BCS1L p.Val79=
c.237C>T · rs757259048 · VCV1124949
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -15 | GERP -4.7 |
| Overall | ||
| CADD | 0.123 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,998 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000743%
12/1,614,092 alleles · very rare
exomes 10/1,461,892 · genomes 2/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,999 |
| African / African-American | 0.00133% | 74,940 |
| European (non-Finnish) | 0.000763% | 131,116 |
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
- BCS1L
- Protein
- p.Val79=
- Coding
- c.237C>T
- MANE Select
- NM_001079866
- dbSNP
- rs757259048
- Type
- single nucleotide variant
- Location
- chr2:218661224 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.10
Similar variants
- BCS1L c.320+1G>T Pathogenic/Likely pathogenic ★★ same type
- BCS1L c.321-2A>G Likely pathogenic ★★ same type
- BCS1L c.889+1G>T Pathogenic/Likely pathogenic ★★ same type
- BCS1L c.889+2T>G Likely pathogenic ★★ same type
- BCS1L c.-50+388C>G Likely pathogenic ★★ same type
- BCS1L c.-50+405A>G Pathogenic/Likely pathogenic ★★ same type
- BCS1L p.Arg109Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- BCS1L p.Arg114Trp Pathogenic/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/bcs1l-p-val79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown