FAR1 p.Ile4=
c.12C>T · rs117395380 · VCV1320619
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.91%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP 0.2, phastCons 1 |
| Overall | ||
| CADD | 10.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.91%
Middle Eastern · 176/6,054 alleles
Filtering AF
2.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.42%
Overall
1.76%
28,333/1,611,654 alleles · low-frequency
exomes 26,330/1,459,418 · genomes 2,003/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.91% | 34 |
| European (non-Finnish) | 2.02% | 49 |
| Remaining individualsnot grpmax-eligible | 1.76% | 57 |
| Admixed American | 1.46% | 69 |
| South Asian | 1.2% | 84 |
| Finnishnot grpmax-eligible | 1.04% | 96 |
| Ashkenazi Jewishnot grpmax-eligible | 0.961% | 104 |
| African / African-American | 0.39% | 257 |
| East Asian | 0.00446% | 22,412 |
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
- FAR1
- Protein
- p.Ile4=
- Coding
- c.12C>T
- MANE Select
- NM_032228
- dbSNP
- rs117395380
- Type
- single nucleotide variant
- Location
- chr11:13694777 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
Similar variants
- FAR1 c.-7-2A>G Likely pathogenic ★★ same type
- FAR1 p.Arg480Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- FAR1 p.Arg480His Pathogenic/Likely pathogenic ★★ same type
- FAR1 p.Arg480Leu Pathogenic ★★ same type
- FAR1 c.546-13A>G Uncertain significance ★★ same type
- FAR1 p.Ala361Val Uncertain significance ★★ ⚠ same type
- FAR1 p.Arg133Gln Uncertain significance ★★ ⚠ same type
- FAR1 p.Arg160Cys Uncertain significance ★★ ⚠ 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/far1-p-ile4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown