LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-08-06
Case ID: NM_006231.4_c.2561_21G_A_20260806_121423
Framework: ACMG/AMP 2015 with custom gene-specific criterion specifications
Variant classification summary

NM_006231.4:c.2561+21G>A

POLE  · NP_006222.2:p.?  · NM_006231.4
GRCh37: chr12:133240935 C>T  ·  GRCh38: chr12:132664349 C>T
Gene: POLE Transcript: NM_006231.4
Final call
VUS
All criteria require review: For research and educational purposes only.
Variant details
Gene
POLE
Transcript
NM_006231.4
Protein
NP_006222.2:p.?
gnomAD AF
3.173177071991299e-05 (v4.1)
ClinVar
OncoKB
Classification rationale
Interpretation summary
Generated evidence synthesis
1
NM_006231.4:c.2561+21G>A is an intronic variant in POLE located 21 bases into intron 22.
2
SpliceAI predicts no splicing impact (max delta score = 0.00), consistent with a functionally silent intronic change.
3
The variant is rare in population databases (gnomAD v2.1 AF = 0.0085%, 24/282,148 alleles; v4.1 AF = 0.0032%, 51/1,607,222 alleles), but rarity is expected for functionally silent intronic variants and is not informative for pathogenicity.
4
The variant is absent from ClinVar; no germline clinical classification is available.
5
It has been observed once as a somatic event in COSMIC (COSV114455825), which does not inform germline pathogenicity.
6
The León-Castillo 2020 custom POLE framework applies exclusively to missense variants; this intronic variant falls outside its scope.
7
No functional, segregation, de novo, case-control, or phenotypic data exist for this variant.
8
No ACMG/AMP pathogenic or benign criteria are met; the variant is classified as a Variant of Uncertain Significance (VUS).
Final determination: No criteria of any strength are met; zero pathogenic and zero benign criteria are satisfied, resulting in VUS by default under ACMG/AMP 2015 combination rules.
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 Intronic variant at c.2561+21 position, 21 bases into intron 22, with no predicted splicing impact (SpliceAI max delta = 0.00). Does not meet null-variant criteria (nonsense, frameshift, canonical ±1/2 splice) per ClinGen PVS1 framework (PMC6185798).
spliceai pvs1_generic_framework
PS1 Not met No previously classified pathogenic variant at nucleotide position c.2561+21 is reported in ClinVar or the literature.
clinvar
PS2 Not met No de novo observation data are available for this variant.
PS3 Not met No functional studies have characterized this intronic variant. No experimental data exist for c.2561+21G>A or a systematically characterized range that includes this position.
PS4 Not met The León-Castillo 2020 custom POLE framework restricts PS4 to exact missense variants recurrent in COSMIC and TCGA endometrial carcinoma cohorts with combined EC count ≥10. This is an intronic variant with no protein change and is absent from the supplementary recurrence table. No germline case-control enrichment data exist.
vcep_path_250_323_s002 vcep_path_250_323
PS5 Not met No alternate pathogenic variant at position c.2561+21 has been identified in ClinVar or the literature.
clinvar
PM1 Not met The León-Castillo 2020 custom POLE PM1 framework applies only to exact exonuclease-domain missense substitutions. This is an intronic variant located 21 bases into intron 22, outside the exonuclease domain and not in any established mutational hotspot or critical functional domain. The variant is also absent from the supplementary hotspot tables.
vcep_path_250_323_s002 vcep_path_250_323
PM2 Not met Although the variant is rare in population databases (gnomAD v2.1 AF = 0.0085%, 24/282,148 alleles; v4.1 AF = 0.0032%, 51/1,607,222 alleles), rarity of a deep intronic variant with no predicted functional consequence (SpliceAI delta = 0.00) is expected of most intronic polymorphisms and is not informative for pathogenicity.
gnomad_v2 gnomad_v4 spliceai
PM5 N/A Intronic variant with no protein change (p.?); PM5 requires a same-residue missense comparator with a different pathogenic amino acid change.
pm5_candidates
PM6 Not met No de novo observation data are available for this variant.
PP1 Not met No segregation data are available for this variant.
PP2 N/A PP2 applies to missense variants in genes with low benign missense variation. This is an intronic variant.
PP3 Not met SpliceAI predicts no splicing impact (max delta = 0.00). REVEL and BayesDel scores are unavailable for this non-coding variant. No computational evidence supports a deleterious effect. The León-Castillo custom PP3 framework applies only to missense variants in the supplementary in silico tables.
spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4 Not met No proband phenotype or clinical specificity data are available to assess whether the variant is in an individual with a phenotype specific for POLE-related disease.
PP5 Not met This variant is absent from ClinVar; no reputable source has classified it as pathogenic.
clinvar
BA1 Not met Global allele frequency in gnomAD v2.1 is 0.0085% (24/282,148 alleles), far below the 1% BA1 threshold.
gnomad_v2 gnomad_v4
BS1 Not met Global allele frequency in gnomAD v2.1 is 0.0085%, far below the 0.3% BS1 threshold.
gnomad_v2 gnomad_v4
BS2 Not met No confirmed observation in a healthy adult individual with full penetrance POLE-related disorder phenotype data is available. Presence in gnomAD population cohorts does not alone satisfy BS2 without disease-phenotype exclusion data.
BS3 Not met No functional studies demonstrating a neutral or benign effect exist for this variant.
BS4 Not met No segregation data are available to assess lack of cosegregation with disease.
BP1 N/A BP1 applies to missense variants in genes where primarily truncating variants cause disease. This is an intronic variant.
BP2 Not met No observation of this variant in trans with a known pathogenic POLE variant has been reported.
BP4 Not met SpliceAI predicts no splicing impact (max delta = 0.00), but BP4 requires multiple lines of computational evidence suggesting no impact. Only one predictor (SpliceAI) is available for this non-coding variant; REVEL and BayesDel do not apply to intronic variants. The León-Castillo custom BP4 framework applies only to missense variants in the supplementary tables.
spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
BP5 Not met No evidence of an alternate molecular basis for disease has been identified in this case.
BP6 Not met This variant is absent from ClinVar; no reputable source has classified it as benign.
clinvar
BP7 N/A BP7 applies to synonymous (silent) coding variants. This is an intronic variant, not a synonymous variant.
BP3 N/A BP3 applies to in-frame insertions/deletions; this is a substitution variant.
PM3 N/A PM3 applies to recessive disorders; POLE-associated disorders follow autosomal dominant inheritance.
PM4 N/A PM4 applies to protein-length changes (stop-loss, in-frame del/ins); this is an intronic substitution.
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