Variant chr2-202287632-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015934.5(NOP58):c.435-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 1,564,552 control chromosomes in the GnomAD database, including 60,469 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.34 ( 10063 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50406 hom. )

Consequence

NOP58
NM_015934.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.359

Variant links:

Genes affected

NOP58 (HGNC:29926): (NOP58 ribonucleoprotein) The protein encoded by this gene is a core component of box C/D small nucleolar ribonucleoproteins. Some box C/D small nucleolar RNAs (snoRNAs), such as U3, U8, and U14, are dependent upon the encoded protein for their synthesis. This protein is SUMOylated, which is necessary for high affinity binding to snoRNAs. [provided by RefSeq, Nov 2015]

NOP58 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 0 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOP58	NM_015934.5 linkuse as main transcript	c.435-28G>A		intron_variant		ENST00000264279.10	NP_057018.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
NOP58	ENST00000264279.10 linkuse as main transcript	c.435-28G>A	intron_variant	1	NM_015934.5	ENSP00000264279	P1
NOP58	ENST00000433543.2 linkuse as main transcript	c.45-28G>A	intron_variant, NMD_transcript_variant	3		ENSP00000388126
NOP58	ENST00000478941.1 linkuse as main transcript	n.459-2691G>A	intron_variant, non_coding_transcript_variant	3
NOP58	ENST00000492688.5 linkuse as main transcript	n.341-28G>A	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51049

AN:

151762

Hom.:

10045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.305

GnomAD3 exomes

AF:

0.280

AC:

70081

AN:

250234

Hom.:

11036

AF XY:

0.276

AC XY:

37357

AN XY:

135256

show subpopulations

Gnomad AFR exome

AF:

0.556

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.130

Gnomad SAS exome

AF:

0.358

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.239

GnomAD4 exome

AF:

0.258

AC:

363933

AN:

1412672

Hom.:

50406

Cov.:

AF XY:

0.259

AC XY:

182531

AN XY:

705750

show subpopulations

Gnomad4 AFR exome

AF:

0.552

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.0897

Gnomad4 SAS exome

AF:

0.356

Gnomad4 FIN exome

AF:

0.298

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.337

AC:

51112

AN:

151880

Hom.:

10063

Cov.:

AF XY:

0.336

AC XY:

24963

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.547

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.350

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.247

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.241

Hom.:

4880

Bravo

AF:

0.345

Asia WGS

AF:

0.287

AC:

997

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.75

BranchPoint Hunter

0.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over