CD96 c.61+4A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00933%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.55 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.1 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 20.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00933%
African / African-American · 7/75,024 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00308%
Overall
0.000496%
8/1,612,382 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00933% | 10,718 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,446 |
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
- Coding
- c.61+4A>G
- MANE Select
- NM_005816
- Type
- single nucleotide variant
- Location
- chr3:111542313 (GRCh38)
- Gene constraint
- LOEUF 1.16 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.81 · 1 PDB
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-c-61-plus-4a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown