POMP c.*5del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00772%, nfe)
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 1.1 | GERP -0.57, phastCons 0.004 |
| Non-coding constraint | Z 0.24 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 3.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00772%
European (non-Finnish) · 91/1,178,894 alleles
Filtering AF
0.0064%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00593%
Overall
0.00595%
96/1,612,788 alleles · very rare
exomes 94/1,460,566 · genomes 2/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00772% | 12,955 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,607 |
| African / African-American | 0.00134% | 74,900 |
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
- POMP
- Coding
- c.*5del
- MANE Select
- NM_015932
- Type
- Deletion
- Location
- chr13:28678107 (GRCh38)
- Gene constraint
- LOEUF 1.191 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 81.76 · 11 PDB
Similar variants
- POMP p.Ile112fs Pathogenic ★★ same type
- POMP c.163-5del Uncertain significance ★ same type
- POMP p.Glu9_Lys11del Uncertain significance ★ same type
- POMP p.Pro15fs Uncertain significance ★ same type
- POMP c.102-10_102-9del Likely benign ★ same type
- POMP c.163-16del Likely benign ★ same type
- POMP c.359-8_359-5del Likely benign ★ same type
- POMP c.4-14del 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/pomp-c-star-5del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown