CLPB c.1680+78CA[5]
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 22%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +78 | deep intronic (+78 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.68 | GERP -1.9 |
| Overall | ||
| CADD | 0.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22%
African / African-American · 16,458/74,824 alleles
Filtering AF
21.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 21.6%
Overall
4.43%
71,258/1,609,620 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 22% | 5 |
| East Asian | 13.8% | 7 |
| Admixed American | 9.1% | 11 |
| Middle Eastern | 6% | 17 |
| South Asian | 5.83% | 17 |
| Remaining individualsnot grpmax-eligible | 5.3% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 4.13% | 24 |
| Finnishnot grpmax-eligible | 3.16% | 32 |
| Amishnot grpmax-eligible | 2.64% | 38 |
| European (non-Finnish) | 2.63% | 38 |
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
- CLPB
- Coding
- c.1680+78CA[5]
- MANE Select
- NM_001258392
- dbSNP
- rs59806404
- Type
- Microsatellite
- Location
- chr11:72294239 (GRCh38)
- Gene constraint
- LOEUF 0.643 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.52 · 7 PDB
Similar variants
- CLPB p.Glu624del Uncertain significance ★★ same type
- CLPB c.456-5081_456-5079del Uncertain significance ★ same type
- CLPB c.456-99GCCATACACTGAAAATATTCCTCTGTCTTGTTTTAGGCTGTTGTCAGAAGGTGCAGATGTCAA[4] Uncertain significance ★ same type
- CLPB p.Asn566del Uncertain significance ★ same type
- CLPB c.1487-248_1487-244del Benign ★ same type
- CLPB c.456-14_456-13del Likely benign ★ same type
- CLPB c.542+8ACC[3] Likely benign ★ 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/clpb-c-1680-plus-78ca-5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown