AIP c.99+9C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.5 | GERP 0.9 |
| Non-coding constraint | Z -0.48 | 1 kb window · o/e 1.04 · regional · uncalibrated |
| Overall | ||
| CADD | 12.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,920 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000248%
4/1,612,764 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,973 |
| Admixed American | 0.00167% | 60,004 |
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
- AIP
- Coding
- c.99+9C>T
- MANE Select
- NM_017900 · reported on NM_003977
- dbSNP
- rs374003812
- Type
- single nucleotide variant
- Location
- chr11:67483266 (GRCh38)
- Structure
- AlphaFold pLDDT 70.14 · 81 PDB
Similar variants
- AIP p.Arg271Trp Pathogenic/Likely pathogenic ★★ same type
- AIP p.Arg304Ter Pathogenic ★★ same type
- AIP p.Arg81Ter Pathogenic ★★ same type
- AIP p.Cys238Tyr Likely pathogenic ★★ same type
- AIP p.Gln126Ter Pathogenic ★★ same type
- AIP p.Gln14Ter Pathogenic ★★ same type
- AIP p.Gln217Ter Pathogenic ★★ same type
- AIP p.Gln229Ter Pathogenic/Likely pathogenic ★★ 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/aip-c-99-plus-9c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown