Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.759%, mid)
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 -9.5 | GERP -3.7 |
| Overall | ||
| CADD | 5.866 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.759%
Middle Eastern · 46/6,062 alleles
Filtering AF
0.585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.523%
Overall
0.433%
6,983/1,612,558 alleles · rare
exomes 6,401/1,460,194 · genomes 582/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.759% | 132 |
| Admixed American | 0.553% | 181 |
| Remaining individualsnot grpmax-eligible | 0.491% | 203 |
| European (non-Finnish) | 0.489% | 204 |
| Ashkenazi Jewishnot grpmax-eligible | 0.466% | 214 |
| Finnishnot grpmax-eligible | 0.414% | 242 |
| South Asian | 0.0823% | 1,214 |
| African / African-American | 0.0639% | 1,564 |
| East Asian | 0.00668% | 14,959 |
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
- SSTR5
- Protein
- p.Phe107=
- Coding
- c.321C>T
- MANE Select
- NM_001172560
- dbSNP
- rs4988486
- Type
- single nucleotide variant
- Location
- chr16:1079189 (GRCh38)
- Gene constraint
- LOEUF 1.931 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 81.91 · 7 PDB
Similar variants
- SSTR5 p.Thr98Met Uncertain significance ★★ ⚠ same type
- SSTR5 p.Ala161= Benign ★★ same type
- SSTR5 p.Ala231= Benign/Likely benign ★★ same type
- SSTR5 p.Arg240Trp Benign/Likely benign ★★ same type
- SSTR5 p.Leu219= Benign ★★ same type
- SSTR5 p.Leu48Met Benign ★★ same type
- SSTR5 p.Pro335Leu Benign ★★ same type
- SSTR5 p.Ser134= Benign ★★ 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/sstr5-p-phe107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown