rs367543043
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000057.4(BLM):βc.1544delβ(p.Asn515MetfsTer16) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000933 in 1,608,492 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (β β ). Synonymous variant affecting the same amino acid position (i.e. G512G) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000057.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLM | NM_000057.4 | c.1544del | p.Asn515MetfsTer16 | frameshift_variant | 7/22 | ENST00000355112.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLM | ENST00000355112.8 | c.1544del | p.Asn515MetfsTer16 | frameshift_variant | 7/22 | 1 | NM_000057.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 150032Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1458460Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725626
GnomAD4 genome AF: 0.00000667 AC: 1AN: 150032Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73124
ClinVar
Submissions by phenotype
Bloom syndrome Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Oct 30, 2017 | Variant summary: The BLM c.1544delA (p.Asn515MetfsX16) variant results in a premature termination codon, predicted to cause a truncated or absent BLM 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 (e.g. c.2824-1077_3019+310del1583, p.V942fs; c.2207_2212del6insTAGATTC, p.Tyr736fsX5; c.772_773delCT, p.Leu258fsX7). One in silico tool predicts a damaging outcome for this variant.This variant is absent in 245606 control chromosomes (gnomAD). A different variant (BLM c.1544_1545dupA) leading to the same protein change, p.Asn515MetfsX16, was reported in multiple Bloom Syndrome patients (German_2007). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 30, 2024 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 29, 2023 | This sequence change creates a premature translational stop signal (p.Asn515Metfs*16) 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). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with congenital anomalies (PMID: 27959697). ClinVar contains an entry for this variant (Variation ID: 374315). For these reasons, this variant has been classified as Pathogenic. - |
BLM-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2023 | The BLM c.1544delA variant is predicted to result in a frameshift and premature protein termination (p.Asn515Metfs*16). This variant was reported in compound heterozygous state in an individual with Bloom syndrome (Deng M et al 2021. PubMed ID: 34177791). Of note, another truncating variant affecting the same amino acid (reported as c.1544_1545dupA, p.Asn515fs) has also been reported to be pathogenic for Bloom syndrome (German J et al 2007. PubMed ID: 17407155). This variant is reported in 0.017% of alleles in individuals of African descent in gnomAD and it is classified as pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/374315/). Frameshift variants in BLM are expected to be pathogenic. This variant is interpreted as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.1544delA pathogenic mutation, located in coding exon 6 of the BLM gene, results from a deletion of one nucleotide at nucleotide position 1544, causing a translational frameshift with a predicted alternate stop codon (p.N515Mfs*16). This alteration has been detected in trans with a pathogenic BLM variant in an individual with Bloom syndrome (Deng M et al. Front Endocrinol (Lausanne), 2021 Jun;12:524242). 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at