BLM p.Phe619del
c.1856_1858del · rs1555419996 · VCV454088
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 8.73e-05%, nfe)
Conditions
2
hereditary neoplastic syndrome
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 | GERP -1, phastCons 0.014 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.73e-05%
European (non-Finnish) · 1/1,145,430 alleles
Overall
6.51e-05%
1/1,535,580 alleles · very rare
exomes 1/1,383,232 · genomes 0/152,348 · joint denominator
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
- BLM
- Protein
- p.Phe619del
- Coding
- c.1856_1858del
- MANE Select
- NM_000057
- dbSNP
- rs1555419996
- Type
- Deletion
- Location
- chr15:90761227 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 16 PDB
Similar variants
- BLM p.Phe619Leu Uncertain significance ★★ ⚠ same residue
- BLM p.Phe619Tyr Uncertain significance ★ ⚠ same residue
- BLM p.Phe619= Likely benign ★ same residue
- BLM c.2193+1_2193+9del Pathogenic/Likely pathogenic ★★ same condition
- BLM c.3013_3019+4del Likely pathogenic ★★ same condition
- BLM c.3210+2del Pathogenic/Likely pathogenic ★★ same condition
- BLM c.99-8_112del Pathogenic/Likely pathogenic ★★ same condition
- BLM p.Arg545fs Pathogenic/Likely pathogenic ★★ same condition
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/blm-p-phe619del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown