IFT80 p.Ala154=
c.462G>A · rs34182424 · VCV343980
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.44%, mid)
Conditions
3
connective tissue disorder
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 -6.7 | GERP -3.2 |
| Overall | ||
| CADD | 1.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.44%
Middle Eastern · 265/5,968 alleles
Filtering AF
4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.83%
Overall
1.94%
31,304/1,610,788 alleles · low-frequency
exomes 27,847/1,459,770 · genomes 3,457/151,018 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 4.44% | 23 |
| African / African-American | 3.67% | 27 |
| Ashkenazi Jewishnot grpmax-eligible | 3.62% | 28 |
| European (non-Finnish) | 2.05% | 49 |
| Remaining individualsnot grpmax-eligible | 1.97% | 51 |
| Admixed American | 1.48% | 67 |
| Amishnot grpmax-eligible | 1.43% | 70 |
| South Asian | 0.704% | 142 |
| Finnishnot grpmax-eligible | 0.532% | 188 |
| East Asian | 0.0112% | 8,961 |
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
- IFT80
- Protein
- p.Ala154=
- Coding
- c.462G>A
- MANE Select
- NM_020800
- dbSNP
- rs34182424
- Type
- single nucleotide variant
- Location
- chr3:160366130 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.50
Similar variants
- IFT80 p.Ala154Val Uncertain significance ★★ ⚠ same residue
- IFT80 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT80 p.Trp155Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT80 c.1076+6C>A Uncertain significance ★★ same condition
- IFT80 c.1836+5T>C Uncertain significance ★★ same condition
- IFT80 c.370+6T>C Uncertain significance ★★ same condition
- IFT80 c.*108A>G Uncertain significance ★★ same condition
- IFT80 p.Ala236Val Uncertain significance ★★ ⚠ same condition
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/ift80-p-ala154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown