Variant 8-56073068-TC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The ENST00000009589.8(RPS20):c.*21del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,587,442 control chromosomes in the GnomAD database, including 128 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0090 ( 8 hom., cov: 32)

Exomes 𝑓: 0.013 ( 120 hom. )

Consequence

RPS20
ENST00000009589.8 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.25

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-56073068-TC-T is Benign according to our data. Variant chr8-56073068-TC-T is described in ClinVar as [Benign]. Clinvar id is 1802762.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0127 (18281/1435104) while in subpopulation MID AF= 0.0195 (80/4104). AF 95% confidence interval is 0.0161. There are 120 homozygotes in gnomad4_exome. There are 8913 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1378 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS20	NM_001023.4 linkuse as main transcript	c.*21del		3_prime_UTR_variant	4/4	ENST00000009589.8	NP_001014.1
RPS20	NM_001146227.3 linkuse as main transcript	c.333+48del		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.*21del		3_prime_UTR_variant	4/4	1	NM_001023.4	ENSP00000009589	P1	P60866-1

Frequencies

GnomAD3 genomes

AF:

0.00907

AC:

1381

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00759

Gnomad ASJ

AF:

0.00577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00684

Gnomad FIN

AF:

0.0133

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0138

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0107

AC:

2478

AN:

231954

Hom.:

AF XY:

0.0108

AC XY:

1366

AN XY:

127062

show subpopulations

Gnomad AFR exome

AF:

0.00246

Gnomad AMR exome

AF:

0.00899

Gnomad ASJ exome

AF:

0.00427

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00882

Gnomad FIN exome

AF:

0.0133

Gnomad NFE exome

AF:

0.0145

Gnomad OTH exome

AF:

0.0168

GnomAD4 exome

AF:

0.0127

AC:

18281

AN:

1435104

Hom.:

120

Cov.:

AF XY:

0.0125

AC XY:

8913

AN XY:

713070

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00886

Gnomad4 ASJ exome

AF:

0.00526

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00856

Gnomad4 FIN exome

AF:

0.0141

Gnomad4 NFE exome

AF:

0.0141

Gnomad4 OTH exome

AF:

0.0124

GnomAD4 genome

AF:

0.00905

AC:

1378

AN:

152338

Hom.:

Cov.:

AF XY:

0.00875

AC XY:

652

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00216

Gnomad4 AMR

AF:

0.00758

Gnomad4 ASJ

AF:

0.00577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00705

Gnomad4 FIN

AF:

0.0133

Gnomad4 NFE

AF:

0.0138

Gnomad4 OTH

AF:

0.0114

Alfa

AF:

0.00555

Hom.:

Bravo

AF:

0.00870

Asia WGS

AF:

0.00404

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Aug 15, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over