Is BLM c.4080delG pathogenic?

BLM c.4080delG is classified Uncertain significance in BLM (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-15). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with BLM c.4080delG?

BLM c.4080delG is associated with hereditary neoplastic syndrome (ClinVar).

How common is BLM c.4080delG in the general population?

BLM c.4080delG is no gnomAD frequency available for this variant (gnomAD).

BLM c.4080delG

rs2151202230 · VCV1737632

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 7.6	GERP 2.6, phastCons 1
Non-coding constraint	Z 4.58	1 kb window · o/e 0.69 · regional · uncalibrated

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BLM
Coding: c.4080delG
MANE Select: NM_000057
dbSNP: rs2151202230
Type: Deletion
Location: chr15:90815101 (GRCh38)
Gene constraint: LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.10 · 16 PDB

Full BLM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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BLM c.99-8_112del Pathogenic/Likely pathogenic ★★ same condition
BLM p.Arg545fs Pathogenic/Likely pathogenic ★★ same condition
BLM p.Arg836fs Pathogenic ★★ same condition
BLM p.Asn448fs Pathogenic ★★ same condition
BLM p.Asp1010fs Pathogenic/Likely pathogenic ★★ same condition
BLM p.Asp159_Phe160insTer 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-c-4080delg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown