IFT57 p.Ala98=
c.294G>A · VCV3645565
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, sas)
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 -1.4 | GERP -5.5, phastCons 0.001 |
| Overall | ||
| CADD | 11.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
South Asian · 19/91,068 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00217%
35/1,613,512 alleles · ultra-rare
exomes 32/1,461,376 · genomes 3/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,793 |
| East Asian | 0.00446% | 22,437 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| African / African-American | 0.00133% | 74,950 |
| European (non-Finnish) | 0.000933% | 107,232 |
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
- IFT57
- Protein
- p.Ala98=
- Coding
- c.294G>A
- MANE Select
- NM_018010
- Type
- single nucleotide variant
- Location
- chr3:108219491 (GRCh38)
- Gene constraint
- LOEUF 1.425 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.92
Similar variants
- IFT57 c.585+3A>G Likely pathogenic ★★ same type
- IFT57 c.981+4A>G Uncertain significance ★★ same type
- IFT57 p.Ala155Thr Uncertain significance ★★ ⚠ same type
- IFT57 p.Ala37Val Uncertain significance ★★ ⚠ same type
- IFT57 p.Arg245Cys Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp110Ala Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp219His Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp228His 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/ift57-p-ala98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown