TRAF7 p.Ser13=
c.39C>T · VCV4928052
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -4.2 |
| Overall | ||
| CADD | 1.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00236%
38/1,612,706 alleles · ultra-rare
exomes 31/1,460,716 · genomes 7/151,990 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.0107% | 9,359 |
| Admixed American | 0.00501% | 19,977 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,816 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
| East Asian | 0.00223% | 44,858 |
| South Asian | 0.0022% | 45,488 |
| European (non-Finnish) | 0.00161% | 62,092 |
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.Ser13=
- Coding
- c.39C>T
- MANE Select
- NM_032271
- Type
- single nucleotide variant
- Location
- chr16:2163959 (GRCh38)
- Gene constraint
- LOEUF 0.675 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.16 · 1 PDB
- Residue 13
- the 'disordered' region
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-ser13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown