SPG7 c.1663+112C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.13%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +112 | deep intronic (+112 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.58 | GERP -1.4 |
| Overall | ||
| CADD | 0.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.13%
African / African-American · 664/58,650 alleles
Filtering AF
1.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.0947%
713/753,284 alleles · low-frequency
exomes 213/600,940 · genomes 500/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.13% | 88 |
| Remaining individualsnot grpmax-eligible | 0.0644% | 1,553 |
| Admixed American | 0.0401% | 2,497 |
| European (non-Finnish) | 0.00141% | 70,883 |
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
- SPG7
- Coding
- c.1663+112C>T
- MANE Select
- NM_003119
- dbSNP
- rs182191298
- Type
- single nucleotide variant
- Location
- chr16:89548225 (GRCh38)
- Gene constraint
- LOEUF 1.547 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.10 · 2 PDB
Similar variants
- SPG7 c.1324+2T>G Pathogenic/Likely pathogenic ★★ same type
- SPG7 c.1552+1G>T Pathogenic/Likely pathogenic ★★ same type
- SPG7 c.1553-2A>G Pathogenic/Likely pathogenic ★★ same type
- SPG7 c.1779+1G>T Pathogenic/Likely pathogenic ★★ same type
- SPG7 c.1936+2T>A Likely pathogenic ★★ same type
- SPG7 c.1937-2A>G Pathogenic ★★ same type
- SPG7 c.2104-2A>G Pathogenic/Likely pathogenic ★★ same type
- SPG7 c.286+1G>T Likely pathogenic ★★ 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/spg7-c-1663-plus-112c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown