NM_006231.4:c.2468+16_2468+21dup

POLE · NP_006222.2:p.? · NM_006231.4

GRCh37: chr12:133241866 T>TCCCGGG · GRCh38: chr12:132665280 T>TCCCGGG

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

7.896094852616591e-05 (v4.1)

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.4:c.2468+16_2468+21dup is an intronic duplication in intron 21 of POLE, located at positions +16 to +21 downstream of exon 21.

This variant is absent from ClinVar and has not been reported in COSMIC or the published literature in association with disease.

The variant is present in gnomAD at very low frequency (v2.1 AF = 0.0078%, v4.1 AF = 0.0079%) with no homozygotes observed, meeting PM2 at supporting strength.

SpliceAI predicts no splicing impact (max delta = 0.02), meeting BP4 at supporting strength.

The custom POLE framework criteria (PM1, PS4, PP3, BP4 via León-Castillo et al. 2020) are missense-specific and do not apply to this intronic duplication.

PVS1 is not applicable as the variant is outside the canonical splice consensus and does not meet null-variant criteria per ClinGen PVS1 framework.

With only PM2_Supporting and BP4_Supporting applied, evidence is insufficient to classify this variant as either pathogenic or benign. The variant is classified as a variant of uncertain significance (VUS).

Final determination: One pathogenic supporting criterion (PM2) plus one benign supporting criterion (BP4) satisfies no pathogenic, likely pathogenic, benign, or likely benign combination in the León-Castillo POLE framework (which uses standard ACMG/AMP 2015 thresholds); conflicting evidence defaults to Variant of 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	NM_006231.4:c.2468+16_2468+21dup is an intronic duplication in intron 21 of POLE, located at positions +16 to +21 downstream of exon 21. This variant is outside the canonical splice consensus (±1,2) and does not fall into the ClinGen PVS1 null-variant buckets (nonsense, frameshift, or canonical splice). Per pvs1_variant_assessment, apply_generic_pvs1_framework is false and variant_bucket is 'other'.	pvs1_generic_framework
PS1	N/A	No known pathogenic variant is reported at this intronic position with a different nucleotide change. PS1 requires a nucleotide change at the same position with a known pathogenic comparator.
PS2	Not assessed	No de novo data available for this variant. No publications report parent-of-origin testing for NM_006231.4:c.2468+16_2468+21dup.
PS3	Not assessed	No functional studies available for this intronic duplication. No publications report in vitro or in vivo functional assessment of NM_006231.4:c.2468+16_2468+21dup.
PS4	Not met	The variant is absent from ClinVar and COSMIC. The custom POLE PS4 rule (from León-Castillo et al. 2020) requires an exact missense variant recurrent in both COSMIC and TCGA endometrial carcinoma cohorts with combined EC count ≥10; this intronic duplication does not meet the missense prerequisite and is not listed in the supplementary tables. Under generic ACMG/AMP 2015, no case-control data are available. PS4 is not met.	clinvar vcep_path_250_323_s002
PS5	Not assessed	No reputable source has recently reported this variant as pathogenic. PS5 requires a reputable source classification where the evidence is not available for independent evaluation.
PM1	Not met	The custom POLE PM1 rules (from León-Castillo et al. 2020) apply exclusively to specific missense variants in the exonuclease domain. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication in intron 21, outside the exonuclease domain and not a missense variant. Under generic ACMG/AMP 2015, the variant does not lie within a well-established mutational hotspot or critical functional domain. The variant is absent from the León-Castillo supplementary tables. PM1 is not met.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	This variant is absent from ClinVar and present in gnomAD at very low allele frequency: v2.1 AF = 7.82 × 10⁻⁵ (22/281,506 alleles) and v4.1 AF = 7.90 × 10⁻⁵ (127/1,608,390 alleles). Both frequencies are well below the 0.1% PM2 threshold for non-VCEP assessment. No homozygotes observed. PM2 is met at supporting strength.	gnomad_v2 gnomad_v4
PM3	N/A	Skipped per adjudication instructions.
PM4	N/A	PM4 applies to in-frame deletions/insertions in a nonrepeat region or stop-loss variants that alter protein length. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication that does not change protein length.
PM5	N/A	PM5 requires a different pathogenic amino acid change at the same residue. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication with no amino acid change (NP_006222.2:p.?). No same-residue comparator can be identified. Per pm5_candidates, eligible_for_classic_pm5_search is false.	pm5_candidates
PM6	Not assessed	No de novo data available. No publications report a confirmed de novo occurrence of NM_006231.4:c.2468+16_2468+21dup with maternity and paternity confirmed.
PP1	Not assessed	No segregation data available. No family studies have been reported for NM_006231.4:c.2468+16_2468+21dup.
PP2	N/A	PP2 is specific to missense variants in genes where missense is a common disease mechanism and benign missense variation is low. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication, not a missense variant.
PP3	Not met	The custom POLE PP3 rule requires an exact missense variant in Supplementary Tables S2 or S3 with REVEL class 'likely disease causing' and ≤1 benign in silico result. This intronic duplication is not a missense variant and does not appear in the León-Castillo supplementary tables. Under generic ACMG/AMP 2015: REVEL and BayesDel are unavailable (not an SNV), HCI prior does not support POLE, and SpliceAI predicts no splicing impact (max delta = 0.02). No computational evidence supports a deleterious effect. PP3 is not met.	spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not assessed	No phenotype or family history data are available for individuals carrying NM_006231.4:c.2468+16_2468+21dup. PP4 requires that the variant phenotype is highly specific for the disease.
PP5	Not assessed	The variant is absent from ClinVar. No expert panel or reputable source has classified NM_006231.4:c.2468+16_2468+21dup. PP5 cannot be applied.
BA1	Not met	gnomAD allele frequency is well below the 1% BA1 threshold. v2.1 AF = 0.0078%, v4.1 AF = 0.0079%. BA1 is not met.	gnomad_v2 gnomad_v4
BS1	Not met	gnomAD allele frequency is below the 0.3% BS1 threshold. v2.1 AF = 0.0078%, v4.1 AF = 0.0079%. BS1 is not met.	gnomad_v2 gnomad_v4
BS2	Not assessed	BS2 requires observation of the variant in a healthy adult individual for a fully penetrant disorder. No such data are available for NM_006231.4:c.2468+16_2468+21dup.
BS3	Not assessed	No functional studies demonstrating no deleterious effect are available for this intronic duplication.
BS4	Not assessed	No segregation data are available. BS4 requires non-segregation with disease in affected family members.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the primary disease mechanism. This is an intronic duplication, not a missense variant.
BP2	Not assessed	No data on in cis observation with a known pathogenic variant in POLE are available for this variant.
BP3	N/A	BP3 is specific to in-frame deletions/insertions in repetitive regions without a known function. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication, not an in-frame coding insertion/deletion.
BP4	Met	SpliceAI predicts no splicing impact for this intronic duplication (max delta score = 0.02, well below the 0.10 threshold). The variant lies at positions +16 to +21, outside the splice consensus region. The most pertinent computational tool for an intronic variant shows no evidence of altered splicing. REVEL and BayesDel are not applicable (not an SNV). BP4 is met at supporting strength based on SpliceAI prediction of no splicing impact.	spliceai
BP5	N/A	BP5 requires that the variant is found in a case with a clear alternate molecular cause of disease. No such data are available for this variant, and no ClinVar entry exists to identify an alternate mechanism.
BP6	Not assessed	No reputable source has classified NM_006231.4:c.2468+16_2468+21dup as benign. BP6 requires a reputable source classification as benign.
BP7	N/A	BP7 is specific to synonymous (silent) variants for which splicing prediction algorithms predict no impact. NM_006231.4:c.2468+16_2468+21dup is an intronic duplication, not a synonymous coding variant. Per ACMG/AMP 2015 guidelines, BP7 applies only to synonymous variants.

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