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LYFE SCIENCES
Project: HERA
NM_000051.4:c.8418+5_8418+8del
p.?  ·  ATM
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Initialising…
0%
Legacy Engine
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Classification rationale
1

The ATM c.8418+5_8418+8del (NP_000042.3:p.?) variant has not been reported in ClinVar.

clinvar ↗
2

This variant is present in gnomAD v4.1 at AF 0.00465% (75/1,613,598 alleles; grpmax FAF 0.005111%) and in gnomAD v2.1 at AF 0.00071% (2/282,394 alleles), which is above the ATM PM2_Supporting threshold of 0.001% and below the BS1 threshold of 0.05%.

gnomad_v4 ↗ gnomad_v2 ↗ cspec ↗
3

SpliceAI predicts an adverse splicing effect with a maximum delta score of 0.89, which exceeds the ATM PP3 threshold of 0.2 for intronic variants outside the donor ±1,2 positions and supports PP3.

spliceai ↗ cspec ↗
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 v2.1This variant is present in gnomAD v2.1 (AF= 7.0823e-06; MAF= 0.00071%, 2/282394 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.55222e-05; MAF= 0.00155%, 2/128848 alleles, homozygotes = 0).
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 4.648e-05; MAF= 0.00465%, 75/1613598 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.27221e-05; MAF= 0.00627%, 74/1179808 alleles, homozygotes = 0); grpmax FAF= 5.111e-05.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.89).
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.