AFG2B p.Ala162=
c.486C>G · VCV4084426
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, 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 -0.82 | GERP 1.4, phastCons 0.001 |
| Overall | ||
| CADD | 6.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,050 alleles
Filtering AF
0.00583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00277%
40/1,445,806 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,025 |
| European (non-Finnish) | 0.00297% | 33,692 |
| East Asian | 0.00223% | 44,792 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,346 |
| South Asian | 0.0011% | 90,942 |
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.Ala162=
- Coding
- c.486C>G
- MANE Select
- NM_024063
- Type
- single nucleotide variant
- Location
- chr15:45402915 (GRCh38)
- Structure
- AlphaFold pLDDT 77.37 · 2 PDB
- Residue 162
- the 'required for interaction with afg2a and cinp' region
Similar variants
- 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
- AFG2B p.Tyr738Cys 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-ala162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown