ANXA11 p.Pro15=
c.45A>G · VCV4699989
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, nfe)
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 -1.1 | GERP -3 |
| Overall | ||
| CADD | 6.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
European (non-Finnish) · 40/1,179,964 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00225%
Overall
0.00248%
40/1,613,954 alleles · very rare
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
- ANXA11
- Protein
- p.Pro15=
- Coding
- c.45A>G
- MANE Select
- NM_145868
- Type
- single nucleotide variant
- Location
- chr10:80172817 (GRCh38)
- Gene constraint
- LOEUF 1.086 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.32 · 2 PDB
- Residue 15
- the 'disordered' region
Similar variants
- ANXA11 p.Asp40Gly Pathogenic ★★ ⚠ same type
- ANXA11 p.Asp40Tyr Pathogenic/Likely pathogenic ★★ ⚠ same type
- ANXA11 p.Gly38Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- ANXA11 c.171+1G>A Uncertain significance ★★ same type
- ANXA11 c.744+2C>T Uncertain significance ★★ same type
- ANXA11 c.744+3G>A Uncertain significance ★★ same type
- ANXA11 p.Ala361Thr Uncertain significance ★★ ⚠ same type
- ANXA11 p.Ala443Asp 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/anxa11-p-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown