ADCY10 p.Phe675=
c.2025C>T · VCV4748430
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0356%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.28 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.41 | GERP -3.2 |
| Overall | ||
| CADD | 11.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0356%
East Asian · 16/44,892 alleles
Filtering AF
0.0223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00217%
35/1,614,090 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0356% | 2,806 |
| African / African-American | 0.00933% | 10,714 |
| Admixed American | 0.00167% | 60,010 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
| European (non-Finnish) | 0.000847% | 118,000 |
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
- ADCY10
- Protein
- p.Phe675=
- Coding
- c.2025C>T
- MANE Select
- NM_018417
- Type
- single nucleotide variant
- Location
- chr1:167856311 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.17 · 37 PDB
Similar variants
- ADCY10 c.1139+6T>G Uncertain significance ★★ same type
- ADCY10 c.253+4A>G Uncertain significance ★★ same type
- ADCY10 p.Ala103Ser Uncertain significance ★★ ⚠ same type
- ADCY10 p.Ala1278Asp Uncertain significance ★★ ⚠ same type
- ADCY10 p.Ala862Gly Uncertain significance ★★ ⚠ same type
- ADCY10 p.Ala991Ser Uncertain significance ★★ ⚠ same type
- ADCY10 p.Arg1207Trp Uncertain significance ★★ ⚠ same type
- ADCY10 p.Arg1217His 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/adcy10-p-phe675 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown