AOPEP p.Pro547=
c.1641C>T · rs545129535 · VCV3025026
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.634%, sas)
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 -11 | GERP -4.3 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.634%
South Asian · 533/84,046 alleles
Filtering AF
0.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.572%
Overall
0.0402%
623/1,550,704 alleles · rare
exomes 581/1,398,424 · genomes 42/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.634% | 158 |
| Remaining individualsnot grpmax-eligible | 0.0598% | 1,673 |
| Middle Eastern | 0.0334% | 2,998 |
| East Asian | 0.00733% | 13,639 |
| European (non-Finnish) | 0.0041% | 24,403 |
| African / African-American | 0.00273% | 36,573 |
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
- AOPEP
- Protein
- p.Pro547=
- Coding
- c.1641C>T
- MANE Select
- NM_001193329
- dbSNP
- rs545129535
- Type
- single nucleotide variant
- Location
- chr9:94928511 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36
- Residue 547
- a UniProt-annotated variant site (in dyt31)
Similar variants
- FANCC p.Ala547Val Uncertain significance ★★ ⚠ same residue
- FANCC p.Ala547Gly Uncertain significance ★ ⚠ same residue
- FANCC p.Ala547Ser Uncertain significance ★ ⚠ same residue
- AOPEP p.Gln235Ter Likely pathogenic ★★ same type
- FANCC c.1072+2T>A Likely pathogenic ★★ same type
- FANCC c.1155-2A>G Likely pathogenic ★★ same type
- FANCC c.522-1G>C Likely pathogenic ★★ same type
- FANCC c.687-1G>A Likely pathogenic ★★ 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/aopep-p-pro547 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown