BMS1 c.779+8A>G
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0431%, eas)
Conditions
1
BMS1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.034 | GERP -3.4 |
| Non-coding constraint | Z 2.07 | 1 kb window · o/e 0.85 · regional · uncalibrated |
| Overall | ||
| CADD | 2.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0431%
East Asian · 19/44,072 alleles
Filtering AF
0.0281%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0234%
Overall
0.00559%
89/1,591,698 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0431% | 2,320 |
| South Asian | 0.022% | 4,553 |
| Remaining individualsnot grpmax-eligible | 0.0195% | 5,119 |
| African / African-American | 0.0178% | 5,611 |
| Admixed American | 0.0169% | 5,900 |
| European (non-Finnish) | 0.00145% | 69,096 |
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
- BMS1
- Coding
- c.779+8A>G
- MANE Select
- NM_014753
- dbSNP
- rs565927861
- Type
- single nucleotide variant
- Location
- chr10:42791777 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
Disease context
BMS1-related disorder
Similar variants
- BMS1 c.779+7T>A Likely benign same condition
- BMS1 p.Ala549Thr Benign same condition
- BMS1 p.Ala864Thr Benign ⚠ same condition
- BMS1 p.Asp505= Likely benign same condition
- BMS1 p.Gln419Glu Benign same condition
- BMS1 p.Lys399= Benign same condition
- BMS1 p.Phe1047Leu Benign same condition
- BMS1 p.Thr583= Benign 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/bms1-c-779-plus-8a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown