CD55 c.853+20A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0899%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +20 | near-intronic (+20 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.66 | GERP -3.4 |
| Non-coding constraint | Z 2.18 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 0.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0899%
South Asian · 81/90,104 alleles
Filtering AF
0.0741%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0683%
Overall
0.00543%
87/1,602,236 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0899% | 1,112 |
| Remaining individualsnot grpmax-eligible | 0.00805% | 12,415 |
| European (non-Finnish) | 8.54e-05% | 1,171,005 |
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.853+20A>G
- MANE Select
- NM_000574
- dbSNP
- rs560219490
- Type
- single nucleotide variant
- Location
- chr1:207331316 (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-853-plus-20a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown