ATIC c.1503+48A>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 100%, nfe) — too common for a highly-penetrant pathogenic allele
Conditions
1
AICA-ribosiduria
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +48 | near-intronic (+48 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -4.3 |
| Non-coding constraint | Z 1.64 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 0.553 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
European (non-Finnish) · 1,162,864/1,162,864 alleles
Filtering AF
99.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.8%
Overall
100%
1,594,284/1,594,362 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asian | 100% | 1 |
| European (non-Finnish)grpmax | 100% | 1 |
| Finnishnot grpmax-eligible | 100% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| Middle Eastern | 100% | 1 |
| South Asian | 100% | 1 |
| Admixed American | 100% | 1 |
| Remaining individualsnot grpmax-eligible | 100% | 1 |
| African / African-American | 99.9% | 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
- ATIC
- Coding
- c.1503+48A>T
- MANE Select
- NM_004044
- dbSNP
- rs10932609
- Type
- single nucleotide variant
- Location
- chr2:215346989 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 5 PDB
Disease context
AICA-ribosiduria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor AICA-ribosiduria (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Infancy, Neonatal
Similar variants
- ATIC p.Ala183Glu Uncertain significance ★★ ⚠ same condition
- ATIC p.His584Arg Uncertain significance ★★ ⚠ same condition
- ATIC c.1098+60C>G Benign ★★ same condition
- ATIC c.1228-30A>G Benign ★★ same condition
- ATIC c.147-111A>T Benign ★★ same condition
- ATIC c.380-18G>A Likely benign ★★ same condition
- ATIC c.380-19A>C Benign ★★ same condition
- ATIC c.-218A>G Benign ★★ 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/atic-c-1503-plus-48a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown