Variant: NM_000051.4(ATM):c.8494C>T (p.Arg2832Cys)

CA287019

127459 (ClinVar)

Gene: ATM

Condition: hereditary breast cancer

Inheritance Mode: Autosomal dominant inheritance

UUID: a1f4fda0-ab77-4c22-a6be-6dc2f95f8e60

Approved on: 2024-01-25

Published on: 2024-02-14

HGVS expressions

NM_000051.4:c.8494C>T
NM_000051.4(ATM):c.8494C>T (p.Arg2832Cys)
NC_000011.10:g.108345818C>T
CM000673.2:g.108345818C>T
NC_000011.9:g.108216545C>T
CM000673.1:g.108216545C>T
NC_000011.8:g.107721755C>T
NG_009830.1:g.127987C>T
NG_054724.1:g.129015G>A
ENST00000452508.7:c.8494C>T
ENST00000713593.1:c.*7965C>T
ENST00000278616.9:c.8494C>T
ENST00000638786.2:n.1192C>T
ENST00000682286.1:n.3251C>T
ENST00000682302.1:n.2912C>T
ENST00000683174.1:n.9978C>T
ENST00000683524.1:n.3718C>T
ENST00000684152.1:n.3910C>T
ENST00000684180.1:n.968C>T
ENST00000684447.1:n.4987C>T
ENST00000527805.6:c.*3558C>T
ENST00000675595.1:c.*3629C>T
ENST00000675843.1:c.8494C>T
ENST00000278616.8:c.8494C>T
ENST00000452508.6:c.8494C>T
ENST00000524755.5:c.227-10526G>A
ENST00000524792.5:n.4709C>T
ENST00000525729.5:c.641-36747G>A
ENST00000526725.1:n.272-5454G>A
ENST00000527531.5:c.*1196+9097G>A
ENST00000615746.4:c.*1196+9097G>A
NM_000051.3:c.8494C>T
NM_001330368.1:c.641-36747G>A
NM_001351110.1:c.695-10526G>A
NM_001351834.1:c.8494C>T
NR_147053.2:n.2301+9097G>A
NM_001330368.2:c.641-36747G>A
NM_001351110.2:c.695-10526G>A
NM_001351834.2:c.8494C>T
NR_147053.3:n.2299+9097G>A

Likely Pathogenic

• Met criteria codes: PS3_Supporting PM3_Strong PP3

• Not Met criteria codes: PM2

Expert Panel

Hereditary Breast, Ovarian and Pancreatic Cancer VCEP

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 1.2.0

Evidence submitted by expert panel

Hereditary Breast, Ovarian and Pancreatic Cancer VCEP

The c.8494C>T variant in ATM is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 2832 (p.Arg2832Cys). This variant has been detected in at least 3 individuals with Ataxia-Telangiectasia (PMID: 26896183, 22017321, 26846839). The highest minor allele frequency in gnomAD v2.1.1 of 0.01% (2/16244 alleles) in the African/African American population (PM2_Supporting, BS1, and BA1 are not met). The computational predictor, Revel (Score: 0.83), predicts a damaging effect on ATM function. Additionally, experimental studies showed that this variant has impact on ATM kinase activity and protein levels but radiosensitivity was found to be intermediate compared to wild type (PMID: 18634022). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant hereditary breast cancer and autosomal recessive Ataxia-Telangiectasia based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP. (PM3_Strong, PP3, PS3_supporting)

Met criteria codes

• PS3_Supporting: Experimental studies showed that this variant has impact on ATM kinase activity and protein levels but radiosensitivity was found to be intermediate compared to wild type
• PM3_Strong: This variant has been detected in atleast 3 individuals with Ataxia-Telangiectasia.( PMID: 26896183, 22017321, 26846839)
• PP3: REVEL predicted the score of 0.83 which is above thresholds defined by the HBOP VCEP for PP3

Not Met criteria codes

• PM2: This variant has a minor allele frequency in gnomAD v2.1.1 of 0.01% (2/16244 alleles) in the African/African American population (PM2_Supporting, BS1, and BA1 are not met).