SLC19A1 p.Ala324=
c.972G>A · rs79091853 · VCV1637940
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 10.5%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.042 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.79 | acceptor gain · deltas |
| Pangolin | Δ0.30 | gain · loss 0.11 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.4 |
| Overall | ||
| CADD | 17.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.5%
South Asian · 7,051/67,200 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.2%
Overall
1.63%
23,381/1,433,842 alleles · common
exomes 20,322/1,285,852 · genomes 3,059/147,990 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 10.5% | 10 |
| East Asian | 9.07% | 11 |
| Admixed American | 5.37% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 5.06% | 20 |
| Middle Eastern | 3.05% | 33 |
| Remaining individualsnot grpmax-eligible | 2.43% | 41 |
| Finnishnot grpmax-eligible | 2.37% | 42 |
| Amishnot grpmax-eligible | 1.92% | 52 |
| European (non-Finnish) | 0.657% | 152 |
| African / African-American | 0.214% | 467 |
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
- SLC19A1
- Protein
- p.Ala324=
- Coding
- c.972G>A
- MANE Select
- NM_194255
- dbSNP
- rs79091853
- Type
- single nucleotide variant
- Location
- chr21:45530949 (GRCh38)
- Gene constraint
- LOEUF 1.585 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.30 · 19 PDB
- Residue 324
- a turn
Similar variants
- SLC19A1 p.Ala324Val Uncertain significance ★ same residue
- COL18A1 p.Arg1081Ter Pathogenic/Likely pathogenic ★★ same type
- COL18A1 p.Arg915Ter Pathogenic/Likely pathogenic ★★ same type
- RFC1 p.Arg383Ter Pathogenic/Likely pathogenic ★★ same type
- COL18A1 c.*30G>A Uncertain significance ★★ same type
- COL18A1 p.Ala1089Thr Uncertain significance ★★ ⚠ same type
- COL18A1 p.Ala1254Val Uncertain significance ★★ ⚠ same type
- COL18A1 p.Arg1081Gln 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/slc19a1-p-ala324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown