BSCL2 p.Ser140=
c.420C>T · rs780093151 · VCV246596
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000594%, nfe)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 8.934 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000594%
European (non-Finnish) · 7/1,178,714 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000434%
7/1,612,084 alleles · very rare
exomes 4/1,459,940 · genomes 3/152,144 · 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
- BSCL2
- Protein
- p.Ser140=
- Coding
- c.420C>T
- MANE Select
- NM_001122955
- dbSNP
- rs780093151
- Type
- single nucleotide variant
- Location
- chr11:62702534 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.09 · 1 PDB
Similar variants
- BSCL2 p.Ser140Cys Uncertain significance ★★ ⚠ same residue
- BSCL2 c.1006-2A>C Likely pathogenic ★★ same condition
- BSCL2 c.486+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BSCL2 p.Ala276Pro Pathogenic ★★ same condition
- BSCL2 p.Arg329Ter Pathogenic ★★ same condition
- BSCL2 p.Asn152Ser Pathogenic ★★ ⚠ same condition
- BSCL2 p.Glu253Ter Pathogenic ★★ same condition
- BSCL2 p.Ser154Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/bscl2-p-ser140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown