The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: ATM vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: ATM CSPEC Genes: [ 'ATM' ] * Message MONDOs: MONDO:0700270 CSPEC MONDO: [ 'MONDO:0016419', 'MONDO:0008840', 'MONDO:0018266' ]
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000051.4(ATM):c.8480T>G (p.Phe2827Cys)

CA115928

3022 (ClinVar)

Gene: ATM
Condition: ATM-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 3d40ca22-dc53-407e-8b14-a96f224ae3a4
Approved on: 2025-06-19
Published on: 2025-07-10

HGVS expressions

NM_000051.4:c.8480T>G
NM_000051.4(ATM):c.8480T>G (p.Phe2827Cys)
NC_000011.10:g.108345804T>G
CM000673.2:g.108345804T>G
NC_000011.9:g.108216531T>G
CM000673.1:g.108216531T>G
NC_000011.8:g.107721741T>G
NG_009830.1:g.127973T>G
NG_054724.1:g.129029A>C
ENST00000452508.7:c.8480T>G
ENST00000713593.1:c.*7951T>G
ENST00000278616.9:c.8480T>G
ENST00000638786.2:n.1178T>G
ENST00000682286.1:n.3237T>G
ENST00000682302.1:n.2898T>G
ENST00000683174.1:n.9964T>G
ENST00000683524.1:n.3704T>G
ENST00000684152.1:n.3896T>G
ENST00000684180.1:n.954T>G
ENST00000684447.1:n.4973T>G
ENST00000527805.6:c.*3544T>G
ENST00000675595.1:c.*3615T>G
ENST00000675843.1:c.8480T>G
ENST00000278616.8:c.8480T>G
ENST00000452508.6:c.8480T>G
ENST00000524755.5:c.227-10512A>C
ENST00000524792.5:n.4695T>G
ENST00000525729.5:c.641-36733A>C
ENST00000526725.1:n.272-5440A>C
ENST00000527531.5:c.*1196+9111A>C
ENST00000615746.4:c.*1196+9111A>C
NM_000051.3:c.8480T>G
NM_001330368.1:c.641-36733A>C
NM_001351110.1:c.695-10512A>C
NM_001351834.1:c.8480T>G
NR_147053.2:n.2301+9111A>C
NM_001330368.2:c.641-36733A>C
NM_001351110.2:c.695-10512A>C
NM_001351834.2:c.8480T>G
NR_147053.3:n.2299+9111A>C
More

Likely Pathogenic

Met criteria codes 3
PP3 PM3_Strong PS3_Supporting
Not Met criteria codes 23
BA1 PP4 PP1 PP2 PVS1 PM5 PM4 PM1 PM6 PM2 BS2 BS3 BS4 BS1 BP2 BP3 BP4 BP1 BP7 BP5 PS2 PS1 PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.8480T>G variant in ATM is a missense variant predicted to cause the substitution of phenylalanine by cysteine at amino acid 2827 (p.Phe2827Cys). This variant has been detected in at least one individual with Ataxia-Telangiectasia, who was described having a mild presentation (PMIDs: 8755918, 9000145, 9463314, 15928302, 19431188, 25040471, 30549301). The highest population minor allele frequency in gnomAD v4.1 is 0.00002196 in the South Asian population (PM2_Supporting, BS1, and BA1 are not met). Stable transfection of ATM-based cDNA constructs in an ATM-null lymphoblastoid cell line showed slightly decreased levels of kinase activity (caused by protein instability) indicating that this variant impacts protein function (PMID 19431188). The computational predictor, REVEL, gives a score of 0.889, which is above the threshold of 0.7333, evidence that correlates with impact on ATM function. In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant ATM-related cancer predisposition and autosomal recessive Ataxia-Telangiectasia based on the ACMG/AMP criteria applied as specified by the HBOP VCEP. (PS3_Supporting, PM3_Strong, PP3)
Met criteria codes
PP3
The computational predictor, REVEL gives a score of 0.889, which is above the threshold of 0.73, evidence that correlates with impact to ATM function (PP3).
PM3_Strong
This variant has been detected in at least 1 individual with an A-T phenotype (reported to be variant A-T (milder phenotype)). The individual is compound heterozygous for the variant and a pathogenic variant (c.1563_1564delAG) with phase in trans (PMID: 8755918). It is highly likely that the same individual is reported in studies, PMID 30549301, PMID: 25040471, PMID:19431188, PMID:15928302, PMID: 9463314, PMID:8755918, PMID: 9000145.
PS3_Supporting
Stable transfection of ATM-based cDNA constructs in an ATM-null lymphoblastoid cell line showed slightly decreased levels of kinase activity (caused by protein instability) indicating that this variant impacts protein function (PMID:19431188).
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Not applicable to ATM
PP1
Not applicable to ATM
PP2
Not applicable for ATM according to HBOP_VCEP
PVS1
This is a missense variant and therefore not applicable
PM5
other variants at this position have conflicting classifications/VUS
PM4
This is missense variant therefore not applicable
PM1
Not applicable for HBOP_VCEP specifications for ATM
PM6
Not applicable to ATM
PM2
The highest population minor allele frequency in gnomAD v4.1 is 0.00002196 in the South Asian population (PM2_Supporting, BS1, and BA1 are not met).
BS2
not applicable to ATM
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
Not applicable to ATM
BS1
gnomAD v4.1 FAF of 0.00000385 (SAS) is less than BS1 threshold of 0.0005
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
Not applicable to ATM
BP4
The computational predictor, REVEL gives a score of 0.889, which is above the threshold of 0.73, evidence that correlates with impact to ATM function (PP3).
BP1
Not applicable for ATM according to HBOP_VCEP
BP7
missense variant therefore does not apply
BP5
not applicable to ATM
PS2
Not applicable to ATM
PS1
no variants resulting in same amino acid change.
PS4
case-control data not available for this variant
Curation History
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