NM_015710.5:c.309C>G
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015710.5(NOP53):c.309C>G(p.Thr103Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,611,162 control chromosomes in the GnomAD database, including 167 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 87 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 80 hom. )
Consequence
NOP53
NM_015710.5 synonymous
NM_015710.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.101
Genes affected
NOP53 (HGNC:4333): (NOP53 ribosome biogenesis factor) Enables 5S rRNA binding activity; identical protein binding activity; and p53 binding activity. Involved in several processes, including negative regulation of transcription, DNA-templated; regulation of cellular protein metabolic process; and regulation of intracellular signal transduction. Located in cytosol; fibrillar center; and nucleoplasm. Colocalizes with rDNA heterochromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 19-47750197-C-G is Benign according to our data. Variant chr19-47750197-C-G is described in ClinVar as [Benign]. Clinvar id is 788027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.101 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0604 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2746AN: 152104Hom.: 87 Cov.: 32
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GnomAD3 exomes AF: 0.00499 AC: 1254AN: 251422Hom.: 36 AF XY: 0.00375 AC XY: 509AN XY: 135906
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GnomAD4 exome AF: 0.00183 AC: 2674AN: 1458940Hom.: 80 Cov.: 28 AF XY: 0.00168 AC XY: 1220AN XY: 725984
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GnomAD4 genome AF: 0.0181 AC: 2752AN: 152222Hom.: 87 Cov.: 32 AF XY: 0.0169 AC XY: 1256AN XY: 74422
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Jan 25, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at