NCOR2 p.Pro1906=
c.5718G>A · rs2229842 · VCV1301427
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 44.7%, eas) — 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. | ||
| REVEL | 0.009 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5 | GERP -2.5 |
| Overall | ||
| CADD | 3.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
44.7%
East Asian · 18,221/40,798 alleles
Filtering AF
44.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 43.9%
Overall
16.8%
255,694/1,519,722 alleles · common
exomes 228,334/1,367,654 · genomes 27,360/152,068 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 44.7% | 2 |
| Finnishnot grpmax-eligible | 30.1% | 3 |
| Admixed American | 21.4% | 5 |
| South Asian | 20.2% | 5 |
| Remaining individualsnot grpmax-eligible | 18% | 6 |
| African / African-American | 15.7% | 6 |
| European (non-Finnish) | 14.9% | 7 |
| Amishnot grpmax-eligible | 11.5% | 9 |
| Middle Eastern | 10.5% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 9.14% | 11 |
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
- NCOR2
- Protein
- p.Pro1906=
- Coding
- c.5718G>A
- MANE Select
- NM_006312
- dbSNP
- rs2229842
- Type
- single nucleotide variant
- Location
- chr12:124337150 (GRCh38)
- Gene constraint
- LOEUF 0.448 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 41.00 · 36 PDB
Similar variants
- NCOR2 p.Ala1526Thr Uncertain significance ★★ ⚠ same type
- NCOR2 p.Arg2174Cys Uncertain significance ★★ ⚠ same type
- NCOR2 p.Arg2467Gln Uncertain significance ★★ ⚠ same type
- NCOR2 p.Gly1520Ser Uncertain significance ★★ ⚠ same type
- NCOR2 c.3986-17C>T Benign ★★ same type
- NCOR2 c.6265+16T>C Benign ★★ same type
- NCOR2 c.-36G>C Benign ★★ same type
- NCOR2 p.Ala1699Thr 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/ncor2-p-pro1906 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown