FGFR1 c.1663+341T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +341 | deep intronic (+341 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.36 | GERP -0.44 |
| Overall | ||
| CADD | 1.406 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
African / African-American · 574/41,036 alleles
Filtering AF
1.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.27%
Overall
0.436%
658/150,942 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.4% | 71 |
| Remaining individualsnot grpmax-eligible | 0.624% | 160 |
| Admixed American | 0.33% | 303 |
| European (non-Finnish) | 0.031% | 3,225 |
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
- FGFR1
- Coding
- c.1663+341T>C
- MANE Select
- NM_023110
- dbSNP
- rs112034315
- Type
- single nucleotide variant
- Location
- chr8:38416965 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 74.30 · 86 PDB
Similar variants
- FGFR1 c.1977+1G>A Pathogenic/Likely pathogenic ★★ same type
- FGFR1 c.1977+1G>T Pathogenic/Likely pathogenic ★★ same type
- FGFR1 c.448+1G>A Likely pathogenic ★★ same type
- FGFR1 c.449-6G>A Likely pathogenic ★★ same type
- FGFR1 c.91+1G>A Pathogenic/Likely pathogenic ★★ same type
- FGFR1 p.Ala343= Pathogenic/Likely pathogenic ★★ same type
- FGFR1 p.Arg209Cys Likely pathogenic ★★ same type
- FGFR1 p.Arg250Gln Pathogenic ★★ 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/fgfr1-c-1663-plus-341t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown