Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 15%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -5.2 |
| Overall | ||
| CADD | 0.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15%
African / African-American · 10,921/73,044 alleles
Filtering AF
14.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.6%
Overall
0.825%
12,783/1,548,678 alleles · common
exomes 6,260/1,396,436 · genomes 6,523/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 15% | 7 |
| Admixed American | 1.26% | 80 |
| Middle Eastern | 1.24% | 81 |
| Remaining individualsnot grpmax-eligible | 1.05% | 95 |
| South Asian | 0.0488% | 2,048 |
| European (non-Finnish) | 0.041% | 2,442 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0105% | 9,545 |
| Finnishnot grpmax-eligible | 0.00339% | 29,469 |
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
- ACOD1
- Protein
- p.Pro77=
- Coding
- c.231G>T
- MANE Select
- NM_001258406
- dbSNP
- rs611161
- Type
- single nucleotide variant
- Location
- chr13:76953656 (GRCh38)
- Gene constraint
- LOEUF 1.53 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.45 · 6 PDB
Similar variants
- ACOD1 p.Arg273His Benign ★★ same type
- ACOD1 p.Asn152Ser Benign ★★ same type
- ACOD1 c.265-3C>T Benign ★ same type
- ACOD1 p.Ser61Arg Likely 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/acod1-p-pro77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown