ERBB2 c.2085+7del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00754%, nfe)
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 1.3 | GERP -4.3, phastCons 0.7 |
| Non-coding constraint | Z 6.15 | 1 kb window · o/e 0.60 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00754%
European (non-Finnish) · 89/1,180,012 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00616%
90/1,461,806 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00754% | 13,259 |
| South Asian | 0.0011% | 91,086 |
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
- ERBB2
- Coding
- c.2085+7del
- MANE Select
- NM_004448
- Type
- Deletion
- Location
- chr17:39723464 (GRCh38)
- Gene constraint
- LOEUF 0.518 · pLI 0.06 (gnomAD)
- Structure
- AlphaFold pLDDT 74.65 · 63 PDB
Similar variants
- ERBB2 p.Met774fs Likely pathogenic ★ same type
- ERBB2 c.2726del Uncertain significance ★ same type
- ERBB2 p.Gln1225_Asp1226del Conflicting classifications of pathogenicity ★ same type
- ERBB2 p.Pro128fs Uncertain significance ★ same type
- ERBB2 p.Thr718fs Uncertain significance ★ same type
- ERBB2 c.1021+9del Likely benign ★ same type
- ERBB2 c.1314-16del Likely benign ★ same type
- ERBB2 c.1738-3del 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/erbb2-c-2085-plus-7del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown