Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 81%, amr) — 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 +145 | deep intronic (+145 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.6 | GERP -0.54, phastCons 0.095 |
| Non-coding constraint | Z 1.87 | 1 kb window · o/e 0.82 · regional · uncalibrated |
| Overall | ||
| CADD | 0.265 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
81%
Admixed American · 40,420/49,912 alleles
Filtering AF
80.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 80%
Overall
71.8%
539,748/752,254 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 81% | 1 |
| Finnishnot grpmax-eligible | 78.6% | 1 |
| Amishnot grpmax-eligible | 76.8% | 1 |
| European (non-Finnish) | 73.3% | 1 |
| Remaining individualsnot grpmax-eligible | 71% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 68.1% | 1 |
| Middle Eastern | 67.7% | 1 |
| South Asian | 67% | 1 |
| African / African-American | 61.7% | 2 |
| East Asian | 60.3% | 2 |
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
- AGPS
- Coding
- c.1285+145C>T
- MANE Select
- NM_003659
- dbSNP
- rs1348849
- Type
- single nucleotide variant
- Location
- chr2:177493344 (GRCh38)
- Gene constraint
- LOEUF 0.408 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.27
Similar variants
- AGPS p.Arg182Ter Pathogenic/Likely pathogenic ★★ same type
- AGPS p.Thr309Ile Likely pathogenic ★★ same type
- AGPS c.1855+6C>A Uncertain significance ★★ same type
- AGPS c.*118A>G Uncertain significance ★★ same type
- AGPS p.Arg265Gln Uncertain significance ★★ ⚠ same type
- AGPS p.Asn649Ser Uncertain significance ★★ ⚠ same type
- AGPS p.Asp28Val Uncertain significance ★★ ⚠ same type
- AGPS p.Asp590His 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/agps-c-1285-plus-145c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown