnomAD AF

1.761828475930277e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.4:c.6531+4C>T is an intronic variant at position +4 of intron 46 in POLE. SpliceAI predicts no significant splicing impact (max delta score 0.13).

This variant is present in gnomAD at extremely low frequency (v2.1: 8/245,768 alleles, AF=3.26e-05; v4.1: 28/1,589,258 alleles, AF=1.76e-05). The frequency does not reach BA1 (>1%) or BS1 (>0.3%) thresholds.

Invitae (Labcorp Genetics) reports this variant as Likely benign with criteria provided in ClinVar (SCV000772749). Ambry Genetics reports it as Uncertain significance (SCV000671346). Both are single-submitter clinical testing classifications without expert panel review.

The only criterion met is BP6 (Supporting benign) based on the Invitae ClinVar submission reporting Likely benign. No pathogenic criteria are met. Under ACMG/AMP 2015 combination rules, a single Supporting benign criterion is insufficient for a Likely benign classification (requires ≥2 Supporting benign or 1 Strong benign + 1 Supporting benign). The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Under the custom POLE framework (León-Castillo et al. 2020, mirroring ACMG/AMP 2015), Likely Benign requires ≥2 Supporting benign criteria or 1 Strong benign + 1 Supporting benign; a single Supporting benign criterion 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	Intronic variant at c.6531+4 (intron 46), outside the canonical ±1,2 splice consensus. SpliceAI predicts no significant splicing impact (max delta score 0.13). Does not meet ClinGen SVI PVS1 null-variant criteria (PMC6185798).	spliceai pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	Intronic variant with no amino acid change; PS1 requires a different nucleotide change at the same codon producing the same missense as an established pathogenic variant.
PS2	Not assessed	No de novo data available for this variant.
PS3	N/A	Intronic variant with no predicted protein change (NP_006222.2:p.?); SpliceAI predicts no significant splicing impact. No functional studies are relevant for a variant with no predicted molecular consequence.	spliceai
PS4	Not met	Two single-submitter ClinVar entries (Likely benign from Invitae, Uncertain significance from Ambry) do not constitute significantly increased prevalence in affected individuals. The custom POLE PS4 rule (León-Castillo et al. 2020) applies only to recurrent exonuclease-domain missense variants; this intronic variant does not qualify. No published case-control data are available.	clinvar vcep_path_250_323 vcep_path_250_323_s002
PS5	Not assessed	No validated de novo data available for this variant.
PM1	N/A	The custom POLE PM1 rules (León-Castillo et al. 2020) apply only to exonuclease-domain missense variants. This intronic variant at c.6531+4 is not located in the exonuclease domain (residues 268–471) and is not a missense change.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Not met	Variant is present in gnomAD at extremely low frequency (v2.1: 8/245,768 alleles, AF=3.26e-05; v4.1: 28/1,589,258 alleles, AF=1.76e-05) and SpliceAI predicts no splicing impact. The presence in population databases, combined with absence of predicted functional consequence, does not support PM2.	gnomad_v2 gnomad_v4 spliceai
PM5	N/A	Intronic variant with no amino acid change; PM5 requires a different missense change at the same residue as a known pathogenic missense variant.
PM6	Not assessed	No de novo data available for this variant.
PP1	Not assessed	No segregation data available for this variant.
PP2	N/A	Intronic variant, not a missense change. PP2 is specific to missense variants in genes with a low rate of benign missense variation where missense variants are a common mechanism of disease.
PP3	Not met	SpliceAI predicts no significant splicing impact (max delta 0.13). REVEL and BayesDel scores are not available for this intronic variant. The custom POLE PP3 rule (León-Castillo et al. 2020) applies only to missense variants in Supplementary Tables S2/S3; this variant is not present in those tables. No computational tools predict a deleterious effect.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not met	No patient phenotype or family history data are available to assess whether the phenotype is highly specific for a POLE-related disorder.
PP5	Not met	ClinVar reports this variant as Likely benign (Invitae, 1 submitter) and Uncertain significance (Ambry, 1 submitter). No reputable source has reported this variant as pathogenic. The cited PMID 25394175 (Hampel et al. 2015) is a general guideline for cancer predisposition referral and does not mention this variant.	clinvar PMID:25394175
BA1	Not met	gnomAD v2.1 allele frequency = 3.26e-05 (0.003%) and gnomAD v4.1 = 1.76e-05 (0.002%), both well below the 1% BA1 threshold for a dominant disorder.	gnomad_v2 gnomad_v4
BS1	Not met	The variant frequency (gnomAD v2.1 AF=3.26e-05, 0.003%; v4.1 AF=1.76e-05, 0.002%) is well below the 0.3% BS1 threshold. The frequency is not greater than expected for a POLE-related disorder.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data on observation of this variant in healthy adult individuals for a disorder with full penetrance expected at an early age.
BS3	Not assessed	No well-established in vitro or in vivo functional studies are available for this variant. SpliceAI prediction alone does not constitute a functional study.
BS4	Not assessed	No segregation data available to evaluate lack of segregation in affected family members.
BP1	N/A	Intronic variant, not a missense change. BP1 applies to missense variants in genes where primarily truncating variants are known to cause disease.
BP2	Not assessed	No data on observation of this variant in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant.
BP4	Not met	SpliceAI predicts no significant splicing impact (max delta 0.13), but this constitutes only a single line of computational evidence. REVEL and BayesDel scores are not available for this intronic variant. The custom POLE BP4 rule applies only to missense variants in Supplementary Tables S2/S3; this variant is not present in those tables. Multiple lines of computational evidence are not available to meet BP4.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
BP5	Not assessed	No data on observation of this variant in a case with an alternate molecular basis for disease.
BP6	Met	Invitae (Labcorp Genetics), a reputable clinical testing laboratory, reports this variant as Likely benign with criteria provided in ClinVar (SCV000772749, review status: criteria provided, single submitter). Under generic ACMG/AMP, a reputable source reporting the variant as benign supports BP6 at the Supporting level.	clinvar
BP7	N/A	BP7 is specific to synonymous (silent) exonic variants for which splicing algorithms predict no impact and the nucleotide is not highly conserved. This variant is an intronic substitution at c.6531+4, not a synonymous coding variant.
BP3	N/A	Variant is a substitution, not an in-frame deletion or insertion.
PM3	N/A	POLE is not associated with a recessive disorder; PM3 requires recessive disease context.
PM4	N/A	Variant is a substitution, not a protein-length altering change (in-frame deletion/insertion, stop-loss, or initiation codon).

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.