BDNF p.Ser139=
c.417C>T · rs760274076 · VCV709884
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, afr)
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 0.68 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 10.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,878 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00217%
35/1,613,940 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,320 |
| Admixed American | 0.005% | 19,999 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,245 |
| East Asian | 0.00223% | 44,888 |
| European (non-Finnish) | 0.00161% | 62,107 |
| South Asian | 0.0011% | 91,074 |
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.Ser139=
- Coding
- c.417C>T
- MANE Select
- NM_001709
- dbSNP
- rs760274076
- Type
- single nucleotide variant
- Location
- chr11:27658148 (GRCh38)
- Gene constraint
- LOEUF 0.233 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.44 · 2 PDB
- Residue 139
- a β-strand
Similar variants
- BDNF p.Ser139Arg 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-ser139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown