Variant 19-54207461-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_001013.4(RPS9):c.471C>T(p.Ile157=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 1,613,614 control chromosomes in the GnomAD database, including 4,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.038 ( 261 hom., cov: 32)

Exomes 𝑓: 0.047 ( 4202 hom. )

Consequence

RPS9
NM_001013.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.328

Variant links:

Genes affected

RPS9 (HGNC:10442): (ribosomal protein S9) 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 S4P family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, multiple processed pseudogenes derived from this gene are dispersed through the genome. [provided by RefSeq, Jul 2008]

RPS9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 19-54207461-C-T is Benign according to our data. Variant chr19-54207461-C-T is described in ClinVar as [Benign]. Clinvar id is 3056073.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.328 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS9	NM_001013.4 linkuse as main transcript	c.471C>T	p.Ile157=	synonymous_variant	5/5	ENST00000302907.9	NP_001004.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS9	ENST00000302907.9 linkuse as main transcript	c.471C>T	p.Ile157=	synonymous_variant	5/5	1	NM_001013.4	ENSP00000302896	P1

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5719

AN:

152140

Hom.:

260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0191

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.00347

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0353

Gnomad OTH

AF:

0.0445

GnomAD3 exomes

AF:

0.0613

AC:

15364

AN:

250714

Hom.:

1310

AF XY:

0.0742

AC XY:

10053

AN XY:

135572

show subpopulations

Gnomad AFR exome

AF:

0.0185

Gnomad AMR exome

AF:

0.0223

Gnomad ASJ exome

AF:

0.132

Gnomad EAS exome

AF:

0.00174

Gnomad SAS exome

AF:

0.264

Gnomad FIN exome

AF:

0.00933

Gnomad NFE exome

AF:

0.0380

Gnomad OTH exome

AF:

0.0580

GnomAD4 exome

AF:

0.0470

AC:

68723

AN:

1461356

Hom.:

4202

Cov.:

AF XY:

0.0540

AC XY:

39238

AN XY:

726968

show subpopulations

Gnomad4 AFR exome

AF:

0.0198

Gnomad4 AMR exome

AF:

0.0230

Gnomad4 ASJ exome

AF:

0.135

Gnomad4 EAS exome

AF:

0.00111

Gnomad4 SAS exome

AF:

0.259

Gnomad4 FIN exome

AF:

0.0107

Gnomad4 NFE exome

AF:

0.0328

Gnomad4 OTH exome

AF:

0.0543

GnomAD4 genome

AF:

0.0376

AC:

5720

AN:

152258

Hom.:

261

Cov.:

AF XY:

0.0410

AC XY:

3052

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0190

Gnomad4 AMR

AF:

0.0353

Gnomad4 ASJ

AF:

0.144

Gnomad4 EAS

AF:

0.00367

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.0106

Gnomad4 NFE

AF:

0.0353

Gnomad4 OTH

AF:

0.0441

Alfa

AF:

0.0382

Hom.:

Bravo

AF:

0.0334

Asia WGS

AF:

0.113

AC:

393

AN:

3478

EpiCase

AF:

0.0455

EpiControl

AF:

0.0467

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

RPS9-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

6.6

DANN

Benign

0.92

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

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