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LYFE SCIENCES
Project: HERA
NM_000051.4:c.2207C>T
p.Ala736Val  ·  ATM
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Classification rationale
1

The ATM c.2207C>T (p.Ala736Val) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as a variant of uncertain significance by 4 clinical laboratories.

clinvar ↗
2

The variant is present at very low frequency in gnomAD, including 3 of 1458952 alleles in v4.1 with no homozygotes, which supports PM2_Supporting and is well below the ATM BS1 and BA1 frequency thresholds.

gnomad_v4 ↗ gnomad_v2 ↗ cspec ↗
3

In silico evidence argues against a deleterious effect: REVEL is 0.103 and SpliceAI shows a maximum delta score of 0.02, supporting BP4 and arguing against 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
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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= 7.96223e-06; MAF= 0.00080%, 2/251186 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.76013e-05; MAF= 0.00176%, 2/113628 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 2.05627e-06; MAF= 0.00021%, 3/1458952 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.70245e-06; MAF= 0.00027%, 3/1110104 alleles, homozygotes = 0); grpmax FAF= 7.2e-07.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (4 clinical laboratories).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: ATM, a kinase involved in the DNA damage response, is mutated in various solid and hematologic malignancies.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueA736
Hotspots ↗