TLR9 p.Ser147=
c.441C>A · rs116310431 · VCV709661
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.16%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.027 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.36 | GERP 1.1, phastCons 0.01 |
| Overall | ||
| CADD | 2.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.16%
African / African-American · 1,621/74,998 alleles
Filtering AF
2.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.04%
Overall
0.118%
1,896/1,611,864 alleles · low-frequency
exomes 1,002/1,459,540 · genomes 894/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.16% | 46 |
| Middle Eastern | 0.331% | 302 |
| Remaining individualsnot grpmax-eligible | 0.208% | 480 |
| Admixed American | 0.124% | 806 |
| South Asian | 0.0121% | 8,256 |
| European (non-Finnish) | 0.00339% | 29,467 |
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
- TLR9
- Protein
- p.Ser147=
- Coding
- c.441C>A
- MANE Select
- NM_017442
- dbSNP
- rs116310431
- Type
- single nucleotide variant
- Location
- chr3:52223875 (GRCh38)
- Gene constraint
- LOEUF 1.116 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.96 · 3 PDB
Similar variants
- TLR9 p.Arg5Cys Benign ★★ same type
- TLR9 p.Arg863Gln Benign ★★ same type
- TLR9 p.Gly563= Benign ★★ same type
- TLR9 p.Ser509= Benign ★★ same type
- TLR9 p.Thr383= Benign ★★ same type
- TLR9 p.Ala140Val Uncertain significance ★ ⚠ same type
- TLR9 p.Ala191Thr Uncertain significance ★ ⚠ same type
- TLR9 p.Ala236Val 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/tlr9-p-ser147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown