F11 p.Glu398=
c.1194G>A · rs768306785 · VCV1535327
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0176%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.73 | donor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 4.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0176%
South Asian · 16/91,092 alleles
Filtering AF
0.011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.0013%
21/1,614,108 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0176% | 5,693 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.000169% | 590,026 |
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
- F11
- Protein
- p.Glu398=
- Coding
- c.1194G>A
- MANE Select
- NM_001322131 · reported on NM_000128
- dbSNP
- rs768306785
- Type
- single nucleotide variant
- Location
- chr4:186284150 (GRCh38)
- Structure
- AlphaFold pLDDT 68.98
Similar variants
- F11 p.Glu398Ter Likely pathogenic ★ same residue
- F11 p.Glu398Lys Uncertain significance ★ ⚠ same residue
- F11 c.1136-1G>C Likely pathogenic ★★ same type
- F11 c.1480+1G>T Likely pathogenic ★★ same type
- F11 c.1481-1G>T Likely pathogenic ★★ same type
- F11 c.1716+1G>A Pathogenic ★★ same type
- F11 c.325+1G>A Pathogenic ★★ same type
- F11 c.326-1G>A 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/f11-p-glu398 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown