CORO2A p.Pro45=
c.135C>T · rs137868323 · VCV2659344
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.148%, mid)
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 2.6 | GERP 0.81, phastCons 1 |
| Overall | ||
| CADD | 9.583 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.148%
Middle Eastern · 9/6,062 alleles
Filtering AF
0.0774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0578%
Overall
0.0281%
454/1,614,206 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.148% | 674 |
| Ashkenazi Jewishnot grpmax-eligible | 0.108% | 925 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,953 |
| European (non-Finnish) | 0.0293% | 3,411 |
| South Asian | 0.022% | 4,554 |
| Admixed American | 0.0217% | 4,618 |
| African / African-American | 0.00267% | 37,521 |
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
- CORO2A
- Protein
- p.Pro45=
- Coding
- c.135C>T
- MANE Select
- NM_052820
- dbSNP
- rs137868323
- Type
- single nucleotide variant
- Location
- chr9:98157526 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.12
Similar variants
- CORO2A p.Ala105Asp Uncertain significance ★ ⚠ same type
- CORO2A p.Ala132Thr Uncertain significance ★ ⚠ same type
- CORO2A p.Ala144Thr Uncertain significance ★ ⚠ same type
- CORO2A p.Ala145Thr Uncertain significance ★ ⚠ same type
- CORO2A p.Ala218Thr Uncertain significance ★ ⚠ same type
- CORO2A p.Ala280Thr Uncertain significance ★ ⚠ same type
- CORO2A p.Ala59Ser Uncertain significance ★ ⚠ same type
- CORO2A p.Ala59Thr 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/coro2a-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown