Is DMD p.Arg2415His (c.7244G>A) pathogenic?

DMD p.Arg2415His (c.7244G>A) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-20). AlphaMissense: likely benign (0.0552); Ultra-rare (popmax 0.0384%, afr); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg2415His (c.7244G>A)?

DMD p.Arg2415His (c.7244G>A) is associated with Duchenne muscular dystrophy, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Arg2415His (c.7244G>A) in the general population?

DMD p.Arg2415His (c.7244G>A) is ultra-rare (popmax 0.0384%, afr) (gnomAD).

How is Duchenne muscular dystrophy inherited?

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

What do computational predictors say about DMD p.Arg2415His (c.7244G>A)?

AlphaMissense predicts likely benign (score 0.0552) — an in-silico prediction, not a clinical call.

DMD p.Arg2415His

c.7244G>A · rs373749120 · VCV227309

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.0552 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0384%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.0552	likely benign
REVEL	0.041	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.17	GERP -4.6
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	0.627	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0384% African / African-American · 22/57,278 alleles

Filtering AF 0.0259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0219%

Overall 0.00397% 48/1,210,054 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0384%	2,604
Admixed American	0.0197%	5,087
South Asian	0.0158%	6,314
Remaining individualsnot grpmax-eligible	0.0042%	23,805
East Asian	0.00296%	33,751
Finnishnot grpmax-eligible	0.00214%	46,646
European (non-Finnish)	0.000447%	223,775

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
Protein: p.Arg2415His
Coding: c.7244G>A
MANE Select: NM_004006
dbSNP: rs373749120
Type: single nucleotide variant
Location: chrX:31820040 (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 p.Arg2415Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD c.10086+1G>A Pathogenic ★★ same condition
DMD c.10086+1G>T Pathogenic ★★ same condition
DMD c.10086+2T>C Pathogenic ★★ same condition
DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same condition
DMD c.10223+1G>A Pathogenic ★★ same condition
DMD c.10223+1G>C Pathogenic ★★ same condition
DMD c.10224-2A>G 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-p-arg2415his (accessed [today's date]).

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