FLT3 p.Asp96=
c.288C>T · rs7338903 · VCV1280165
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 99.9%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.45 | GERP -2.4 |
| Overall | ||
| CADD | 2.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
99.9%
East Asian · 44,852/44,882 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.8%
Overall
98.5%
1,589,740/1,613,948 alleles · common
exomes 1,442,853/1,461,706 · genomes 146,887/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 99.9% | 1 |
| Finnishnot grpmax-eligible | 99.6% | 1 |
| Amishnot grpmax-eligible | 99.6% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 99.5% | 1 |
| South Asian | 99.5% | 1 |
| European (non-Finnish) | 98.8% | 1 |
| Admixed American | 98.7% | 1 |
| Middle Eastern | 98.6% | 1 |
| Remaining individualsnot grpmax-eligible | 98.4% | 1 |
| African / African-American | 90.5% | 1 |
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
- FLT3
- Protein
- p.Asp96=
- Coding
- c.288C>T
- MANE Select
- NM_004119
- dbSNP
- rs7338903
- Type
- single nucleotide variant
- Location
- chr13:28061947 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.19 · 11 PDB
Similar variants
- FLT3 c.1205+56C>T Benign ★★ same type
- FLT3 c.1310-3T>C Benign ★★ same type
- FLT3 c.1418+75A>G Benign ★★ same type
- FLT3 c.1418+81A>G Benign ★★ same type
- FLT3 c.1419-15T>C Benign ★★ same type
- FLT3 c.1419-36T>A Benign ★★ same type
- FLT3 c.1597+8A>G Likely benign ★★ same type
- FLT3 c.165+118G>T Benign ★★ 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/flt3-p-asp96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown