ANXA11 p.Val158=
c.474G>T · rs139412104 · VCV1603479
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.476%, mid)
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 3.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 8.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.476%
Middle Eastern · 27/5,670 alleles
Filtering AF
0.336%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.289%
Overall
0.187%
2,873/1,540,414 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.476% | 210 |
| Remaining individualsnot grpmax-eligible | 0.222% | 451 |
| European (non-Finnish) | 0.21% | 476 |
| Finnishnot grpmax-eligible | 0.173% | 576 |
| Admixed American | 0.167% | 598 |
| South Asian | 0.0958% | 1,044 |
| African / African-American | 0.0567% | 1,764 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00413% | 24,230 |
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.Val158=
- Coding
- c.474G>T
- MANE Select
- NM_145868
- dbSNP
- rs139412104
- Type
- single nucleotide variant
- Location
- chr10:80169056 (GRCh38)
- Gene constraint
- LOEUF 1.086 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.32 · 2 PDB
- Residue 158
- the 'disordered' region
Similar variants
- ANXA11 p.Val158_Pro159insThrTyrProGlyGlnProProVal Uncertain significance same residue
- 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
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-val158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown