Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.65%, 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 5.4 | GERP -0.99, phastCons 1 |
| Overall | ||
| CADD | 8.919 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.65%
African / African-American · 3,478/74,784 alleles
Filtering AF
4.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.47%
Overall
0.249%
4,007/1,607,060 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.65% | 22 |
| Admixed American | 0.428% | 234 |
| Remaining individualsnot grpmax-eligible | 0.354% | 283 |
| Middle Eastern | 0.149% | 672 |
| South Asian | 0.00662% | 15,115 |
| European (non-Finnish) | 0.00324% | 30,900 |
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
- CCP110
- Protein
- p.Arg845=
- Coding
- c.2535A>G
- MANE Select
- NM_001323572
- dbSNP
- rs8054531
- Type
- single nucleotide variant
- Location
- chr16:19544847 (GRCh38)
- Gene constraint
- LOEUF 0.372 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.11
Similar variants
- CCP110 p.Ala433= Benign ★★ same type
- CCP110 p.Asn740= Benign ★★ same type
- CCP110 p.Ile252Met Benign ★★ same type
- CCP110 p.Lys583= Benign ★★ same type
- CCP110 p.Met375Ile Benign ★★ same type
- CCP110 p.Pro171Leu Benign ★★ same type
- CCP110 p.Thr122= Benign ★★ same type
- CCP110 p.Thr560Met 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/ccp110-p-arg845 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown