DYM c.946+7G>A
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.273%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.53 | GERP -0.35, phastCons 0.007 |
| Non-coding constraint | Z -2.95 | 1 kb window · o/e 1.23 · regional · uncalibrated |
| Overall | ||
| CADD | 8.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.273%
African / African-American · 205/74,992 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.231%
Overall
0.0138%
223/1,613,902 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.273% | 366 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,249 |
| Admixed American | 0.00333% | 30,010 |
| European (non-Finnish) | 0.000424% | 235,975 |
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
- DYM
- Coding
- c.946+7G>A
- MANE Select
- NM_001353214
- dbSNP
- rs150849326
- Type
- single nucleotide variant
- Location
- chr18:49286427 (GRCh38)
- Gene constraint
- LOEUF 1.081 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.91
Similar variants
- DYM c.1728+2T>C Pathogenic/Likely pathogenic ★★ same type
- DYM c.947-2A>G Pathogenic/Likely pathogenic ★★ same type
- DYM p.Arg204Ter Pathogenic ★★ same type
- DYM p.Arg428Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Arg588Ter Pathogenic ★★ same type
- DYM p.Arg70Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Gln306Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Glu87Lys 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/dym-c-946-plus-7g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown