Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.899%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 10.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.899%
African / African-American · 675/75,052 alleles
Filtering AF
0.843%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.821%
Overall
0.0455%
735/1,614,184 alleles · rare
exomes 365/1,461,846 · genomes 370/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.899% | 111 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Admixed American | 0.025% | 4,002 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,546 |
| European (non-Finnish) | 0.000763% | 131,110 |
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
- GHSR
- Protein
- p.Ala144=
- Coding
- c.432C>T
- MANE Select
- NM_198407
- dbSNP
- rs2232168
- Type
- single nucleotide variant
- Location
- chr3:172447982 (GRCh38)
- Gene constraint
- LOEUF 1.033 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.75 · 10 PDB
- Residue 144
- a turn
Similar variants
- GHSR p.Ala144Val Uncertain significance ★ ⚠ same residue
- GHSR p.Arg141Leu Uncertain significance ★★ ⚠ same type
- GHSR p.Arg141Pro Uncertain significance ★★ ⚠ same type
- GHSR p.Arg206Pro Uncertain significance ★★ ⚠ same type
- GHSR p.Arg237Trp Uncertain significance ★★ ⚠ same type
- GHSR p.Arg283Ter Uncertain significance ★★ same type
- GHSR p.Glu73Asp Uncertain significance ★★ ⚠ same type
- GHSR p.Glu9Lys Uncertain significance ★★ ⚠ 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/ghsr-p-ala144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown