BBIP1 p.Leu2=
c.6T>G · rs1186420743 · VCV1615115
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00714%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -3.8, phastCons 0.97 |
| Overall | ||
| CADD | 11.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00714%
South Asian · 6/84,058 alleles
Filtering AF
0.00306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00208%
Overall
0.000391%
6/1,535,978 alleles · very rare
exomes 6/1,383,616 · genomes 0/152,362 · joint denominator
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
- BBIP1
- Protein
- p.Leu2=
- Coding
- c.6T>G
- MANE Select
- NM_001195305
- dbSNP
- rs1186420743
- Type
- single nucleotide variant
- Location
- chr10:110918152 (GRCh38)
- Gene constraint
- LOEUF 1.693 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 82.24 · 1 PDB
- Residue 2
- the 'disordered' region
Similar variants
- BBIP1 c.37+3A>T Uncertain significance ★★ same type
- BBIP1 c.38-6T>C Uncertain significance ★★ same type
- BBIP1 p.Arg31Trp Uncertain significance ★★ ⚠ same type
- BBIP1 p.Arg78His Uncertain significance ★★ ⚠ same type
- BBIP1 p.Arg88Gln Uncertain significance ★★ ⚠ same type
- BBIP1 p.Asn15Lys Uncertain significance ★★ ⚠ same type
- BBIP1 p.Ile17Lys Uncertain significance ★★ ⚠ same type
- BBIP1 p.Lys59Asn 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/bbip1-p-leu2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown