PDE7B p.Arg83=
c.249G>A · rs114553138 · VCV709056
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, 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 7.5 | GERP -0.95, phastCons 1 |
| Overall | ||
| CADD | 11.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
African / African-American · 1,050/74,986 alleles
Filtering AF
1.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3%
Overall
0.0734%
1,184/1,613,450 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.4% | 71 |
| Middle Eastern | 0.116% | 866 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Admixed American | 0.085% | 1,176 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
| South Asian | 0.0011% | 91,054 |
| European (non-Finnish) | 0.000593% | 168,499 |
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
- PDE7B
- Protein
- p.Arg83=
- Coding
- c.249G>A
- MANE Select
- NM_018945
- dbSNP
- rs114553138
- Type
- single nucleotide variant
- Location
- chr6:136147433 (GRCh38)
- Gene constraint
- LOEUF 0.792 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 79.84
Similar variants
- PDE7B p.Lys295Arg Benign/Likely benign ★★ same type
- PDE7B p.Ala212Pro Uncertain significance ★ ⚠ same type
- PDE7B p.Ala318Ser Uncertain significance ★ ⚠ same type
- PDE7B p.Ala318Thr Uncertain significance ★ ⚠ same type
- PDE7B p.Arg124Cys Uncertain significance ★ ⚠ same type
- PDE7B p.Arg255Gln Uncertain significance ★ ⚠ same type
- PDE7B p.Arg293Thr Uncertain significance ★ ⚠ same type
- PDE7B p.Arg347Lys 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/pde7b-p-arg83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown