TMPO c.990+86del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 14.6%, eas) — 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 +86 | deep intronic (+86 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.57 | GERP -0.97 |
| Overall | ||
| CADD | 0.954 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (T)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
14.6%
East Asian · 4,207/28,834 alleles
Filtering AF
14.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.1%
Overall
6.98%
44,437/636,466 alleles · common
exomes 40,737/518,310 · genomes 3,700/118,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 14.6% | 7 |
| African / African-American | 10.9% | 9 |
| Remaining individualsnot grpmax-eligible | 7.92% | 13 |
| Middle Eastern | 7.73% | 13 |
| South Asian | 6.62% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 6.59% | 15 |
| Admixed American | 6.2% | 16 |
| European (non-Finnish) | 6.14% | 16 |
| Finnishnot grpmax-eligible | 5.9% | 17 |
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
- TMPO
- Coding
- c.990+86del
- MANE Select
- NM_001032283
- dbSNP
- rs79128220
- Type
- Deletion
- Location
- chr12:98545130 (GRCh38)
- Gene constraint
- LOEUF 0.736 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.49 · 14 PDB
Similar variants
- TMPO c.565+1536_565+1543del Uncertain significance ★★ same type
- TMPO c.565+1928del Uncertain significance ★★ same type
- TMPO c.565+1983del Uncertain significance ★★ same type
- TMPO c.565+2304del Uncertain significance ★★ same type
- TMPO c.565+1272del Uncertain significance ★ same type
- TMPO c.565+1350_565+1352del Uncertain significance ★ same type
- TMPO c.565+1508_565+1509del Uncertain significance ★ same type
- TMPO c.565+1812_565+1814del 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/tmpo-c-990-plus-86del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown