CLOCK c.1206+10T>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +10 | near-intronic (+10 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.82 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -3.4, phastCons 0.02 |
| Non-coding constraint | Z 1.12 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 5.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
African / African-American · 854/74,220 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0621%
987/1,589,514 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.15% | 87 |
| Admixed American | 0.113% | 885 |
| Remaining individualsnot grpmax-eligible | 0.078% | 1,282 |
| Middle Eastern | 0.0502% | 1,991 |
| European (non-Finnish) | 0.0012% | 83,059 |
| South Asian | 0.00114% | 87,490 |
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
- CLOCK
- Coding
- c.1206+10T>C
- MANE Select
- NM_004898
- dbSNP
- rs141393811
- Type
- single nucleotide variant
- Location
- chr4:55453044 (GRCh38)
- Gene constraint
- LOEUF 0.496 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 61.90 · 2 PDB
Similar variants
- CLOCK c.674-10A>G Benign ★★ same type
- CLOCK p.Ala34= Benign ★★ same type
- CLOCK p.Gly235Glu Likely benign ★★ same type
- CLOCK c.2362-2A>G Uncertain significance ★ same type
- CLOCK p.Ala432Pro Uncertain significance ★ ⚠ same type
- CLOCK p.Ala691Gly Uncertain significance ★ ⚠ same type
- CLOCK p.Arg242Lys Uncertain significance ★ ⚠ same type
- CLOCK p.Arg386Gln 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/clock-c-1206-plus-10t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown