MAF p.Ala162=
c.486C>G · VCV4534647
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00396%, eas)
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 3.3 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 12.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00396%
East Asian · 1/25,244 alleles
Filtering AF
0.001%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000809%
Overall
0.00154%
18/1,165,676 alleles · very rare
exomes 15/1,017,522 · genomes 3/148,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00396% | 25,244 |
| European (non-Finnish) | 0.00169% | 59,212 |
| African / African-American | 0.00162% | 61,540 |
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
- MAF
- Protein
- p.Ala162=
- Coding
- c.486C>G
- MANE Select
- NM_005360
- Type
- single nucleotide variant
- Location
- chr16:79599417 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 62.21
- Residue 162
- the 'represses are-mediated transcription' region
Similar variants
- MAF p.Ala162_Val163insAla Uncertain significance ★ same residue
- MAF p.Ala302Val Pathogenic/Likely pathogenic ★★ same type
- MAF p.Arg299Cys Pathogenic/Likely pathogenic ★★ same type
- MAF p.Arg306Gly Pathogenic/Likely pathogenic ★★ same type
- MAF p.Cys305Phe Likely pathogenic ★★ same type
- MAF p.Pro59His Pathogenic/Likely pathogenic ★★ same type
- MAF p.Ser54Leu Pathogenic ★★ same type
- MAF p.Ser57Phe 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/maf-p-ala162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown