Variant chr8-56073858-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001023.4(RPS20):c.104-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,271,834 control chromosomes in the GnomAD database, including 25,884 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2448 hom., cov: 32)

Exomes 𝑓: 0.19 ( 23436 hom. )

Consequence

RPS20
NM_001023.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

RPS20 (HGNC:10405): (ribosomal protein S20) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10P family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the small nucleolar RNA gene U54, which is located in its second intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Two transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Apr 2009]

RPS20 links:

SNORD54 (HGNC:10204): (small nucleolar RNA, C/D box 54)

SNORD54 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 8-56073858-A-G is Benign according to our data. Variant chr8-56073858-A-G is described in ClinVar as [Benign]. Clinvar id is 1259849.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
RPS20	NM_001023.4 linkuse as main transcript	c.104-90T>C	intron_variant		ENST00000009589.8	NP_001014.1
SNORD54	NR_002437.1 linkuse as main transcript	n.44T>C	non_coding_transcript_exon_variant	1/1
RPS20	NM_001146227.3 linkuse as main transcript	c.104-90T>C	intron_variant			NP_001139699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS20	ENST00000009589.8 linkuse as main transcript	c.104-90T>C		intron_variant		1	NM_001023.4	ENSP00000009589	P1	P60866-1
SNORD54	ENST00000459159.1 linkuse as main transcript	n.44T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23640

AN:

152080

Hom.:

2448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0433

Gnomad AMI

AF:

0.422

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0823

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.187

GnomAD3 exomes

AF:

0.165

AC:

41028

AN:

248794

Hom.:

4275

AF XY:

0.169

AC XY:

22785

AN XY:

135100

show subpopulations

Gnomad AFR exome

AF:

0.0402

Gnomad AMR exome

AF:

0.122

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.000327

Gnomad SAS exome

AF:

0.0850

Gnomad FIN exome

AF:

0.166

Gnomad NFE exome

AF:

0.228

Gnomad OTH exome

AF:

0.212

GnomAD4 exome

AF:

0.194

AC:

216955

AN:

1119636

Hom.:

23436

Cov.:

AF XY:

0.193

AC XY:

110419

AN XY:

573028

show subpopulations

Gnomad4 AFR exome

AF:

0.0416

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.000341

Gnomad4 SAS exome

AF:

0.0872

Gnomad4 FIN exome

AF:

0.166

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.194

GnomAD4 genome

AF:

0.155

AC:

23638

AN:

152198

Hom.:

2448

Cov.:

AF XY:

0.150

AC XY:

11142

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0433

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.312

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0824

Gnomad4 FIN

AF:

0.161

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.172

Hom.:

919

Bravo

AF:

0.155

Asia WGS

AF:

0.0400

AC:

141

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.7

DANN

Benign

0.76

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over