CTCF c.952+141T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.95%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +141 | deep intronic (+141 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3 |
| Non-coding constraint | Z 0.87 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 0.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.95%
African / African-American · 1,072/54,880 alleles
Filtering AF
1.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.82%
Overall
0.183%
1,287/701,768 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.95% | 51 |
| Admixed American | 0.242% | 414 |
| Remaining individualsnot grpmax-eligible | 0.199% | 503 |
| Ashkenazi Jewishnot grpmax-eligible | 0.086% | 1,162 |
| Middle Eastern | 0.0805% | 1,242 |
| European (non-Finnish) | 0.0151% | 6,631 |
| South Asian | 0.00223% | 44,942 |
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
- CTCF
- Coding
- c.952+141T>C
- MANE Select
- NM_006565
- dbSNP
- rs143770196
- Type
- single nucleotide variant
- Location
- chr16:67612262 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
Similar variants
- CTCF c.782-1G>A Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-2A>T Pathogenic ★★ same type
- CTCF p.Arg283His Likely pathogenic ★★ same type
- CTCF p.Arg342Cys Pathogenic/Likely pathogenic ★★ same type
- CTCF p.Arg342His Pathogenic/Likely pathogenic ★★ same type
- CTCF p.Arg368Cys 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/ctcf-c-952-plus-141t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown