AFG2B p.Val151=
c.453C>T · VCV3257011
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -2.8 |
| Overall | ||
| CADD | 4.291 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,820 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000626%
10/1,598,390 alleles · ultra-rare
exomes 8/1,446,090 · genomes 2/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,470 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,338 |
| European (non-Finnish) | 0.000254% | 393,142 |
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
- AFG2B
- Protein
- p.Val151=
- Coding
- c.453C>T
- MANE Select
- NM_024063
- Type
- single nucleotide variant
- Location
- chr15:45402882 (GRCh38)
- Structure
- AlphaFold pLDDT 77.37 · 2 PDB
- Residue 151
- the 'required for interaction with afg2a and cinp' region
Similar variants
- AFG2B p.Val151Ile Uncertain significance ★ ⚠ same residue
- AFG2B p.Ile466Met Pathogenic/Likely pathogenic ★★ ⚠ same type
- AFG2B p.Thr400Ile Pathogenic/Likely pathogenic ★★ same type
- AFG2B p.Arg288Pro Uncertain significance ★★ ⚠ same type
- AFG2B p.Arg28Cys Uncertain significance ★★ ⚠ same type
- AFG2B p.Phe71Leu Uncertain significance ★★ ⚠ same type
- AFG2B p.Pro558Arg Uncertain significance ★★ ⚠ same type
- AFG2B p.Ser333Ile 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/afg2b-p-val151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown