BLM p.Arg899=
c.2695C>A · rs587779884 · VCV1794842
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-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 | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.34 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.45 | GERP -4, phastCons 0.99 |
| Overall | ||
| CADD | 6.513 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,980 alleles
Overall
6.84e-05%
1/1,461,816 alleles · very rare
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.Arg899=
- Coding
- c.2695C>A
- MANE Select
- NM_000057
- dbSNP
- rs587779884
- Type
- single nucleotide variant
- Location
- chr15:90784953 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.10 · 16 PDB
- Residue 899
- the '3' overhang dna-binding' region; an α-helix; the helicase c-terminal domain
Similar variants
- BLM p.Arg899Ter Pathogenic ★★ same residue
- BLM p.Arg899Gln Uncertain significance ★★ ⚠ same residue
- BLM p.Arg899Gly Uncertain significance ★★ ⚠ same residue
- BLM c.1087+1G>A Likely pathogenic ★★ same condition
- BLM c.1088-1G>A Likely pathogenic ★★ same condition
- BLM c.1220+2T>C Likely pathogenic ★★ same condition
- BLM c.1220+2T>G Likely pathogenic ★★ same condition
- BLM c.1882+2T>C 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-arg899 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown