rs1064793210
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Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The ENST00000265433.8(NBN):βc.11delβ(p.Leu4ArgfsTer16) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000372 in 1,613,064 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (β β ). Synonymous variant affecting the same amino acid position (i.e. L4L) has been classified as Likely benign.
Frequency
Genomes: π 0.0000066 ( 0 hom., cov: 33)
Exomes π: 0.0000034 ( 0 hom. )
Consequence
NBN
ENST00000265433.8 frameshift
ENST00000265433.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.30
Genes affected
NBN (HGNC:7652): (nibrin) Mutations in this gene are associated with Nijmegen breakage syndrome, an autosomal recessive chromosomal instability syndrome characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. The encoded protein is a member of the MRE11/RAD50 double-strand break repair complex which consists of 5 proteins. This gene product is thought to be involved in DNA double-strand break repair and DNA damage-induced checkpoint activation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 254 pathogenic variants in the truncated region.
PP5
Variant 8-89984550-CA-C is Pathogenic according to our data. Variant chr8-89984550-CA-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 418370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NBN | NM_002485.5 | c.11del | p.Leu4ArgfsTer16 | frameshift_variant | 1/16 | ENST00000265433.8 | NP_002476.2 | |
NBN | XM_011517046.2 | c.11del | p.Leu4ArgfsTer16 | frameshift_variant | 1/11 | XP_011515348.1 | ||
NBN | XM_047421796.1 | c.11del | p.Leu4ArgfsTer16 | frameshift_variant | 1/10 | XP_047277752.1 | ||
NBN | NM_001024688.3 | c.-286del | 5_prime_UTR_variant | 1/17 | NP_001019859.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NBN | ENST00000265433.8 | c.11del | p.Leu4ArgfsTer16 | frameshift_variant | 1/16 | 1 | NM_002485.5 | ENSP00000265433 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460820Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726738
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Microcephaly, normal intelligence and immunodeficiency Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Oct 27, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 02, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 418370). This premature translational stop signal has been observed in individual(s) with endometrial cancer and a family history of breast cancer (PMID: 27443514). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu4Argfs*16) in the NBN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NBN are known to be pathogenic (PMID: 9590180, 16415040). - |
Pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Aplastic anemia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 06, 2023 | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2023 | 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; Not observed at significant frequency in large population cohorts (gnomAD); Observed in a patient with endometrial cancer (Ring et al., 2016); This variant is associated with the following publications: (PMID: 32427313, 27443514) - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.11delT pathogenic mutation, located in coding exon 1 of the NBN gene, results from a deletion of one nucleotide at nucleotide position 11, causing a translational frameshift with a predicted alternate stop codon (p.L4Rfs*16). This alteration has been previously detected in a cohort of 381 unselected endometrial cancer patients who underwent multi-gene panel testing (Ring KL et al. Mod Pathol, 2016 11;29:1381-1389). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at