BCAS3 p.Ala656=
c.1968A>C · VCV3911288
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.01 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.99 | GERP -4.7, phastCons 0.99 |
| Overall | ||
| CADD | 7.913 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,028 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000205%
3/1,461,842 alleles · very rare
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
- BCAS3
- Protein
- p.Ala656=
- Coding
- c.1968A>C
- MANE Select
- NM_017679
- Type
- single nucleotide variant
- Location
- chr17:61040831 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.25
- Residue 656
- a UniProt-annotated variant site (in hemars)
Similar variants
- BCAS3 p.Ala349Val Uncertain significance ★★ ⚠ same type
- BCAS3 p.Arg254Cys Uncertain significance ★★ ⚠ same type
- BCAS3 p.Asp337Glu Uncertain significance ★★ ⚠ same type
- BCAS3 p.Pro755Leu Uncertain significance ★★ ⚠ same type
- BCAS3 c.1638-10A>G Likely benign ★★ same type
- BCAS3 p.Gly159= Likely benign ★★ same type
- BCAS3 c.1762+1G>A Likely pathogenic ★ same type
- BCAS3 p.Arg544Ter 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/bcas3-p-ala656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown