CAP1 p.Ala73=
c.219G>A · rs34497744 · VCV775536
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.75%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.55 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -4.9 |
| Overall | ||
| CADD | 17.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.75%
African / African-American · 2,064/75,000 alleles
Filtering AF
2.65%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.61%
Overall
0.151%
2,442/1,613,628 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.75% | 36 |
| Middle Eastern | 0.396% | 253 |
| Remaining individualsnot grpmax-eligible | 0.202% | 496 |
| Admixed American | 0.16% | 625 |
| South Asian | 0.0362% | 2,759 |
| European (non-Finnish) | 0.00805% | 12,417 |
| East Asian | 0.00668% | 14,960 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
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
- CAP1
- Protein
- p.Ala73=
- Coding
- c.219G>A
- MANE Select
- NM_006367
- dbSNP
- rs34497744
- Type
- single nucleotide variant
- Location
- chr1:40061737 (GRCh38)
- Gene constraint
- LOEUF 0.361 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85 · 5 PDB
Similar variants
- CAP1 p.Tyr31= Benign ★★ same type
- CAP1 p.Ala145Ser Uncertain significance ★ ⚠ same type
- CAP1 p.Ala161Ser Uncertain significance ★ ⚠ same type
- CAP1 p.Ala259Ser Uncertain significance ★ ⚠ same type
- CAP1 p.Ala259Thr Uncertain significance ★ ⚠ same type
- CAP1 p.Ala270Gly Uncertain significance ★ ⚠ same type
- CAP1 p.Ala302Val Uncertain significance ★ ⚠ same type
- CAP1 p.Ala52Val 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/cap1-p-ala73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown