15-90769536-CAG-C
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000057.4(BLM):c.2506_2507delAG(p.Arg836fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
BLM
NM_000057.4 frameshift
NM_000057.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.68
Genes affected
BLM (HGNC:1058): (BLM RecQ like helicase) The Bloom syndrome is an autosomal recessive disorder characterized by growth deficiency, microcephaly and immunodeficiency among others. It is caused by homozygous or compound heterozygous mutation in the gene encoding DNA helicase RecQ protein on chromosome 15q26. This Bloom-associated helicase unwinds a variety of DNA substrates including Holliday junction, and is involved in several pathways contributing to the maintenance of genome stability. Identification of pathogenic Bloom variants is required for heterozygote testing in at-risk families. [provided by RefSeq, May 2020]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-90769536-CAG-C is Pathogenic according to our data. Variant chr15-90769536-CAG-C is described in ClinVar as [Pathogenic]. Clinvar id is 42071.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251380Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135884
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GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461798Hom.: 0 AF XY: 0.0000110 AC XY: 8AN XY: 727202
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GnomAD4 genome 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:11
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Bloom syndrome Pathogenic:6
| Pathogenic, no assertion criteria provided | clinical testing | Greehey Children's Cancer Research Institute, UT Health San Antonio | Aug 01, 2020 | The proband, a Hispanic male child from the US-Mexico border, had features of Bloom syndrome including short stature, failure to thrive, microcephaly, a long thin face with coarse facial features, little subcutaneous fat, and multi-pigmented skin lesions. At age 3 the proband developed rhabdomyosarcoma, a tumor type not previously observed in Bloom syndrome. He was found to be homozygous for BLM c.2506_2507delAG variant, a variant previously described in two other individuals, one Mexican and one from New Mexico. Using flanking markers a common homozygous haplotype was revealed in our patient as well as his two affected siblings, suggesting that this variant is a previously unrecognized founder mutation in the Mexican population. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 05, 2021 | Variant summary: BLM c.2506_2507delAG (p.Arg836GlyfsX18) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 7.6e-05 in 251380 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in BLM causing Bloom Syndrome (7.6e-05 vs 0.0035), allowing no conclusion about variant significance. c.2506_2507delAG has been reported in the literature in homozygous and compound heterozygous individuals affected with Bloom Syndrome (e.g. German_2007). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 25, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Aug 29, 2016 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2025 | This sequence change creates a premature translational stop signal (p.Arg836Glyfs*18) in the BLM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BLM are known to be pathogenic (PMID: 17407155). This variant is present in population databases (rs367543024, gnomAD 0.06%). This premature translational stop signal has been observed in individual(s) with Bloom syndrome (PMID: 17407155). ClinVar contains an entry for this variant (Variation ID: 42071). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Mar 16, 2017 | - - |
not provided Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Oct 11, 2022 | This frameshift variant alters the translational reading frame of the BLM mRNA and causes the premature termination of BLM protein synthesis. In the published literature, the variant has been reported in individuals affected with advanced cancers (PMID: 29625052 (2018)) and Bloom syndrome with a second pathogenic variant (PMID: 17407155 (2007)). One family study showed the variant segregated with disease (PMID: 33832920 (2021)). Based on the available information, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 03, 2024 | Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 35969835, 36087940, 36451132, 29625052, 33832920, 17407155, 34308104, 26247052, 37594403) - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2024 | The c.2506_2507delAG pathogenic mutation, located in coding exon 11 of the BLM gene, results from a deletion of two nucleotides at nucleotide positions 2506 to 2507, causing a translational frameshift with a predicted alternate stop codon (p.R836Gfs*18). This mutation has been reported in the homozygous and compound heterozygous state in patients with Bloom syndrome (German J et al. Hum. Mutat., 2007 Aug;28:743-53). This alteration has also been reported in one individual with cervical squamous cell carcinoma and another individual with liposarcoma (Huang KL et al. Cell, 2018 04;173:355-370.e14). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
| Pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Dec 14, 2021 | - - |
BLM-related disorder Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 29, 2023 | The BLM c.2506_2507delAG variant is predicted to result in a frameshift and premature protein termination (p.Arg836Glyfs*18). This variant was reported in the homozygous or compound heterozygous state in individuals with Bloom syndrome (German et al. 2007. PubMed ID: 17407155; Sybouts et al. 2021. PubMed ID: 33832920). This variant is reported in 0.055% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in BLM are expected to be pathogenic. This variant is interpreted as pathogenic. - |
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