SAMD9 p.Phe1275=
c.3825T>C · rs3802064 · VCV1165054
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 8.54%, eas) — too common for a highly-penetrant pathogenic allele
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 0.098 | phastCons 0.012 |
| Overall | ||
| CADD | 2.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.54%
East Asian · 3,830/44,848 alleles
Filtering AF
8.31%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.22%
Overall
1.28%
20,678/1,612,824 alleles · common
exomes 18,395/1,460,634 · genomes 2,283/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 8.54% | 12 |
| African / African-American | 1.76% | 57 |
| Ashkenazi Jewishnot grpmax-eligible | 1.39% | 72 |
| Remaining individualsnot grpmax-eligible | 1.37% | 73 |
| European (non-Finnish) | 1.04% | 96 |
| South Asian | 1.02% | 98 |
| Finnishnot grpmax-eligible | 0.809% | 124 |
| Admixed American | 0.805% | 124 |
| Middle Eastern | 0.759% | 132 |
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.Phe1275=
- Coding
- c.3825T>C
- MANE Select
- NM_017654
- dbSNP
- rs3802064
- Type
- single nucleotide variant
- Location
- chr7:93102273 (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.Phe1275Tyr Uncertain significance ★ ⚠ same residue
- SAMD9 p.Arg1293Trp Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg459Gln Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg685Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- SAMD9 p.Arg824Gln Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg982Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- SAMD9 p.Arg982His Pathogenic/Likely pathogenic ★★ ⚠ same type
- SAMD9 p.Leu1511Ser Likely pathogenic ★★ ⚠ 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/samd9-p-phe1275 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown