Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 49.5%, amr) — 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 2.1 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 2.804 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
49.5%
Admixed American · 29,704/59,962 alleles
Filtering AF
49.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 48.9%
Overall
39.4%
636,182/1,613,218 alleles · common
exomes 580,482/1,461,614 · genomes 55,700/151,604 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 49.5% | 2 |
| Amishnot grpmax-eligible | 48% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 42.7% | 2 |
| European (non-Finnish) | 41.4% | 2 |
| Finnishnot grpmax-eligible | 40.3% | 2 |
| Remaining individualsnot grpmax-eligible | 37.9% | 3 |
| Middle Eastern | 32.6% | 3 |
| South Asian | 32.4% | 3 |
| African / African-American | 27.8% | 4 |
| East Asian | 7.58% | 13 |
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
- CAVIN4
- Protein
- p.Arg332=
- Coding
- c.996G>A
- MANE Select
- NM_001018116
- dbSNP
- rs2780956
- Type
- single nucleotide variant
- Location
- chr9:100586352 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 66.21
- Residue 332
- the 'disordered' region
Similar variants
- CAVIN4 p.Arg332Ser Uncertain significance ★ ⚠ same residue
- CAVIN4 p.Arg17Cys Uncertain significance ★★ ⚠ same type
- CAVIN4 p.Arg272Cys Uncertain significance ★★ ⚠ same type
- CAVIN4 p.Asn128Lys Uncertain significance ★★ ⚠ same type
- CAVIN4 p.Pro142Leu Uncertain significance ★★ ⚠ same type
- CAVIN4 p.Ser20Thr Uncertain significance ★★ ⚠ same type
- CAVIN4 c.408+28T>C Likely benign ★★ same type
- CAVIN4 c.408+42T>C 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/cavin4-p-arg332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown