BSPRY p.Phe204=
c.612T>C · rs577779388 · VCV3135323
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.148%, mid)
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 -0.084 | GERP -2.3, phastCons 0.86 |
| Overall | ||
| CADD | 7.393 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.148%
Middle Eastern · 9/6,062 alleles
Filtering AF
0.0774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0578%
Overall
0.00743%
120/1,614,130 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.148% | 674 |
| Admixed American | 0.015% | 6,667 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| European (non-Finnish) | 0.00771% | 12,967 |
| African / African-American | 0.00133% | 75,038 |
| South Asian | 0.0011% | 91,084 |
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
- BSPRY
- Protein
- p.Phe204=
- Coding
- c.612T>C
- MANE Select
- NM_017688
- dbSNP
- rs577779388
- Type
- single nucleotide variant
- Location
- chr9:113368313 (GRCh38)
- Gene constraint
- LOEUF 1.216 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.75
Similar variants
- BSPRY p.Gly373Ser Uncertain significance ★★ ⚠ same type
- BSPRY p.Ala261Pro Uncertain significance ★ ⚠ same type
- BSPRY p.Ala287Gly Uncertain significance ★ ⚠ same type
- BSPRY p.Ala287Ser Uncertain significance ★ ⚠ same type
- BSPRY p.Ala287Val Uncertain significance ★ ⚠ same type
- BSPRY p.Ala45Gly Uncertain significance ★ ⚠ same type
- BSPRY p.Ala82Val Uncertain significance ★ ⚠ same type
- BSPRY p.Arg113Trp 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/bspry-p-phe204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown