CSAD p.Ala103=
c.309C>T · rs57871710 · VCV778640
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.2%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.224 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -4.1 |
| Overall | ||
| CADD | 6.802 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.2%
African / African-American · 2,401/74,986 alleles
Filtering AF
3.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.05%
Overall
0.352%
5,681/1,614,076 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.2% | 31 |
| South Asian | 1.87% | 53 |
| Middle Eastern | 1.29% | 78 |
| Admixed American | 0.703% | 142 |
| Remaining individualsnot grpmax-eligible | 0.547% | 183 |
| Finnishnot grpmax-eligible | 0.17% | 587 |
| Ashkenazi Jewishnot grpmax-eligible | 0.122% | 822 |
| European (non-Finnish) | 0.0487% | 2,052 |
| East Asian | 0.0245% | 4,080 |
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
- CSAD
- Protein
- p.Ala103=
- Coding
- c.309C>T
- MANE Select
- NM_001244705
- dbSNP
- rs57871710
- Type
- single nucleotide variant
- Location
- chr12:53172381 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.67 · 1 PDB
- Residue 103
- an α-helix
Similar variants
- CSAD p.Ala199= Benign ★★ same type
- CSAD p.Glu50= Benign ★★ same type
- CSAD c.-21C>T Uncertain significance ★ same type
- CSAD c.-24G>T Uncertain significance ★ same type
- CSAD c.-27C>T Uncertain significance ★ same type
- CSAD c.-33C>G Uncertain significance ★ same type
- CSAD c.-48A>G Uncertain significance ★ same type
- CSAD c.-90-660A>G 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/csad-p-ala103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown