NM_006231.4:c.6748-18G>A is an intronic variant in POLE (intron 48) that is present at extremely low frequency in population databases (gnomAD v2.1: 8/249,726 alleles, AF=0.0032%; gnomAD v4.1: 13/1,594,924 alleles, AF=0.00082%), meeting PM2 at supporting strength.1 SpliceAI predicts no splice impact (max delta score 0.0), and this variant does not involve canonical splice consensus sequences. No functional studies or computational tools support a deleterious effect.2 This variant has been reported in ClinVar as Likely benign by a single clinical laboratory (Invitae, SCV002332903, VCV001540941). The cited publication (PMID:28492532) is a methodology paper describing the Sherloc classification framework and does not provide variant-specific evidence.3 The custom León-Castillo et al. 2020 POLE framework (PM1, PS4, PP3, BP4) applies only to missense variants in the exonuclease domain; this intronic variant is outside the scope of the custom rules, which rely on specific variant-level evidence from the paper's supplementary tables where this variant is absent.4 Overall, only one criterion is met (PM2_Supporting), which is insufficient to reach a classification under ACMG/AMP 2015 combination rules. The variant remains a Variant of Uncertain Significance (VUS) by default, though the available evidence leans benign (ClinVar Likely benign, SpliceAI no impact).5
POLE
Final classification
VUS
POLE c.6748-18G>A · p.?
POLE
NM_006231.4:c.6748-18G>A is an intronic variant in POLE (intron 48) that is present at extremely low frequency in population databases (gnomAD v2.1: 8/249,726 alleles, AF=0.0032%; gnomAD v4.1: 13/1,594,924 alleles, AF=0.00082%), meeting PM2 at supporting strength.
Only one criterion is met (PM2 at supporting strength). Under generic ACMG/AMP 2015 combination rules, a single supporting criterion is insufficient to satisfy any pathogenic, likely pathogenic, benign, or likely benign combination. The variant defaults to Variant of Uncertain Significance (VUS). The Leon-Castillo et al. 2020 custom POLE framework applies only to missense variants in the exonuclease domain and explicitly directs fallback to generic ACMG/AMP for this intronic variant.
Classification rationale
PM2
VUS
POLE c.6748-18G>A
PM2
→
VUS
4
vcep_path_250_323
5
generic_acmg_combination_rules
Gene diagram
· NM_006231.4 · variants mapped to exon structure
POLE
NM_006231.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.2e-05 (8/249,726 alleles), gnomAD v4.1 AF=8.2e-06 (13/1,594,924 alleles), both well below the 0.1% PM2 threshold. No homozygotes observed.
gnomAD v2.1: AF 3.2e-05 (8/249726 alleles0 homozygotes)
Assessed · not applied
Pathogenic
PS2
No de novo data available for this variant.
PS3
No functional data available for this intronic variant.
PM6
No de novo data available for this variant.
PP1
No segregation data available for this variant.
PP3
SpliceAI predicts no splice impact (max delta 0.0).
PP4
No phenotype or family history data specific to this variant are available.
Benign
BA1
Highest population allele frequency is 0.0327% (gnomAD v2.1, OTH subpopulation), far below the 1% BA1 threshold.
BS1
Global allele frequency is 0.0032% (gnomAD v2.1, 8/249,726 alleles), below the 0.3% BS1 threshold.
BS2
No data available on observation of this variant in healthy adults with expected full-penetrance early-onset disease, either in trans with a pathogenic variant or in homozygous state.
BS3
No well-established functional studies demonstrate no damaging effect for this specific variant.
BS4
No segregation data available to assess lack of cosegregation with disease.
BP2
No data available on observation of this variant in trans with a known pathogenic variant in a recessive disorder, or in cis with a pathogenic variant in any inheritance pattern.
BP4
SpliceAI predicts no splice impact (max delta 0.0), but multiple lines of computational evidence are not available for this intronic variant.
BP5
No data available on an alternative molecular basis for disease in cases carrying this variant.
BP6
No data available from a reputable source classifying this variant as benign.
N/A · 10
PVS1 · PS1 · PS4 · PM1 · PM5 · PP2 · PP5 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 8.15086e-06; MAF= 0.00082%, 13/1594924 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000165948; MAF= 0.01659%, 1/6026 alleles, homozygotes = 0); grpmax FAF= 5.436e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.20351e-05; MAF= 0.00320%, 8/249726 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000327225; MAF= 0.03272%, 2/6112 alleles, homozygotes = 0); grpmax FAF= 7.539e-05.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00082%
· 13 / 1,594,924
0 hom · FAF 0.0054%
0 hom · FAF 0.0054%
Middle Eastern 1 / 6,026 |
0.017% |
Admixed American 7 / 59,972 |
0.012% |
African/African American 3 / 74,612 |
0.004% |
Remaining individuals 2 / 61,860 |
0.0032% |
+ 6 not observed (European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, European (non-Finnish))
gnomAD v2.1
0.0032%
· 8 / 249,726
0 hom · FAF 0.0075%
0 hom · FAF 0.0075%
Remaining individuals 2 / 6,112 |
0.033% |
Admixed American 6 / 34,412 |
0.017% |
+ 6 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 1540941)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
No data
No calibrated functional assay or RNA evidence was identified for this variant.
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Sources & reference links
Triaged references · 1 PMID not cited in assessment
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR