SAMD9 p.Asp13=
c.39T>C · rs779908712 · VCV740407
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00448%, eas)
Conditions
1
Inborn genetic diseases
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 -0.28 | GERP -2.1, phastCons 0.022 |
| Overall | ||
| CADD | 2.552 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00448%
East Asian · 2/44,668 alleles
Filtering AF
0.000883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000722%
Overall
0.00138%
22/1,590,934 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00448% | 22,334 |
| Admixed American | 0.00185% | 54,070 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,438 |
| European (non-Finnish) | 0.00145% | 69,010 |
| African / African-American | 0.00136% | 73,404 |
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
- SAMD9
- Protein
- p.Asp13=
- Coding
- c.39T>C
- MANE Select
- NM_017654
- dbSNP
- rs779908712
- Type
- single nucleotide variant
- Location
- chr7:93106059 (GRCh38)
- Gene constraint
- LOEUF 1.773 · pLI 0.03 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.79 · 10 PDB
Similar variants
- SAMD9 p.Ala1057Val Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1066Thr Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1069Thr Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1082Gly Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1102Asp Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1195Asp Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala123Ser Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1290Val Uncertain significance ★★ ⚠ same condition
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/samd9-p-asp13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown