DOCK7 c.3045+89C>A
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.15%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +89 | deep intronic (+89 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP -0.41, phastCons 0.016 |
| Non-coding constraint | Z 1.77 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 0.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.15%
South Asian · 2,295/72,742 alleles
Filtering AF
3.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3%
Overall
1.35%
17,886/1,323,582 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.15% | 32 |
| European (non-Finnish) | 1.45% | 69 |
| Middle Eastern | 1.35% | 74 |
| Remaining individualsnot grpmax-eligible | 1.27% | 79 |
| Finnishnot grpmax-eligible | 0.938% | 107 |
| Amishnot grpmax-eligible | 0.768% | 130 |
| Admixed American | 0.45% | 222 |
| Ashkenazi Jewishnot grpmax-eligible | 0.389% | 257 |
| African / African-American | 0.224% | 447 |
| East Asian | 0.0047% | 21,282 |
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
- DOCK7
- Coding
- c.3045+89C>A
- MANE Select
- NM_001367561
- dbSNP
- rs116423924
- Type
- single nucleotide variant
- Location
- chr1:62542519 (GRCh38)
- Gene constraint
- LOEUF 0.551 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.60 · 2 PDB
Similar variants
- DOCK7 c.4924-1G>A Pathogenic/Likely pathogenic ★★ same type
- DOCK7 p.Arg1380Ter Pathogenic ★★ same type
- DOCK7 p.Arg1415Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK7 p.Arg429Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK7 p.Arg445Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK7 c.3781+4C>G Uncertain significance ★★ same type
- DOCK7 c.38+6T>C Uncertain significance ★★ same type
- DOCK7 p.Ala1479Thr 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/dock7-c-3045-plus-89c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown