CD96 p.Phe272=
c.816T>C · rs17851826 · VCV1569624
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.045%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 10.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.045%
European (non-Finnish) · 445/989,034 alleles
Filtering AF
0.0415%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0402%
Overall
0.0325%
456/1,403,796 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.045% | 2,223 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,925 |
| African / African-American | 0.00283% | 35,291 |
| Finnishnot grpmax-eligible | 0.00157% | 63,558 |
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
- CD96
- Protein
- p.Phe272=
- Coding
- c.816T>C
- MANE Select
- NM_005816
- dbSNP
- rs17851826
- Type
- single nucleotide variant
- Location
- chr3:111598128 (GRCh38)
- Gene constraint
- LOEUF 1.16 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.81 · 1 PDB
- Residue 272
- the ig-like c2-type domain
Similar variants
- CD96 c.1249+1G>A Uncertain significance ★★ same type
- CD96 c.544-1512C>T Uncertain significance ★★ ⚠ same type
- CD96 p.Asp205Gly Uncertain significance ★★ ⚠ same type
- CD96 p.Asp224Asn Uncertain significance ★★ ⚠ same type
- CD96 p.Ile151Thr Uncertain significance ★★ ⚠ same type
- CD96 p.Leu120Pro Uncertain significance ★★ ⚠ same type
- CD96 p.Lys500Arg Uncertain significance ★★ ⚠ same type
- CD96 p.Pro346Ser 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/cd96-p-phe272 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown