BDNF p.His203=
c.609T>C · rs746089117 · VCV2054554
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, 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 -2.1 | GERP -5.5 |
| Overall | ||
| CADD | 5.374 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,880 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.00118%
19/1,614,002 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,206 |
| Middle Eastern | 0.0164% | 6,084 |
| South Asian | 0.00329% | 30,363 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- BDNF
- Protein
- p.His203=
- Coding
- c.609T>C
- MANE Select
- NM_001709
- dbSNP
- rs746089117
- Type
- single nucleotide variant
- Location
- chr11:27657956 (GRCh38)
- Gene constraint
- LOEUF 0.233 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.44 · 2 PDB
- Residue 203
- a turn; a disulfide bond
Similar variants
- BDNF p.His203Gln Uncertain significance ★ ⚠ same residue
- BDNF c.-21-1044G>C Benign ★★ same type
- BDNF c.-21-1065G>A Benign ★★ same type
- BDNF c.-21-15778G>T Benign ★★ same type
- BDNF c.-22+774G>A Benign ★★ same type
- BDNF p.Ala150= Benign ★★ same type
- BDNF p.Asp86= Likely benign ★★ same type
- BDNF p.Gly161= 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/bdnf-p-his203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown