ADCY3 p.Val204=
c.612C>G · rs79278464 · VCV3033748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0151%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.047 | GERP -2.2 |
| Overall | ||
| CADD | 0.681 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0151%
Admixed American · 9/59,740 alleles
Filtering AF
0.00776%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00581%
Overall
0.00316%
51/1,611,526 alleles · ultra-rare
exomes 48/1,459,332 · genomes 3/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0151% | 6,638 |
| European (non-Finnish) | 0.00331% | 30,227 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,191 |
| African / African-American | 0.00134% | 74,836 |
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
- ADCY3
- Protein
- p.Val204=
- Coding
- c.612C>G
- MANE Select
- NM_004036
- dbSNP
- rs79278464
- Type
- single nucleotide variant
- Location
- chr2:24918376 (GRCh38)
- Gene constraint
- LOEUF 0.695 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.86
Similar variants
- ADCY3 p.Ala512Thr Uncertain significance ★★ ⚠ same type
- ADCY3 p.Ala553Val Uncertain significance ★★ ⚠ same type
- ADCY3 p.Ala97Val Uncertain significance ★★ ⚠ same type
- ADCY3 p.Arg1041His Uncertain significance ★★ ⚠ same type
- ADCY3 p.Arg259Cys Uncertain significance ★★ ⚠ same type
- ADCY3 p.Arg705Lys Uncertain significance ★★ ⚠ same type
- ADCY3 p.Asp474Asn Uncertain significance ★★ ⚠ same type
- ADCY3 p.Cys727Arg 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/adcy3-p-val204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown