AGPS c.260+62A>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.33%, afr) — 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 +62 | deep intronic (+62 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.44 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.097 | GERP -3.2 |
| Non-coding constraint | Z 2.33 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 7.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.33%
African / African-American · 4,631/73,110 alleles
Filtering AF
6.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.12%
Overall
0.349%
5,414/1,549,908 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.33% | 16 |
| Middle Eastern | 0.773% | 129 |
| Admixed American | 0.488% | 205 |
| Remaining individualsnot grpmax-eligible | 0.451% | 222 |
| South Asian | 0.0214% | 4,664 |
| European (non-Finnish) | 0.0174% | 5,762 |
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.260+62A>C
- MANE Select
- NM_003659
- dbSNP
- rs114901772
- Type
- single nucleotide variant
- Location
- chr2:177393111 (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-260-plus-62a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown