HTT c.608+7del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0976%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.54 | GERP -0.45 |
| Non-coding constraint | Z 0.77 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 0.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0976%
African / African-American · 73/74,782 alleles
Filtering AF
0.0796%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0729%
Overall
0.00537%
86/1,601,326 alleles · ultra-rare
exomes 34/1,449,018 · genomes 52/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0976% | 1,024 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,524 |
| Admixed American | 0.005% | 20,002 |
| European (non-Finnish) | 0.000514% | 194,710 |
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
- HTT
- Coding
- c.608+7del
- MANE Select
- NM_001388492
- dbSNP
- rs773551460
- Type
- Deletion
- Location
- chr4:3105442 (GRCh38)
- Structure
- AlphaFold pLDDT 85.38 · 30 PDB
Similar variants
- HTT c.5369-9del Likely benign ★★ same type
- HTT p.Gln33fs Likely pathogenic ★ same type
- HTT p.Gly697fs Pathogenic ★ same type
- HTT p.Ser1941fs Pathogenic ★ same type
- HTT c.2099-21_2099-13del Uncertain significance ★ same type
- HTT c.747+4del Uncertain significance ★ same type
- HTT c.7766-13_7766-8del Uncertain significance ★ same type
- SLC6A4 c.*2091del 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/htt-c-608-plus-7del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown