Is DMD c.3603+15del pathogenic?

DMD c.3603+15del is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-25). Common (popmax 6.07%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Duchenne muscular dystrophy.

What condition is associated with DMD c.3603+15del?

DMD c.3603+15del is associated with Duchenne muscular dystrophy, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How is Duchenne muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DMD c.3603+15del

Q: How common is DMD c.3603+15del in the general population?

DMD c.3603+15del is common (popmax 6.07%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs5902031 · VCV94599

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 6.07%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +15	near-intronic (+15 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.15	GERP -2
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained
Overall
CADD	0.298	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(ATTT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.07% African / African-American · 2,662/43,826 alleles

Filtering AF 5.88% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.8%

Overall 3.82% 34,009/889,388 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.07%	16
Ashkenazi Jewishnot grpmax-eligible	4.98%	20
Remaining individualsnot grpmax-eligible	4.74%	21
Admixed American	4.09%	24
European (non-Finnish)	3.69%	27
Middle Eastern	3.38%	30
South Asian	3.14%	32
Finnishnot grpmax-eligible	3.12%	32
East Asian	3.08%	32

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.3603+15del
MANE Select: NM_004006
dbSNP: rs5902031
Type: Deletion
Location: chrX:32454647 (GRCh38)

Full DMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy Becker muscular dystrophy

For Duchenne muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

DMD c.1813-29_1813-2del Likely pathogenic ★★ same condition
DMD c.2804-1del Pathogenic ★★ same condition
DMD c.3433-5_3434del Pathogenic ★★ same condition
DMD c.4519-2_4523del Pathogenic ★★ same condition
DMD c.9650-4_9655del Likely pathogenic ★★ same condition
DMD p.Ala192fs Pathogenic ★★ same condition
DMD p.Ala324fs Pathogenic ★★ same condition
DMD p.Ala3522fs Pathogenic/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-3603-plus-15del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown