CS p.Phe96=
c.288T>C · rs141833651 · VCV728964
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.448%, 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 0.17 | GERP -3.7, phastCons 0.61 |
| Overall | ||
| CADD | 7.304 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.448%
African / African-American · 336/75,068 alleles
Filtering AF
0.408%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.393%
Overall
0.0225%
363/1,614,200 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.448% | 223 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| Admixed American | 0.0167% | 6,000 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
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
- CS
- Protein
- p.Phe96=
- Coding
- c.288T>C
- MANE Select
- NM_004077
- dbSNP
- rs141833651
- Type
- single nucleotide variant
- Location
- chr12:56282971 (GRCh38)
- Gene constraint
- LOEUF 0.356 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.56 · 11 PDB
Similar variants
- CS p.Leu257= Benign ★★ same type
- CS p.Ala2Gly Uncertain significance ★ ⚠ same type
- CS p.Ala8Ser Uncertain significance ★ ⚠ same type
- CS p.Arg183Gly Uncertain significance ★ ⚠ same type
- CS p.Arg191Gln Uncertain significance ★ ⚠ same type
- CS p.Arg218Gln Uncertain significance ★ ⚠ same type
- CS p.Arg329Gln Uncertain significance ★ ⚠ same type
- CS p.Arg340Gln 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/cs-p-phe96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown