Variant 19-49498026-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001015.5(RPS11):c.333A>T(p.Val111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,612,732 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 21 hom. )

Consequence

RPS11
NM_001015.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.824

Variant links:

Genes affected

RPS11 (HGNC:10384): (ribosomal protein S11) 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 member of the S17P family of ribosomal proteins that is a component of the 40S subunit. This gene is co-transcribed with the small nucleolar RNA gene U35B, which is located in the third intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed throughout the genome. [provided by RefSeq, Jul 2012]

RPS11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00798586).

BP6

Variant 19-49498026-A-T is Benign according to our data. Variant chr19-49498026-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650249.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 180 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS11	NM_001015.5 linkuse as main transcript	c.333A>T	p.Val111=	synonymous_variant	4/5	ENST00000270625.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS11	ENST00000270625.7 linkuse as main transcript	c.333A>T	p.Val111=	synonymous_variant	4/5	1	NM_001015.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00119

AC:

181

AN:

152058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000787

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00828

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00160

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00219

AC:

550

AN:

251376

Hom.:

AF XY:

0.00272

AC XY:

370

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.000549

Gnomad ASJ exome

AF:

0.00308

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0101

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.00153

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.00175

AC:

2557

AN:

1460556

Hom.:

Cov.:

AF XY:

0.00207

AC XY:

1503

AN XY:

726598

show subpopulations

Gnomad4 AFR exome

AF:

0.000209

Gnomad4 AMR exome

AF:

0.000693

Gnomad4 ASJ exome

AF:

0.00230

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.000131

Gnomad4 NFE exome

AF:

0.00129

Gnomad4 OTH exome

AF:

0.00197

GnomAD4 genome

AF:

0.00118

AC:

180

AN:

152176

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.000145

Gnomad4 AMR

AF:

0.000786

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00808

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00160

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00122

Hom.:

Bravo

AF:

0.000956

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.00241

AC:

292

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.00142

EpiControl

AF:

0.00261

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

RPS11: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.56

CADD

Benign

5.8

DANN

Benign

0.85

DEOGEN2

Benign

0.030

FATHMM_MKL

Benign

0.73

LIST_S2

Benign

0.20

MetaRNN

Benign

0.0080

MutationTaster

Benign

1.0

Sift4G

Benign

0.19

Vest4

0.20

MVP

0.65

GERP RS

-1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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