MYO7A c.5326+101A>C
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +101 | deep intronic (+101 nt into the intron) |
|---|---|---|
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.27 | GERP -2.9 |
| Overall | ||
| CADD | 0.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
African / African-American · 713/68,996 alleles
Filtering AF
0.971%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.945%
Overall
0.0678%
920/1,357,240 alleles · low-frequency
exomes 497/1,204,920 · genomes 423/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.03% | 97 |
| Middle Eastern | 0.418% | 239 |
| Remaining individualsnot grpmax-eligible | 0.107% | 932 |
| Admixed American | 0.0583% | 1,716 |
| European (non-Finnish) | 0.0104% | 9,658 |
| South Asian | 0.00563% | 17,767 |
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
- MYO7A
- Coding
- c.5326+101A>C
- MANE Select
- NM_000260
- dbSNP
- rs139786600
- Type
- single nucleotide variant
- Location
- chr11:77203318 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
Similar variants
- MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
- MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type
- MYO7A p.Arg668Cys Pathogenic ★★★ same type
- MYO7A p.Arg853His Likely pathogenic ★★★ same type
- MYO7A p.Glu968Asp Likely pathogenic ★★★ ⚠ same type
- MYO7A p.Gly2187Asp Likely 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/myo7a-c-5326-plus-101a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown