CHRD p.Thr301=
c.903C>G · rs77289593 · VCV709673
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.82%, 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 -1.1 | GERP -0.81 |
| Overall | ||
| CADD | 2.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.82%
African / African-American · 2,115/74,982 alleles
Filtering AF
2.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.68%
Overall
0.191%
3,078/1,613,912 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.82% | 35 |
| Middle Eastern | 0.528% | 189 |
| Admixed American | 0.317% | 316 |
| Remaining individualsnot grpmax-eligible | 0.301% | 332 |
| European (non-Finnish) | 0.0456% | 2,193 |
| South Asian | 0.0165% | 6,071 |
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
- CHRD
- Protein
- p.Thr301=
- Coding
- c.903C>G
- MANE Select
- NM_003741
- dbSNP
- rs77289593
- Type
- single nucleotide variant
- Location
- chr3:184382695 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.95 · 3 PDB
- Residue 301
- the chrd 2 domain
Similar variants
- CHRD p.Thr301Ala Likely benign ★ same residue
- CHRD p.Gln608= Benign ★★ same type
- CHRD p.Gly387Ser Benign ★★ same type
- CHRD p.Pro772= Benign ★★ same type
- CHRD p.Thr457Ser Likely benign ★★ same type
- CHRD p.Ala251Glu Uncertain significance ★ ⚠ same type
- CHRD p.Ala251Thr Uncertain significance ★ ⚠ same type
- CHRD p.Ala27Pro 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/chrd-p-thr301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown