FLT3 p.Leu561=
c.1683A>G · rs34374211 · VCV1226610
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 22.7%, afr) — 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 -3.1 | GERP -4.4 |
| Overall | ||
| CADD | 1.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.7%
African / African-American · 17,017/74,962 alleles
Filtering AF
22.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.3%
Overall
6.03%
97,312/1,613,474 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 22.7% | 4 |
| South Asian | 18.4% | 5 |
| East Asian | 18.2% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 7.69% | 13 |
| Middle Eastern | 7.06% | 14 |
| Remaining individualsnot grpmax-eligible | 6.6% | 15 |
| Admixed American | 3.92% | 26 |
| European (non-Finnish) | 3.72% | 27 |
| Finnishnot grpmax-eligible | 3.65% | 27 |
| Amishnot grpmax-eligible | 1.86% | 54 |
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.Leu561=
- Coding
- c.1683A>G
- MANE Select
- NM_004119
- dbSNP
- rs34374211
- Type
- single nucleotide variant
- Location
- chr13:28034322 (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-leu561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown