Is ATM p.Asp899= (c.2697C>T) pathogenic?

ATM p.Asp899= (c.2697C>T) is classified Benign/Likely benign in ATM (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Very rare (popmax 0.00801%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with ATM p.Asp899= (c.2697C>T)?

ATM p.Asp899= (c.2697C>T) is associated with hereditary neoplastic syndrome, ataxia telangiectasia, hereditary breast carcinoma (ClinVar).

How common is ATM p.Asp899= (c.2697C>T) in the general population?

ATM p.Asp899= (c.2697C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

ATM p.Asp899=

c.2697C>T · rs786202978 · VCV186473

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.081	GERP -0.56, phastCons 0.91
Overall
CADD	7.745	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,910 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.00062% 10/1,613,920 alleles · very rare exomes 5/1,461,756 · genomes 5/152,164 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,485
Admixed American	0.00167%	60,000
South Asian	0.0011%	91,078
European (non-Finnish)	0.000169%	589,998

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ATM
Protein: p.Asp899=
Coding: c.2697C>T
MANE Select: NM_000051
dbSNP: rs786202978
Type: single nucleotide variant
Location: chr11:108268468 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 899: a UniProt-annotated variant site (in at); an α-helix; a UniProt-annotated variant site (in at; uncertain significance)

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ataxia telangiectasia hereditary breast carcinoma

Similar variants

ATM p.Asp899Gly Uncertain significance ★★ same residue
ATM p.Asp899Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
ATM p.Asp899His Uncertain significance ★ same residue
ATM p.Asp899_Met900insIleLeuPheLeuAsp Uncertain significance ★ 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
ATM c.3078-1G>A 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-asp899 (accessed [today's date]).

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