ATF2 p.Asp440=
c.1320C>T · rs36047041 · VCV775788
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.84%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.457 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.48, phastCons 1 |
| Overall | ||
| CADD | 6.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.84%
African / African-American · 1,382/74,992 alleles
Filtering AF
1.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.73%
Overall
0.0953%
1,538/1,613,456 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.84% | 54 |
| Admixed American | 0.112% | 894 |
| Remaining individualsnot grpmax-eligible | 0.104% | 961 |
| Middle Eastern | 0.0495% | 2,019 |
| South Asian | 0.00769% | 13,011 |
| European (non-Finnish) | 0.00119% | 84,258 |
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
- ATF2
- Protein
- p.Asp440=
- Coding
- c.1320C>T
- MANE Select
- NM_000514 · reported on NM_001880
- dbSNP
- rs36047041
- Type
- single nucleotide variant
- Location
- chr2:175074807 (GRCh38)
- Structure
- AlphaFold pLDDT 75.29 · 4 PDB
Similar variants
- GDNF c.*2213G>A Uncertain significance ★★ same type
- GDNF c.*2828T>A Uncertain significance ★★ same type
- GDNF p.Arg116Gln Uncertain significance ★★ ⚠ same type
- ATF1 p.Tyr109= Benign ★★ same type
- ATF2 p.Asn348= Benign ★★ same type
- GDNF c.152-73C>T Benign ★★ same type
- GDNF c.-51A>G Benign ★★ same type
- GDNF c.*1264C>T Benign ★★ same type
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/atf2-p-asp440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown