DMD c.960+50del
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 19.1%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +50 | near-intronic (+50 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.92 | GERP 0.61, phastCons 0.001 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.145 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
19.1%
African / African-American · 10,884/56,838 alleles
Filtering AF
18.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 18.7%
Overall
1.05%
12,631/1,202,413 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 19.1% | 5 |
| Remaining individualsnot grpmax-eligible | 1.55% | 64 |
| Admixed American | 1.44% | 70 |
| Middle Eastern | 0.923% | 108 |
| South Asian | 0.0855% | 1,170 |
| European (non-Finnish) | 0.0302% | 3,307 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00913% | 10,954 |
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.960+50del
- MANE Select
- NM_004006
- dbSNP
- rs72470512
- Type
- Deletion
- Location
- chrX:32697820 (GRCh38)
Similar variants
- DMD c.1813-29_1813-2del Likely pathogenic ★★ same type
- DMD c.2804-1del Pathogenic ★★ same type
- DMD c.3276+2del Pathogenic/Likely pathogenic ★★ same type
- DMD c.3433-5_3434del Pathogenic ★★ same type
- DMD c.4519-2_4523del Pathogenic ★★ same type
- DMD c.6438+1_6438+5del Pathogenic ★★ same type
- DMD c.9650-4_9655del Likely pathogenic ★★ same type
- DMD p.Ala192fs 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-960-plus-50del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown