CLIP2 p.Asn205=
c.615C>T · rs116688438 · VCV782490
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.89%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 6.8, phastCons 1 |
| Overall | ||
| CADD | 10.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.89%
African / African-American · 1,419/75,044 alleles
Filtering AF
1.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.78%
Overall
0.103%
1,643/1,600,420 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.89% | 53 |
| Admixed American | 0.175% | 571 |
| Remaining individualsnot grpmax-eligible | 0.138% | 726 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00186% | 53,631 |
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.Asn205=
- Coding
- c.615C>T
- MANE Select
- NM_003388
- dbSNP
- rs116688438
- Type
- single nucleotide variant
- Location
- chr7:74338941 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 2 PDB
- Residue 205
- the 'disordered' region
Similar variants
- CLIP2 p.Asn205Lys Uncertain significance ★ ⚠ same residue
- CLIP2 p.Asn205Ser Uncertain significance ★ ⚠ same residue
- CLIP2 p.Arg12His Uncertain significance ★★ ⚠ same type
- CLIP2 p.Ala123= Benign ★★ same type
- CLIP2 p.Arg932= 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
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-asn205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown