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LYFE SCIENCES
Project: HERA
NM_006231.4:c.6111C>T
p.Ala2037=  ·  POLE
ACMG/AMP
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Initialising…
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Legacy Engine
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Classification rationale
1

NM_006231.4:c.6111C>T is a synonymous POLE variant, NP_006222.2:p.(Ala2037=), and SpliceAI predicts no significant splice impact with a maximum delta score of 0.05, supporting BP7.

spliceai ↗
2

The variant has been submitted to ClinVar as Likely benign by 4 clinical laboratories and as Benign by 1 clinical laboratory, supporting BP6 under the generic ACMG/AMP framework.

clinvar ↗
3

Population frequency is low in gnomAD v4.1 at 4.15156e-05 (0.00415%), which is below the BS1 threshold of 0.3% and the BA1 threshold of 1.0%, so benign frequency criteria stronger than supporting are not met.

gnomad_v4 ↗
4

Using the retrieved generic ACMG/AMP final classification combination rules, BP6 plus BP7 constitutes two supporting benign criteria and is consistent with a Likely benign classification.

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
Rationale
Select a criterion to inspect its explanation.
Evidence used
Gaps remaining
Rule
Publications
Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 4.97368e-05; MAF= 0.00497%, 14/281482 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000228698; MAF= 0.02287%, 7/30608 alleles, homozygotes = 0); grpmax FAF= 0.00010658.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 4.15156e-05; MAF= 0.00415%, 67/1613852 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 9.88099e-05; MAF= 0.00988%, 9/91084 alleles, homozygotes = 0); grpmax FAF= 6.806e-05.
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (1 clinical laboratory).
Functional evidence
03
Functional
OncoKB oncogenicity for this specific variant: Unknown Oncogenic Effect (variant has not been individually curated).
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05).
COSMIC evidence
05
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV107342250, n = 1 times).
Cancer hotspots evidence
06
Cancer hotspots
No cancer hotspot summary recorded.