FLT3 p.Ser993=
c.2979G>A · rs142922228 · VCV776787
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, afr)
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 -4.7 | GERP -3.7 |
| Overall | ||
| CADD | 0.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
African / African-American · 953/75,020 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0688%
1,111/1,614,086 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.27% | 79 |
| Admixed American | 0.105% | 953 |
| Remaining individualsnot grpmax-eligible | 0.0832% | 1,202 |
| Middle Eastern | 0.0496% | 2,017 |
| South Asian | 0.00878% | 11,384 |
| European (non-Finnish) | 0.00263% | 38,065 |
| East Asian | 0.00223% | 44,888 |
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.Ser993=
- Coding
- c.2979G>A
- MANE Select
- NM_004119
- dbSNP
- rs142922228
- Type
- single nucleotide variant
- Location
- chr13:28004055 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.19 · 11 PDB
- Residue 993
- a modified residue (phosphoserine)
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-ser993 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown