BICC1 p.Val593=
c.1779G>A · rs145584701 · VCV2141175
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0693%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 6.384 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0693%
African / African-American · 52/75,034 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0489%
Overall
0.00415%
67/1,612,584 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0693% | 1,443 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,676 |
| Middle Eastern | 0.0165% | 6,054 |
| Admixed American | 0.00167% | 59,954 |
| South Asian | 0.0011% | 91,000 |
| European (non-Finnish) | 8.48e-05% | 1,178,844 |
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
- BICC1
- Protein
- p.Val593=
- Coding
- c.1779G>A
- MANE Select
- NM_001080512
- dbSNP
- rs145584701
- Type
- single nucleotide variant
- Location
- chr10:58800247 (GRCh38)
- Gene constraint
- LOEUF 0.541 · pLI 0.30 (gnomAD)
- Structure
- AlphaFold pLDDT 61.02 · 3 PDB
- Residue 593
- the 'disordered' region
Similar variants
- BICC1 p.Ala190Thr Uncertain significance ★★ ⚠ same type
- BICC1 p.Ala276Ser Uncertain significance ★★ ⚠ same type
- BICC1 p.Ala523Val Uncertain significance ★★ ⚠ same type
- BICC1 p.Arg302Gln Uncertain significance ★★ ⚠ same type
- BICC1 p.Arg657Lys Uncertain significance ★★ ⚠ same type
- BICC1 p.Arg804His Uncertain significance ★★ ⚠ same type
- BICC1 p.Arg839His Uncertain significance ★★ ⚠ same type
- BICC1 p.Arg961Cys 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/bicc1-p-val593 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown