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POLD1
Final classification
VUS
POLD1 c.2716_2717del · p.Arg906AspfsTer47
POLD1

NM_002691.4:c.2716_2717del (NP_002682.2:p.(Arg906AspfsTer47)) is a frameshift variant in exon 21 of 27 coding exons of POLD1. The deletion is predicted to cause a premature termination codon subject to nonsense-mediated decay, meeting PVS1 at very strong strength under the ClinGen SVI framework (PMC6185798). POLD1 loss of function is an established germline disease mechanism for polymerase proofreading-associated polyposis and cancer predisposition.

Gene
POLD1
Transcript
NM_002691.4
HGVS · transcript:coding
NM_002691.4:c.2716_2717del
Consequence
N/A
GRCh38
chr19:50415585 CGA>C
GRCh37
chr19:50918842 CGA>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
POLD1 c.2716_2717del

NM_002691.4:c.2716_2717del (NP_002682.2:p.(Arg906AspfsTer47)) is a frameshift variant in exon 21 of 27 coding exons of POLD1. The deletion is predicted to cause a premature termination codon subject to nonsense-mediated decay, meeting PVS1 at very strong strength under the ClinGen SVI framework (PMC6185798). POLD1 loss of function is an established germline disease mechanism for polymerase proofreading-associated polyposis and cancer predisposition.1 The variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (allele frequency 0.00%), meeting PM2 at supporting strength under generic ACMG/AMP 2015 criteria (threshold <0.1%).2 No additional pathogenic criteria are met. The variant is absent from ClinVar, has no published functional data, no de novo reports, no segregation data, and no case-control evidence. SpliceAI predicts no splice impact (max delta = 0.04). OncoKB shows Unknown Oncogenic Effect. No cancerhotspots.org hotspot at this residue. No benign criteria are met.3 Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), PVS1 (very strong) with only one supporting criterion (PM2) does not formally reach the Likely Pathogenic threshold (requires 1 very strong + 1 moderate, or 1 strong + 1-2 moderate, etc.). However, a frameshift variant in a known tumor suppressor gene, absent from all population databases, is strongly indicative of pathogenicity. Many clinical laboratories would classify this as Likely Pathogenic using professional judgment. Formal classification under the strict combination rules is Variant of Uncertain Significance (VUS).4

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
4 generic_acmg_combination_rules
Gene diagram · NM_002691.4 · variants mapped to exon structure
POLD1 NM_002691.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_002691.4:c.2716_2717del is a frameshift variant in exon 21 of 27 coding exons, predicted to cause a premature termination codon (NP_002682.2:p.(Arg906AspfsTer47)) subject to nonsense-mediated decay. POLD1 loss of function is an established germline disease mechanism supported by literature evidence for polymerase proofreading-associated polyposis (PPAP) and cancer predisposition. The variant meets PVS1 at full strength under the ClinGen SVI PVS1 framework (PMC6185798).
Frameshift variant (2bp deletion) causing predicted NMD in a gene where LoF is an established disease mechanismPOLD1 germline LoF is associated with polymerase proofreading-associated polyposis and cancer predisposition per supporting literatureNM_002691.4 is MANE Select transcript
PM2 supporting Pathogenic
NM_002691.4:c.2716_2717del is completely absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency 0.00%), far below the generic ACMG PM2 threshold of <0.1%.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (genomes + exomes)Absent from gnomAD-Canada v1.0 (genomes)
Assessed · not applied
Pathogenic
PS2 No de novo data are available for this variant.
PS3 No variant-specific functional data are available.
PS4 No case-control or cohort data available.
PM1 The variant lies at codon 906 in the C-terminal region of POLD1, which is part of the polymerase domain.
PM4 PM4 applies to protein length changes from in-frame deletions/insertions in non-repeat regions or stop-loss variants.
PM6 No de novo data are available.
PP1 No segregation data are available.
PP3 Multiple in silico tools predict no significant effect.
PP4 No patient phenotype or clinical data are available in the case materials to assess phenotype specificity or fit.
PP5 The variant is absent from ClinVar — it has not been submitted by any laboratory and has no expert panel classification.
Benign
BA1 The variant is absent from gnomAD (allele frequency 0.00%), far below the BA1 threshold of >1%.
BS1 The variant is absent from gnomAD (allele frequency 0.00%), far below the BS1 threshold of >0.3%.
BS2 No observations in healthy adults or co-occurrence data are available.
BS3 No functional studies demonstrating no deleterious effect are available for this variant.
BS4 No segregation data are available to assess lack of co-segregation with disease.
BP2 No data on co-occurrence with a known pathogenic variant in trans are available.
BP4 Multiple in silico tools predict no significant effect.
BP5 No data indicate this variant is found in a case with an alternative molecular basis for disease.
BP6 The variant is absent from ClinVar — no reputable source has classified it as benign.
N/A · 6 PS1 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. POLD1, a DNA polymerase, is infrequently altered by mutation in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots