ATRIP p.Phe37=
c.111C>T · rs368960700 · VCV789984
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.47%, afr)
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 -0.003 | GERP -3.9, phastCons 0.01 |
| Overall | ||
| CADD | 9.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.47%
African / African-American · 1,734/70,174 alleles
Filtering AF
2.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.34%
Overall
0.135%
2,080/1,537,716 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.47% | 40 |
| Remaining individualsnot grpmax-eligible | 0.206% | 486 |
| Admixed American | 0.193% | 518 |
| Middle Eastern | 0.104% | 962 |
| European (non-Finnish) | 0.0108% | 9,232 |
| South Asian | 0.0012% | 83,044 |
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
- ATRIP
- Protein
- p.Phe37=
- Coding
- c.111C>T
- MANE Select
- NM_130384
- dbSNP
- rs368960700
- Type
- single nucleotide variant
- Location
- chr3:48446956 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
- Residue 37
- the 'disordered' region
Similar variants
- TREX1 p.Leu37Pro Uncertain significance ★ ⚠ same residue
- TREX1 p.Leu37= Likely benign ★ same residue
- TREX1 p.Arg114His Pathogenic/Likely pathogenic ★★ ⚠ same type
- TREX1 p.Arg164Ter Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Asp18Asn Pathogenic ★★ same type
- TREX1 p.Asp200His Likely pathogenic ★★ same type
- TREX1 p.Gln135Ter Pathogenic/Likely pathogenic ★★ same type
- ATRIP p.Ala119Thr Uncertain significance ★★ ⚠ 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/atrip-p-phe37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown