BCAS1 p.Thr578=
c.1734G>A · rs61333971 · VCV777585
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.73%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3.5 |
| Overall | ||
| CADD | 0.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.73%
African / African-American · 5,043/74,886 alleles
Filtering AF
6.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.52%
Overall
0.368%
5,939/1,613,866 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.73% | 15 |
| Admixed American | 0.53% | 189 |
| Remaining individualsnot grpmax-eligible | 0.523% | 191 |
| Middle Eastern | 0.297% | 337 |
| South Asian | 0.0187% | 5,357 |
| European (non-Finnish) | 0.0181% | 5,514 |
| East Asian | 0.00446% | 22,420 |
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
- BCAS1
- Protein
- p.Thr578=
- Coding
- c.1734G>A
- MANE Select
- NM_001366298
- dbSNP
- rs61333971
- Type
- single nucleotide variant
- Location
- chr20:53953513 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.00
- Residue 578
- the 'disordered' region; the 'interacts with dynll1 and dynll2' region
Similar variants
- BCAS1 p.Thr578Met Likely benign ★ ⚠ same residue
- BCAS1 c.1486-10G>A Benign ★★ same type
- BCAS1 p.Ala180= Benign ★★ same type
- BCAS1 p.Ser519= Benign ★★ same type
- BCAS1 p.Thr171Met Benign ★★ ⚠ same type
- BCAS1 p.Thr56Met Benign ★★ ⚠ same type
- BCAS1 p.Thr67Met Benign/Likely benign ★★ ⚠ same type
- BCAS1 p.Ala184Val Uncertain significance ★ ⚠ 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/bcas1-p-thr578 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown