DMD c.649+48A>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.095%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +48 | near-intronic (+48 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.85 | GERP -2.4 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.095%
European (non-Finnish) · 717/754,602 alleles
Filtering AF
0.0892%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0869%
Overall
0.0699%
737/1,054,689 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.095% | 1,052 |
| Remaining individualsnot grpmax-eligible | 0.0285% | 3,510 |
| African / African-American | 0.00925% | 10,816 |
| Finnishnot grpmax-eligible | 0.0065% | 15,392 |
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.649+48A>T
- MANE Select
- NM_004006
- dbSNP
- rs200535651
- Type
- single nucleotide variant
- Location
- chrX:32809445 (GRCh38)
Similar variants
- DMD c.10086+1G>A Pathogenic ★★ same type
- DMD c.10086+1G>T Pathogenic ★★ same type
- DMD c.10086+2T>C Pathogenic ★★ same type
- DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same type
- DMD c.10223+1G>A Pathogenic ★★ same type
- DMD c.10223+1G>C Pathogenic ★★ same type
- DMD c.10224-2A>G Likely pathogenic ★★ same type
- DMD c.10554-2A>G 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/dmd-c-649-plus-48a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown