A2M p.Val129=
c.387C>G · rs56202499 · VCV777428
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.35%, 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 1.2 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 4.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.35%
Middle Eastern · 82/6,062 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.873%
14,090/1,613,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.35% | 74 |
| Ashkenazi Jewishnot grpmax-eligible | 1.25% | 80 |
| European (non-Finnish) | 1.03% | 97 |
| Remaining individualsnot grpmax-eligible | 0.77% | 130 |
| Admixed American | 0.692% | 145 |
| Finnishnot grpmax-eligible | 0.579% | 173 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| African / African-American | 0.172% | 582 |
| South Asian | 0.0933% | 1,071 |
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
- A2M
- Protein
- p.Val129=
- Coding
- c.387C>G
- MANE Select
- NM_000014
- dbSNP
- rs56202499
- Type
- single nucleotide variant
- Location
- chr12:9112420 (GRCh38)
- Gene constraint
- LOEUF 0.765 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.61 · 13 PDB
- Residue 129
- a β-strand
Similar variants
- A2M c.3756+4G>A Benign/Likely benign ★★ same type
- A2M p.Ala844= Benign ★★ same type
- A2M p.Asp277Asn Benign ★★ same type
- A2M p.Ile1000Val Benign ★★ same type
- A2M p.Pro261Leu Benign ★★ same type
- A2M p.Tyr1152= Benign/Likely benign ★★ same type
- A2M p.Val120= Likely benign ★★ same type
- A2M p.Val437= Benign ★★ 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/a2m-p-val129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown