TCERG1 p.Arg96=
c.286A>C · VCV3454058
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0534%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 18.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0534%
African / African-American · 40/74,962 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0356%
Overall
0.00273%
44/1,612,216 alleles · ultra-rare
exomes 25/1,459,840 · genomes 19/152,376 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0534% | 1,874 |
| Admixed American | 0.00335% | 29,825 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,446 |
| European (non-Finnish) | 8.48e-05% | 1,179,272 |
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
- TCERG1
- Protein
- p.Arg96=
- Coding
- c.286A>C
- MANE Select
- NM_001382548
- Type
- single nucleotide variant
- Location
- chr5:146457183 (GRCh38)
- Gene constraint
- LOEUF 0.323 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.35 · 29 PDB
- Residue 96
- the 'disordered' region
Similar variants
- TCERG1 p.Ala189Val Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala191Ser Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala195Val Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala205Val Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala245Val Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala253Val Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala424Ser Uncertain significance ★ ⚠ same type
- TCERG1 p.Ala429Val 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/tcerg1-p-arg96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown