Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.08%, afr) — too common for a highly-penetrant pathogenic allele
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 -3, phastCons 0.027 |
| Overall | ||
| CADD | 8.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.08%
African / African-American · 4,555/74,858 alleles
Filtering AF
5.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.88%
Overall
0.31%
4,974/1,606,316 alleles · common
exomes 2,376/1,454,116 · genomes 2,598/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.08% | 16 |
| Remaining individualsnot grpmax-eligible | 0.348% | 288 |
| Admixed American | 0.272% | 368 |
| Middle Eastern | 0.0827% | 1,209 |
| South Asian | 0.00556% | 17,972 |
| European (non-Finnish) | 0.0028% | 35,660 |
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
- ABI3
- Protein
- p.Pro174=
- Coding
- c.522T>C
- MANE Select
- NM_016428
- dbSNP
- rs2233371
- Type
- single nucleotide variant
- Location
- chr17:49219599 (GRCh38)
- Gene constraint
- LOEUF 1.113 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.31
- Residue 174
- the 'disordered' region
Similar variants
- ABI3 p.Glu87= Benign ★★ same type
- ABI3 p.Ala126Ser Uncertain significance ★ ⚠ same type
- ABI3 p.Ala173Gly Uncertain significance ★ ⚠ same type
- ABI3 p.Ala173Ser Uncertain significance ★ ⚠ same type
- ABI3 p.Ala178Thr Uncertain significance ★ ⚠ same type
- ABI3 p.Ala18Thr Uncertain significance ★ ⚠ same type
- ABI3 p.Ala204Val Uncertain significance ★ ⚠ same type
- ABI3 p.Ala208Glu 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/abi3-p-pro174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown