ADD3 p.Ser104=
c.312G>A · rs147859836 · VCV2075893
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0349%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.92 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.76 | gain · loss 0.41 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -3.4 |
| Overall | ||
| CADD | 19.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0349%
European (non-Finnish) · 412/1,179,886 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.031%
Overall
0.0273%
441/1,613,348 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0349% | 2,864 |
| African / African-American | 0.0201% | 4,987 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,205 |
| East Asian | 0.00223% | 44,852 |
| South Asian | 0.0011% | 90,952 |
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
- ADD3
- Protein
- p.Ser104=
- Coding
- c.312G>A
- MANE Select
- NM_016824
- dbSNP
- rs147859836
- Type
- single nucleotide variant
- Location
- chr10:110112893 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.83
Similar variants
- ADD3 p.Ser104Leu Uncertain significance ★★ ⚠ same residue
- ADD3 p.Gly367Asp Pathogenic/Likely pathogenic ★★ same type
- ADD3 c.1733-1G>A Uncertain significance ★★ same type
- ADD3 p.Ala588Gly Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg27Cys Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg46Gln Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg571His Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg645Gln 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/add3-p-ser104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown