Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00996%, nfe)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00996%
European (non-Finnish) · 89/893,291 alleles
Filtering AF
0.00823%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00758%
Overall
0.00755%
91/1,205,999 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00996% | 10,037 |
| Remaining individualsnot grpmax-eligible | 0.00422% | 23,721 |
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.Arg1844=
- Coding
- c.5530C>A
- MANE Select
- NM_004006
- dbSNP
- rs1064325
- Type
- single nucleotide variant
- Location
- chrX:32345999 (GRCh38)
- Residue 1844
- the 'interaction with synm' region; a UniProt-annotated variant site (in)
Similar variants
- DMD p.Arg1844Ter Pathogenic ★★ same residue
- DMD p.Arg1844Gln Likely benign ★★ ⚠ same residue
- DMD p.Arg1844fs Likely pathogenic ★ 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
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-arg1844 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown