IFT88 p.Ser612=
c.1836A>G · rs539848384 · VCV1618703
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.796%, 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 -4.4 | GERP -4.7 |
| Overall | ||
| CADD | 0.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.796%
South Asian · 665/83,584 alleles
Filtering AF
0.746%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.726%
Overall
0.049%
699/1,425,136 alleles · rare
exomes 659/1,272,790 · genomes 40/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.796% | 126 |
| Middle Eastern | 0.0751% | 1,331 |
| Remaining individualsnot grpmax-eligible | 0.0231% | 4,324 |
| African / African-American | 0.00987% | 10,136 |
| European (non-Finnish) | 0.000985% | 101,559 |
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
- IFT88
- Protein
- p.Ser612=
- Coding
- c.1836A>G
- MANE Select
- NM_006531
- dbSNP
- rs539848384
- Type
- single nucleotide variant
- Location
- chr13:20644845 (GRCh38)
- Gene constraint
- LOEUF 1.023 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 77.20
Similar variants
- IFT88 p.Ser612Leu Uncertain significance ★ ⚠ same residue
- IFT88 p.Ala327Thr Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala37Gly Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala458Val Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala510Pro Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala546Thr Uncertain significance ★★ ⚠ same type
- IFT88 p.Ala628Ser Uncertain significance ★★ ⚠ same type
- IFT88 p.Arg369His 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/ift88-p-ser612 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown