BDNF p.Ser213=
c.639G>A · rs78572035 · VCV718660
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.323%, 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 -0.006 | GERP 0.013, phastCons 0.66 |
| Overall | ||
| CADD | 13.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.323%
East Asian · 145/44,874 alleles
Filtering AF
0.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.264%
Overall
0.0177%
285/1,614,168 alleles · rare
exomes 230/1,461,892 · genomes 55/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.323% | 309 |
| Remaining individualsnot grpmax-eligible | 0.13% | 772 |
| African / African-American | 0.028% | 3,573 |
| Admixed American | 0.025% | 4,002 |
| European (non-Finnish) | 0.00186% | 53,638 |
| South Asian | 0.0011% | 91,086 |
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.Ser213=
- Coding
- c.639G>A
- MANE Select
- NM_001709
- dbSNP
- rs78572035
- Type
- single nucleotide variant
- Location
- chr11:27657926 (GRCh38)
- Gene constraint
- LOEUF 0.233 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.44 · 2 PDB
- Residue 213
- a β-strand
Similar variants
- BDNF p.Ser213Leu 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-ser213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown