DMD c.*489C>T
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.223%, nfe)
Conditions
1
dilated cardiomyopathy 3B
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 0.81 | GERP 4.6, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 4.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.223%
European (non-Finnish) · 122/54,603 alleles
Filtering AF
0.191%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.179%
Overall
0.128%
133/103,924 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.223% | 448 |
| Remaining individualsnot grpmax-eligible | 0.107% | 935 |
| African / African-American | 0.0332% | 3,013 |
| South Asian | 0.0309% | 3,232 |
| Finnishnot grpmax-eligible | 0.0169% | 5,919 |
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
- DMD
- Coding
- c.*489C>T
- MANE Select
- NM_004006
- dbSNP
- rs45549534
- Type
- single nucleotide variant
- Location
- chrX:31121430 (GRCh38)
Similar variants
- DMD c.10086+1G>A Pathogenic ★★ same condition
- DMD c.1603-2A>T Pathogenic ★★ same condition
- DMD c.1812+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DMD c.2623-2A>G Pathogenic ★★ same condition
- DMD c.2804-1G>T Pathogenic ★★ same condition
- DMD c.31+1G>C Pathogenic ★★ same condition
- DMD c.31+1G>T Pathogenic ★★ same condition
- DMD c.4846-1G>C Likely pathogenic ★★ same condition
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/dmd-c-star-489c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown