Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 40.7%, sas) — too common for a highly-penetrant pathogenic allele
Conditions
1
colon carcinoma
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 -3.5 | GERP -5.5 |
| Overall | ||
| CADD | 0.818 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
40.7%
South Asian · 37,004/90,918 alleles
Filtering AF
40.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 40.2%
Overall
20.2%
325,346/1,612,098 alleles · common
exomes 293,329/1,459,922 · genomes 32,017/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 40.7% | 2 |
| Amishnot grpmax-eligible | 30.8% | 3 |
| African / African-American | 27.4% | 4 |
| Middle Eastern | 26.2% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.4% | 4 |
| Remaining individualsnot grpmax-eligible | 21.9% | 5 |
| European (non-Finnish) | 18.9% | 5 |
| East Asian | 16.3% | 6 |
| Finnishnot grpmax-eligible | 13.3% | 8 |
| Admixed American | 10.8% | 9 |
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
- FLT1
- Protein
- p.Pro1068=
- Coding
- c.3204T>C
- MANE Select
- NM_002019
- dbSNP
- rs2296189
- Type
- single nucleotide variant
- Location
- chr13:28319505 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.86 · 12 PDB
- Residue 1068
- an α-helix; the protein kinase domain
Similar variants
- FLT1 p.Tyr815fs Uncertain significance same condition
- FLT1 p.Asp6Asn Benign ★★ same type
- FLT1 p.Cys107= Likely benign ★★ same type
- FLT1 p.Ile548Met Likely benign ★★ same type
- FLT1 p.Leu492= Benign ★★ same type
- FLT1 p.Met938Val Likely benign ★★ same type
- FLT1 p.Pro1201Leu Likely benign ★★ same type
- FLT1 p.Thr260= 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/flt1-p-pro1068 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown