AFG2A p.Ser832=
c.2496A>C · rs2530450385 · VCV3250664
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00161%, 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 -0.38 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 0.712 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00161%
European (non-Finnish) · 19/1,179,586 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00137%
20/1,461,362 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00161% | 62,084 |
| African / African-American | 0.00133% | 75,016 |
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
- AFG2A
- Protein
- p.Ser832=
- Coding
- c.2496A>C
- MANE Select
- NM_145207
- dbSNP
- rs2530450385
- Type
- single nucleotide variant
- Location
- chr4:123256171 (GRCh38)
- Structure
- AlphaFold pLDDT 73.21 · 2 PDB
- Residue 832
- a UniProt-annotated variant site (in nedhsb)
Similar variants
- AFG2A c.1714+1G>A Pathogenic ★★ same type
- AFG2A c.446+1G>A Likely pathogenic ★★ same type
- AFG2A p.Ala844Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- AFG2A p.Arg445Ter Pathogenic/Likely pathogenic ★★ same type
- AFG2A p.Arg510Ter Pathogenic/Likely pathogenic ★★ same type
- AFG2A p.Arg514Ter Pathogenic/Likely pathogenic ★★ same type
- AFG2A p.Arg538Ter Pathogenic/Likely pathogenic ★★ same type
- AFG2A p.Arg655Ter Pathogenic/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/afg2a-p-ser832 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown