3-50347546-AC-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_006545.5(NPRL2):c.*59del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0404 in 1,596,450 control chromosomes in the GnomAD database, including 12,239 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.087 ( 1898 hom., cov: 31)
Exomes 𝑓: 0.036 ( 10341 hom. )
Consequence
NPRL2
NM_006545.5 3_prime_UTR
NM_006545.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.150
Genes affected
NPRL2 (HGNC:24969): (NPR2 like, GATOR1 complex subunit) Enables protein kinase activity. Contributes to GTPase activator activity. Involved in cellular response to amino acid starvation; negative regulation of TOR signaling; and negative regulation of kinase activity. Located in lysosomal membrane. Part of GATOR1 complex. Implicated in focal epilepsy. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 3-50347546-AC-A is Benign according to our data. Variant chr3-50347546-AC-A is described in ClinVar as [Benign]. Clinvar id is 1249338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPRL2 | NM_006545.5 | c.*59del | 3_prime_UTR_variant | 11/11 | ENST00000232501.8 | ||
NPRL2 | XM_011533288.4 | c.*59del | 3_prime_UTR_variant | 10/10 | |||
NPRL2 | XM_017005556.3 | c.*59del | 3_prime_UTR_variant | 9/9 | |||
NPRL2 | XM_047447310.1 | c.*59del | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPRL2 | ENST00000232501.8 | c.*59del | 3_prime_UTR_variant | 11/11 | 1 | NM_006545.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0872 AC: 13238AN: 151852Hom.: 1897 Cov.: 31
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GnomAD4 exome AF: 0.0355 AC: 51304AN: 1444480Hom.: 10341 Cov.: 28 AF XY: 0.0322 AC XY: 23192AN XY: 719758
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GnomAD4 genome AF: 0.0873 AC: 13263AN: 151970Hom.: 1898 Cov.: 31 AF XY: 0.0936 AC XY: 6953AN XY: 74262
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 31, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 45% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 42. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at