TRRAP p.Ala3696=
c.11088G>A · rs200919131 · VCV2919825
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.127%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.095 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.555 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.127%
East Asian · 57/44,876 alleles
Filtering AF
0.101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0912%
Overall
0.0083%
134/1,614,086 alleles · rare
exomes 114/1,461,892 · genomes 20/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.127% | 787 |
| South Asian | 0.0417% | 2,397 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| African / African-American | 0.00933% | 10,715 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Admixed American | 0.00167% | 60,006 |
| European (non-Finnish) | 0.000847% | 118,002 |
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
- TRRAP
- Protein
- p.Ala3696=
- Coding
- c.11088G>A
- MANE Select
- NM_001375524
- dbSNP
- rs200919131
- Type
- single nucleotide variant
- Location
- chr7:99011201 (GRCh38)
- Gene constraint
- LOEUF 0.115 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Residue 3696
- the pi3k/pi4k catalytic domain; a β-strand
Similar variants
- TRRAP p.Ala3696Thr Uncertain significance ★ same residue
- TRRAP p.Ala3696Val Uncertain significance ★ same residue
- TRRAP p.Arg1035Gln Pathogenic/Likely pathogenic ★★ same type
- TRRAP p.Glu1104Gly Pathogenic/Likely pathogenic ★★ same type
- TRRAP p.Glu1106Lys Likely pathogenic ★★ same type
- TRRAP p.Met3318Val Pathogenic/Likely pathogenic ★★ same type
- TRRAP p.Val1030Ile Likely pathogenic ★★ same type
- TRRAP c.2622+3A>G 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/trrap-p-ala3696 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown