TRRAP p.Ala1920=
c.5760A>G · rs34111364 · VCV1553823
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.39%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.005 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -0.71 |
| Overall | ||
| CADD | 1.913 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.39%
South Asian · 3,085/91,082 alleles
Filtering AF
3.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.25%
Overall
0.357%
5,761/1,614,146 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.39% | 30 |
| Ashkenazi Jewishnot grpmax-eligible | 2.5% | 40 |
| Remaining individualsnot grpmax-eligible | 0.47% | 213 |
| Middle Eastern | 0.363% | 276 |
| European (non-Finnish) | 0.129% | 772 |
| Admixed American | 0.0916% | 1,091 |
| African / African-American | 0.032% | 3,127 |
| Finnishnot grpmax-eligible | 0.0219% | 4,574 |
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.Ala1920=
- Coding
- c.5760A>G
- MANE Select
- NM_001375524
- dbSNP
- rs34111364
- Type
- single nucleotide variant
- Location
- chr7:98955127 (GRCh38)
- Gene constraint
- LOEUF 0.115 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Residue 1920
- an α-helix
Similar variants
- 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
- TRRAP c.7176+4A>G Uncertain significance ★★ same type
- TRRAP c.8247+5G>T 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-ala1920 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown