BICC1 p.Ser860=
c.2580G>A · rs1419690703 · VCV1932354
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.43 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -5.2 |
| Overall | ||
| CADD | 6.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,832 alleles
Overall
0.000274%
4/1,461,252 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,832 |
| Admixed American | 0.00167% | 59,950 |
| South Asian | 0.0011% | 91,070 |
| European (non-Finnish) | 8.48e-05% | 1,179,631 |
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.Ser860=
- Coding
- c.2580G>A
- MANE Select
- NM_001080512
- dbSNP
- rs1419690703
- Type
- single nucleotide variant
- Location
- chr10:58817608 (GRCh38)
- Gene constraint
- LOEUF 0.541 · pLI 0.30 (gnomAD)
- Structure
- AlphaFold pLDDT 61.02 · 3 PDB
Similar variants
- BICC1 p.Ser860Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser860 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown