BCAS4 p.Pro9=
c.27G>A · rs936862957 · VCV799459
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.111%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -2.1 |
| Overall | ||
| CADD | 9.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
Middle Eastern · 6/5,382 alleles
Filtering AF
0.0485%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0331%
Overall
0.00508%
76/1,494,920 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.111% | 897 |
| Remaining individualsnot grpmax-eligible | 0.026% | 3,839 |
| African / African-American | 0.0144% | 6,963 |
| European (non-Finnish) | 0.00374% | 26,707 |
| South Asian | 0.00252% | 39,681 |
| Admixed American | 0.00209% | 47,736 |
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
- BCAS4
- Protein
- p.Pro9=
- Coding
- c.27G>A
- MANE Select
- NM_198799
- dbSNP
- rs936862957
- Type
- single nucleotide variant
- Location
- chr20:50795110 (GRCh38)
- Gene constraint
- LOEUF 1.081 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.40
- Residue 9
- the 'disordered' region
Similar variants
- BCAS4 p.Ser130Thr Benign ★★ same type
- BCAS4 p.Ser130Tyr Benign/Likely benign ★★ ⚠ same type
- BCAS4 p.Thr142Met Likely benign ★★ same type
- BCAS4 c.-15C>T Uncertain significance ★ ⚠ same type
- BCAS4 c.-6C>T Uncertain significance ★ ⚠ same type
- BCAS4 p.Ala118Ser Uncertain significance ★ ⚠ same type
- BCAS4 p.Ala126Thr Uncertain significance ★ ⚠ same type
- BCAS4 p.Ala29Ser 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/bcas4-p-pro9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown