COBL p.Ser47=
c.141G>A · rs115321263 · VCV786107
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.82%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2 | GERP -3.7 |
| Overall | ||
| CADD | 0.655 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.82%
African / African-American · 3,616/74,988 alleles
Filtering AF
4.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.64%
Overall
0.262%
4,228/1,613,920 alleles · low-frequency
exomes 2,074/1,461,708 · genomes 2,154/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.82% | 21 |
| Admixed American | 0.36% | 278 |
| Remaining individualsnot grpmax-eligible | 0.354% | 283 |
| Middle Eastern | 0.166% | 602 |
| European (non-Finnish) | 0.0129% | 7,763 |
| South Asian | 0.0121% | 8,279 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| East Asian | 0.00223% | 44,862 |
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
- COBL
- Protein
- p.Ser47=
- Coding
- c.141G>A
- MANE Select
- NM_015198
- dbSNP
- rs115321263
- Type
- single nucleotide variant
- Location
- chr7:51219845 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.88 · 1 PDB
- Residue 47
- a modified residue (phosphoserine)
Similar variants
- COBL p.Ala57= Benign ★★ same type
- COBL p.Ala655Pro Benign ★★ same type
- COBL p.Gly534Ser Likely benign ★★ same type
- COBL p.His601Tyr Benign ★★ same type
- COBL p.Ser513Phe Benign ★★ same type
- COBL p.Thr1234= Benign ★★ same type
- COBL p.Tyr222= Benign ★★ same type
- COBL p.Ala1130Ser 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/cobl-p-ser47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown