Is ATM p.Asp2913= (c.8739T>C) pathogenic?

ATM p.Asp2913= (c.8739T>C) is classified Benign/Likely benign in ATM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-08-27). Absent from gnomAD v4.1; Associated with ataxia telangiectasia.

What condition is associated with ATM p.Asp2913= (c.8739T>C)?

ATM p.Asp2913= (c.8739T>C) is associated with ataxia telangiectasia, hereditary neoplastic syndrome, hereditary breast carcinoma (ClinVar).

How common is ATM p.Asp2913= (c.8739T>C) in the general population?

ATM p.Asp2913= (c.8739T>C) is absent from gnomAD v4.1 (gnomAD).

How is Ataxia-telangiectasia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ATM p.Asp2913=

c.8739T>C · rs764778912 · VCV822695

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ataxia telangiectasia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.69	GERP -1.7, phastCons 1
Overall
CADD	7.337	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ATM
Protein: p.Asp2913=
Coding: c.8739T>C
MANE Select: NM_000051
dbSNP: rs764778912
Type: single nucleotide variant
Location: chr11:108353833 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 2913: a UniProt-annotated variant site (in at; uncertain significance; reduces protein abundance); a UniProt-annotated variant site (in at); a UniProt-annotated variant site (in at; uncertain significance); the pi3k/pi4k catalytic domain; an α-helix; a UniProt-annotated variant site (in at; uncertain significance; increases protein abundance)

Full ATM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ataxia telangiectasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome hereditary breast carcinoma

For Ataxia-telangiectasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: 1-5 / 10 000 (Norway)

Similar variants

ATM p.Asp2913Tyr Pathogenic/Likely pathogenic ★★ same residue
ATM p.Asp2913Glu Uncertain significance ★★ same residue
ATM p.Asp2913His Uncertain significance ★★ ⚠ same residue
ATM p.Asp2913Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Asp2913fs Pathogenic ★ same residue
ATM c.1607+1G>T Pathogenic ★★★ same condition
ATM c.2251-4A>G Likely pathogenic ★★★ same condition
ATM c.2466+5G>C Likely pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/atm-p-asp2913 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown