Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.38%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.4 |
| Overall | ||
| CADD | 0.016 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.38%
East Asian · 1,962/44,828 alleles
Filtering AF
4.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.15%
Overall
0.256%
4,128/1,612,290 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.38% | 23 |
| Admixed American | 2.7% | 37 |
| Finnishnot grpmax-eligible | 0.339% | 295 |
| Remaining individualsnot grpmax-eligible | 0.224% | 446 |
| South Asian | 0.0418% | 2,395 |
| African / African-American | 0.0374% | 2,673 |
| European (non-Finnish) | 0.0108% | 9,282 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,574 |
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.Ser519=
- Coding
- c.1557A>G
- MANE Select
- NM_001366298
- dbSNP
- rs3746788
- Type
- single nucleotide variant
- Location
- chr20:53953690 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.00
- Residue 519
- the 'disordered' region
Similar variants
- BCAS1 c.1486-10G>A Benign ★★ same type
- BCAS1 p.Ala180= Benign ★★ same type
- BCAS1 p.Thr171Met Benign ★★ ⚠ same type
- BCAS1 p.Thr56Met Benign ★★ ⚠ same type
- BCAS1 p.Thr578= Benign ★★ same type
- BCAS1 p.Thr67Met Benign/Likely benign ★★ ⚠ same type
- BCAS1 p.Ala184Val Uncertain significance ★ ⚠ same type
- BCAS1 p.Ala257Ser 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-ser519 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown