AP1S2 c.288+73T>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +73 | deep intronic (+73 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.48 | GERP -3.4, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 7.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 32,371/32,371 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.9%
Overall
99.4%
924,975/930,927 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Middle Eastern | 100% | 1 |
| Admixed American | 99.9% | 1 |
| African / African-American | 99.9% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 99.9% | 1 |
| South Asian | 99.8% | 1 |
| Finnishnot grpmax-eligible | 99.5% | 1 |
| Remaining individualsnot grpmax-eligible | 99.4% | 1 |
| European (non-Finnish) | 99.2% | 1 |
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
- AP1S2
- Coding
- c.288+73T>A
- MANE Select
- NM_001272071
- dbSNP
- rs798169
- Type
- single nucleotide variant
- Location
- chrX:15845830 (GRCh38)
- Structure
- AlphaFold pLDDT 94.36
Similar variants
- AP1S2 c.-1+1G>A Pathogenic/Likely pathogenic ★★ same type
- AP1S2 p.Arg52Ter Pathogenic ★★ same type
- AP1S2 p.Gln123Ter Pathogenic ★★ same type
- AP1S2 p.Asn129Thr Uncertain significance ★★ ⚠ same type
- AP1S2 p.Gly158Arg Uncertain significance ★★ ⚠ same type
- AP1S2 p.Ile134Thr Uncertain significance ★★ ⚠ same type
- AP1S2 p.Ile82Val Uncertain significance ★★ ⚠ same type
- AP1S2 p.Leu54Val 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/ap1s2-c-288-plus-73t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown