PDE2A c.144+9del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0115%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.064 | GERP -3.4, phastCons 0.004 |
| Non-coding constraint | Z 3.02 | 1 kb window · o/e 0.75 · regional · uncalibrated |
| Overall | ||
| CADD | 12.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0115%
Admixed American · 5/43,614 alleles
Filtering AF
0.00445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00293%
Overall
0.00239%
36/1,506,230 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0115% | 8,723 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00778% | 12,856 |
| South Asian | 0.0065% | 15,388 |
| East Asian | 0.00522% | 19,159 |
| Finnishnot grpmax-eligible | 0.00344% | 29,093 |
| African / African-American | 0.00289% | 34,632 |
| Remaining individualsnot grpmax-eligible | 0.00173% | 57,904 |
| European (non-Finnish) | 0.0015% | 66,448 |
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
- PDE2A
- Coding
- c.144+9del
- MANE Select
- NM_002599
- dbSNP
- rs776647324
- Type
- Deletion
- Location
- chr11:72642245 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17 · 44 PDB
Similar variants
- PDE2A c.2616-12del Benign/Likely benign ★★ same type
- PDE2A c.1070+8_1070+37del Likely benign ★ same type
- PDE2A c.2616-13del 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/pde2a-c-144-plus-9del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown