EXOSC9 p.Phe90=
c.270C>T · rs766608315 · VCV2084162
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -0.52, phastCons 1 |
| Overall | ||
| CADD | 14.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,970 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00273%
44/1,613,898 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00834% | 11,994 |
| South Asian | 0.00329% | 30,357 |
| European (non-Finnish) | 0.00288% | 34,705 |
| Finnishnot grpmax-eligible | 0.00156% | 64,024 |
| African / African-American | 0.00133% | 74,908 |
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
- EXOSC9
- Protein
- p.Phe90=
- Coding
- c.270C>T
- MANE Select
- NM_005033
- dbSNP
- rs766608315
- Type
- single nucleotide variant
- Location
- chr4:121802782 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.44 · 8 PDB
- Residue 90
- the 'are binding' region
Similar variants
- EXOSC9 p.Phe90Ser Uncertain significance ★ ⚠ same residue
- EXOSC9 p.Arg161Ter Pathogenic/Likely pathogenic ★★ same type
- EXOSC9 p.Arg212Ter Pathogenic ★★ same type
- EXOSC9 p.Arg229Ter Pathogenic/Likely pathogenic ★★ same type
- EXOSC9 p.Leu14Pro Pathogenic/Likely pathogenic ★★ same type
- EXOSC9 p.Ser7Ter Pathogenic/Likely pathogenic ★★ same type
- EXOSC9 c.1157-172A>G Uncertain significance ★★ same type
- EXOSC9 p.Ala148Val 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/exosc9-p-phe90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown