NCAPD3 p.Pro228=
c.684A>G · rs34328388 · VCV779384
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.08%, 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 0.59 | GERP -5, phastCons 0.99 |
| Overall | ||
| CADD | 7.883 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.08%
African / African-American · 3,060/75,054 alleles
Filtering AF
3.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.91%
Overall
0.219%
3,539/1,614,172 alleles · low-frequency
exomes 1,758/1,461,802 · genomes 1,781/152,370 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.08% | 25 |
| Admixed American | 0.325% | 308 |
| Remaining individualsnot grpmax-eligible | 0.269% | 372 |
| Middle Eastern | 0.215% | 466 |
| South Asian | 0.00878% | 11,385 |
| European (non-Finnish) | 0.0078% | 12,826 |
| East Asian | 0.00669% | 14,958 |
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
- NCAPD3
- Protein
- p.Pro228=
- Coding
- c.684A>G
- MANE Select
- NM_015261
- dbSNP
- rs34328388
- Type
- single nucleotide variant
- Location
- chr11:134209361 (GRCh38)
- Gene constraint
- LOEUF 0.643 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.29 · 1 PDB
Similar variants
- NCAPD3 c.4388+1G>A Likely pathogenic ★★ same type
- NCAPD3 p.Ala334Thr Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Arg519Cys Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Gly1451Arg Uncertain significance ★★ ⚠ same type
- NCAPD3 p.Lys221Asn Uncertain significance ★★ ⚠ same type
- NCAPD3 c.1090-33A>G Benign ★★ same type
- NCAPD3 c.1215+28G>A Benign ★★ same type
- NCAPD3 c.1525+18T>A 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/ncapd3-p-pro228 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown