ADCY6 p.Ser2=
c.6A>G · rs780803395 · VCV749869
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -4.7 |
| Overall | ||
| CADD | 4.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,018 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000372%
6/1,614,178 alleles · very rare
exomes 6/1,461,868 · genomes 0/152,310 · joint denominator
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
- ADCY6
- Protein
- p.Ser2=
- Coding
- c.6A>G
- MANE Select
- NM_015270
- dbSNP
- rs780803395
- Type
- single nucleotide variant
- Location
- chr12:48783429 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.33
Similar variants
- ADCY6 p.Arg1065Trp Uncertain significance ★★ ⚠ same type
- ADCY6 p.Arg538His Uncertain significance ★★ ⚠ same type
- ADCY6 c.1376+168C>T Benign ★★ same type
- ADCY6 c.1377-56G>A Benign ★★ same type
- ADCY6 c.1833-29A>T Benign ★★ same type
- ADCY6 c.1981-11C>G Benign ★★ same type
- ADCY6 c.2283+57C>G Benign ★★ same type
- ADCY6 c.2442+40G>T Benign ★★ 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/adcy6-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown