RAB7A c.*165AC[7]
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | phastCons 0.009 |
| Non-coding constraint | Z 1.04 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 0.335 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (CA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
African / African-American · 615/53,814 alleles
Filtering AF
1.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.04%
Overall
0.707%
4,251/601,672 alleles · low-frequency
exomes 3,833/451,874 · genomes 418/149,798 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.14% | 88 |
| East Asian | 0.997% | 100 |
| Remaining individualsnot grpmax-eligible | 0.896% | 112 |
| Ashkenazi Jewishnot grpmax-eligible | 0.827% | 121 |
| Middle Eastern | 0.722% | 139 |
| European (non-Finnish) | 0.695% | 144 |
| Finnishnot grpmax-eligible | 0.651% | 154 |
| Admixed American | 0.487% | 206 |
| South Asian | 0.304% | 328 |
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
- RAB7A
- Coding
- c.*165AC[7]
- MANE Select
- NM_004637
- dbSNP
- rs3830294
- Type
- Microsatellite
- Location
- chr3:128813586 (GRCh38)
- Gene constraint
- LOEUF 0.242 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.98 · 10 PDB
Similar variants
- RAB7A c.400-13CTT[2] Likely benign ★ same type
- RAB7A c.-70CTC[2] Benign ★ same type
- RAB7A c.*165AC[9] Likely benign ★ same type
- RAB7A c.*182CA[9] Likely 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/rab7a-c-star-165ac-7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown