ADGRA3 p.Ser161=
c.483G>A · VCV3677289
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00492%, sas)
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 -0.35 | GERP -4.3, phastCons 0.25 |
| Overall | ||
| CADD | 7.662 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00492%
South Asian · 4/81,236 alleles
Filtering AF
0.00165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000975%
Overall
0.000831%
13/1,564,494 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00492% | 20,309 |
| African / African-American | 0.00412% | 24,268 |
| East Asian | 0.00228% | 43,834 |
| European (non-Finnish) | 0.000434% | 230,651 |
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
- ADGRA3
- Protein
- p.Ser161=
- Coding
- c.483G>A
- MANE Select
- NM_145290
- Type
- single nucleotide variant
- Location
- chr4:22447502 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.20
Similar variants
- ADGRA3 p.Ser161Leu Uncertain significance ★ ⚠ same residue
- ADGRA3 p.Ala1008Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala1120Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala1127Ser Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala177Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala26Pro Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala316Pro Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala37Gly 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/adgra3-p-ser161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown