GHR p.Val628=
c.1884G>A · rs145815104 · VCV2907826
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.028%, 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 2.9 | GERP 0.2, phastCons 1 |
| Overall | ||
| CADD | 7.141 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.028%
African / African-American · 21/74,926 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00136%
22/1,613,724 alleles · ultra-rare
exomes 10/1,461,520 · genomes 12/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.028% | 3,568 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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
- GHR
- Protein
- p.Val628=
- Coding
- c.1884G>A
- MANE Select
- NM_000163
- dbSNP
- rs145815104
- Type
- single nucleotide variant
- Location
- chr5:42719391 (GRCh38)
- Gene constraint
- LOEUF 0.65 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 59.70 · 11 PDB
Similar variants
- GHR c.266+83G>T Pathogenic/Likely pathogenic ★★ same type
- GHR c.267-2A>G Pathogenic/Likely pathogenic ★★ same type
- GHR c.440-1G>A Pathogenic/Likely pathogenic ★★ same type
- GHR c.618+792A>G Pathogenic/Likely pathogenic ★★ same type
- GHR p.Arg235Ter Pathogenic ★★ same type
- GHR p.Arg61Ter Pathogenic ★★ same type
- GHR p.Asn115Thr Pathogenic/Likely pathogenic ★★ same type
- GHR p.Asp170His Pathogenic/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/ghr-p-val628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown