TRAF7 p.Ser535=
c.1605C>T · rs200042334 · VCV2646049
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0783%, amr)
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 -8.7 | GERP -4.2 |
| Overall | ||
| CADD | 1.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0783%
Admixed American · 47/60,016 alleles
Filtering AF
0.0604%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.0114%
184/1,612,384 alleles · ultra-rare
exomes 167/1,460,098 · genomes 17/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0783% | 1,277 |
| Middle Eastern | 0.066% | 1,515 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,462 |
| European (non-Finnish) | 0.00983% | 10,171 |
| African / African-American | 0.00266% | 37,524 |
| South Asian | 0.0011% | 91,068 |
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
- TRAF7
- Protein
- p.Ser535=
- Coding
- c.1605C>T
- MANE Select
- NM_032271
- dbSNP
- rs200042334
- Type
- single nucleotide variant
- Location
- chr16:2175601 (GRCh38)
- Gene constraint
- LOEUF 0.675 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.16 · 1 PDB
Similar variants
- TRAF7 p.Arg524Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Arg655Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Leu402Val Pathogenic ★★ ⚠ same type
- TRAF7 p.Leu625Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Ser558Phe Pathogenic ★★ ⚠ same type
- TRAF7 p.Ser629Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRAF7 p.Arg316Cys Uncertain significance ★★ ⚠ same type
- TRAF7 p.Arg371Trp 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/traf7-p-ser535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown