CLIP2 p.Arg932=
c.2796T>C · rs76865959 · VCV785220
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.24%, 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. | ||
| REVEL | 0.247 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -12 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.24%
African / African-American · 4,663/74,760 alleles
Filtering AF
6.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.03%
Overall
0.333%
5,375/1,613,376 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.24% | 16 |
| Admixed American | 0.499% | 200 |
| Remaining individualsnot grpmax-eligible | 0.44% | 227 |
| Middle Eastern | 0.297% | 337 |
| South Asian | 0.00988% | 10,116 |
| European (non-Finnish) | 0.00941% | 10,630 |
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
- CLIP2
- Protein
- p.Arg932=
- Coding
- c.2796T>C
- MANE Select
- NM_003388
- dbSNP
- rs76865959
- Type
- single nucleotide variant
- Location
- chr7:74397149 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 2 PDB
Similar variants
- CLIP2 p.Arg932Cys Uncertain significance ★ same residue
- CLIP2 p.Arg12His Uncertain significance ★★ ⚠ same type
- CLIP2 p.Ala123= Benign ★★ same type
- CLIP2 p.Asn205= Benign ★★ same type
- CLIP2 p.Asn910= Benign/Likely benign ★★ same type
- CLIP2 p.His159= Benign/Likely benign ★★ same type
- CLIP2 p.Ile396= Benign ★★ same type
- CLIP2 p.Leu169= 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/clip2-p-arg932 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown