PARK7 c.252+46del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 23.7%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +46 | near-intronic (+46 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.99 | GERP -1.9 |
| Non-coding constraint | Z -5.56 | 1 kb window · o/e 1.39 · regional · uncalibrated |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
23.7%
African / African-American · 15,111/63,760 alleles
Filtering AF
23.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 23.3%
Overall
7.73%
57,252/740,616 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 23.7% | 4 |
| Remaining individualsnot grpmax-eligible | 9.31% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 8.9% | 11 |
| Middle Eastern | 8.15% | 12 |
| European (non-Finnish) | 6.62% | 15 |
| Finnishnot grpmax-eligible | 5.74% | 17 |
| South Asian | 5.56% | 18 |
| Admixed American | 4.07% | 25 |
| East Asian | 2.43% | 41 |
| Amishnot grpmax-eligible | 0.478% | 209 |
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
- PARK7
- Coding
- c.252+46del
- MANE Select
- NM_007262
- dbSNP
- rs147617838
- Type
- Deletion
- Location
- chr1:7969441 (GRCh38)
- Gene constraint
- LOEUF 1.025 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 98.43 · 88 PDB
Similar variants
- PARK7 p.Pro158del Likely pathogenic ★★ same type
- PARK7 c.-24+75_-24+92del Benign ★★ same type
- PARK7 c.410delG Uncertain significance ★ same type
- PARK7 c.252+193_252+194del Benign ★ same type
- PARK7 c.252+194del Benign ★ same type
- PARK7 c.252+45_252+46del Likely benign ★ same type
- PARK7 c.409+267_409+276del Benign ★ same type
- PARK7 c.409+274_409+276del 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/park7-c-252-plus-46del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown