CD55 c.664+13A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00839%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.97 | GERP 0.6 |
| Non-coding constraint | Z 0.97 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 13.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00839%
Admixed American · 5/59,578 alleles
Filtering AF
0.00325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00208%
Overall
0.00119%
17/1,429,904 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00839% | 11,916 |
| Remaining individualsnot grpmax-eligible | 0.00651% | 15,350 |
| European (non-Finnish) | 0.000694% | 144,002 |
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
- CD55
- Coding
- c.664+13A>C
- MANE Select
- NM_000574
- dbSNP
- rs779388813
- Type
- single nucleotide variant
- Location
- chr1:207326850 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.99 · 33 PDB
Similar variants
- CD55 c.286+1G>A Likely pathogenic ★★ same type
- CD55 c.286+2T>G Likely pathogenic ★★ same type
- CD55 p.Glu50Ter Pathogenic/Likely pathogenic ★★ same type
- CD55 p.Trp213Ter Pathogenic/Likely pathogenic ★★ same type
- CD55 c.1081+1G>C Uncertain significance ★★ same type
- CD55 p.Arg221Ser Uncertain significance ★★ ⚠ same type
- CD55 p.Arg357Cys Uncertain significance ★★ ⚠ same type
- CD55 p.Arg357His Uncertain significance ★★ ⚠ 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/cd55-c-664-plus-13a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown