Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.32%, afr)
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 -1.9 | GERP -3.8 |
| Overall | ||
| CADD | 6.961 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.32%
African / African-American · 3,240/74,996 alleles
Filtering AF
4.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.15%
Overall
0.316%
5,096/1,614,076 alleles · low-frequency
exomes 3,075/1,461,852 · genomes 2,021/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.32% | 23 |
| Middle Eastern | 2.95% | 34 |
| Admixed American | 0.683% | 146 |
| Remaining individualsnot grpmax-eligible | 0.486% | 206 |
| European (non-Finnish) | 0.0764% | 1,310 |
| South Asian | 0.0637% | 1,570 |
| East Asian | 0.00446% | 22,440 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Finnishnot grpmax-eligible | 0.00156% | 64,026 |
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
- GRM8
- Protein
- p.Phe119=
- Coding
- c.357C>T
- MANE Select
- NM_000845
- dbSNP
- rs769200
- Type
- single nucleotide variant
- Location
- chr7:127242848 (GRCh38)
- Gene constraint
- LOEUF 0.687 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.11 · 10 PDB
- Residue 119
- an α-helix
Similar variants
- GRM8 c.1495-9T>C Benign ★★ same type
- GRM8 p.Arg561= Benign ★★ same type
- GRM8 p.Gly231= Benign ★★ same type
- GRM8 p.His32Gln Benign ★★ same type
- GRM8 p.Ile265Thr Benign ★★ same type
- GRM8 p.Ile488= Benign ★★ same type
- GRM8 p.Phe21Cys Benign ★★ same type
- GRM8 p.Pro512Ala 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/grm8-p-phe119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown