ADAM9 p.Phe704del
c.2104TTC[2] · rs746548581 · VCV1010974
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP -0.31, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00116%
17/1,461,690 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,058 |
| Admixed American | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,248 |
| Finnishnot grpmax-eligible | 0.00156% | 63,994 |
| South Asian | 0.0011% | 91,068 |
| European (non-Finnish) | 0.000509% | 196,650 |
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
- ADAM9
- Protein
- p.Phe704del
- Coding
- c.2104TTC[2]
- MANE Select
- NM_003816
- dbSNP
- rs746548581
- Type
- Microsatellite
- Location
- chr8:39090080 (GRCh38)
- Gene constraint
- LOEUF 0.575 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 76.14
Similar variants
- ADAM9 p.Glu183fs Pathogenic/Likely pathogenic ★★ same type
- ADAM9 p.Cys428_Asp429delinsTer Pathogenic ★ same type
- ADAM9 p.Arg205del Uncertain significance ★ same type
- ADAM9 p.Gly624del Uncertain significance ★ same type
- ADAM9 c.410+22_410+24del Likely benign ★ same type
- ADAM9 c.672+25_672+27del Likely benign ★ same type
- ADAM9 p.Arg6fs Pathogenic same type
- ADAM9 p.Ser42del 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/adam9-p-phe704del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown