SAMD9L p.Ser39=
c.117T>C · rs141858354 · VCV2972220
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.161%, 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 -4 | GERP -4.1 |
| Overall | ||
| CADD | 0.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.161%
East Asian · 72/44,856 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.12%
Overall
0.00446%
72/1,613,946 alleles · rare
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
- SAMD9L
- Protein
- p.Ser39=
- Coding
- c.117T>C
- MANE Select
- NM_152703
- dbSNP
- rs141858354
- Type
- single nucleotide variant
- Location
- chr7:93135855 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.85
- Residue 39
- the sam domain
Similar variants
- SAMD9L p.Ser39Arg Uncertain significance ★ ⚠ same residue
- SAMD9L p.Ser39Gly Uncertain significance ★ ⚠ same residue
- SAMD9L p.Ser39Ile Uncertain significance ★ ⚠ same residue
- SAMD9L p.Ala1073Thr Uncertain significance ★★ ⚠ same condition
- SAMD9L p.Ala1087Asp Uncertain significance ★★ ⚠ same condition
- SAMD9L p.Ala1106Thr Uncertain significance ★★ ⚠ same condition
- SAMD9L p.Ala1106Val Uncertain significance ★★ ⚠ same condition
- SAMD9L p.Ala1109Pro 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/samd9l-p-ser39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown