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LYFE SCIENCES
Project: HERA
NM_006231.4:c.4952+9A>G
p.?  ·  POLE
León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
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Classification rationale
1

The POLE c.4952+9A>G (p.?) variant has not been identified in the León-Castillo endometrial carcinoma recurrence table and has been reported in ClinVar as Likely benign by one clinical laboratory.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and present once in gnomAD v4.1 (1/1613298 alleles; AF 6.20e-07), which supports rarity but does not establish pathogenic enrichment.

gnomad_v2 ↗ gnomad_v4 ↗
3

SpliceAI predicts low splice impact for NM_006231.4 with a maximum delta score of 0.07, arguing against a clinically meaningful splicing effect.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1Absent from gnomAD v2.1.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 6.19848e-07; MAF= 0.00006%, 1/1613298 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09813e-05; MAF= 0.00110%, 1/91064 alleles, homozygotes = 0).
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
06
Cancer hotspots
No cancer hotspot summary recorded.