AMPD2 c.91+78C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.83%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.04 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +78 | deep intronic (+78 nt into the intron) |
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.4 | GERP -3 |
| Overall | ||
| CADD | 4.144 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.83%
African / African-American · 2,015/71,130 alleles
Filtering AF
2.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.69%
Overall
0.157%
2,300/1,465,614 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.83% | 35 |
| Admixed American | 0.253% | 395 |
| Remaining individualsnot grpmax-eligible | 0.22% | 454 |
| Middle Eastern | 0.123% | 815 |
| South Asian | 0.00833% | 12,006 |
| European (non-Finnish) | 0.000844% | 118,423 |
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
- AMPD2
- Coding
- c.91+78C>A
- MANE Select
- NM_001368809
- dbSNP
- rs112387076
- Type
- single nucleotide variant
- Location
- chr1:109621344 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 5 PDB
Similar variants
- AMPD2 c.1698+1G>A Pathogenic/Likely pathogenic ★★ same type
- AMPD2 p.Arg353Ter Pathogenic/Likely pathogenic ★★ same type
- AMPD2 p.Arg449Ter Pathogenic/Likely pathogenic ★★ same type
- AMPD2 p.Arg620His Pathogenic/Likely pathogenic ★★ same type
- AMPD2 p.Arg789His Likely pathogenic ★★ same type
- AMPD2 p.Glu174Ter Pathogenic/Likely pathogenic ★★ same type
- AMPD2 c.1080+3G>A Uncertain significance ★★ same type
- AMPD2 c.353+3G>A 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/ampd2-c-91-plus-78c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown