NM_015710.5:c.309C>G

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.101
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NOP53NM_015710.5 linkc.309C>G p.Thr103Thr synonymous_variant Exon 3 of 13 ENST00000246802.10 NP_056525.2 Q9NZM5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NOP53ENST00000246802.10 linkc.309C>G p.Thr103Thr synonymous_variant Exon 3 of 13 1 NM_015710.5 ENSP00000246802.4 Q9NZM5

Frequencies

GnomAD3 genomes
AF:
0.0181
AC:
2746
AN:
152104
Hom.:
87
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0625
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00766
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00499
AC:
1254
AN:
251422
Hom.:
36
AF XY:
0.00375
AC XY:
509
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.0643
Gnomad AMR exome
AF:
0.00405
Gnomad ASJ exome
AF:
0.0000993
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00118
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000141
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00183
AC:
2674
AN:
1458940
Hom.:
80
Cov.:
28
AF XY:
0.00168
AC XY:
1220
AN XY:
725984
show subpopulations
Gnomad4 AFR exome
AF:
0.0612
Gnomad4 AMR exome
AF:
0.00443
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00109
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000577
Gnomad4 OTH exome
AF:
0.00450
GnomAD4 genome
AF:
0.0181
AC:
2752
AN:
152222
Hom.:
87
Cov.:
32
AF XY:
0.0169
AC XY:
1256
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0624
Gnomad4 AMR
AF:
0.00765
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.00529
Hom.:
6
Bravo
AF:
0.0205
Asia WGS
AF:
0.0170
AC:
59
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
8.5
DANN
Benign
0.61
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs79458115; hg19: chr19-48253454; API