FAR1 p.Ile101=
c.303C>T · rs1021529208 · VCV1646429
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000512%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.47 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.26 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 17.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000512%
European (non-Finnish) · 6/1,172,138 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000377%
6/1,592,272 alleles · very rare
exomes 5/1,440,236 · genomes 1/152,036 · joint denominator
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.Ile101=
- Coding
- c.303C>T
- MANE Select
- NM_032228
- dbSNP
- rs1021529208
- Type
- single nucleotide variant
- Location
- chr11:13700430 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
Similar variants
- FAR1 p.Ile101Met Uncertain significance ★ ⚠ same residue
- FAR1 p.Ile101Val Uncertain significance ★ ⚠ same residue
- 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
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-ile101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown