DMD c.3786+2T>A
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Duchenne muscular dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | Δ0.80 | donor loss · deltas |
| Pangolin | Δ0.62 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.2, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 26.7 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DMD
- Coding
- c.3786+2T>A
- MANE Select
- NM_004006
- dbSNP
- rs2148287085
- Type
- single nucleotide variant
- Location
- chrX:32448454 (GRCh38)
Disease context
Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Duchenne muscular dystrophy (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- 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
- DMD c.10554-2A>G 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-3786-plus-2t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown