Variant rs17628 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001020.6(RPS16):c.27T>G(p.Ser9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,607,704 control chromosomes in the GnomAD database, including 115,015 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.

Frequency

Genomes: 𝑓 0.44 ( 16482 hom., cov: 33)

Exomes 𝑓: 0.36 ( 98533 hom. )

Consequence

RPS16
NM_001020.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.377

Variant links:

Genes affected

RPS16 (HGNC:10396): (ribosomal protein S16) 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 S9P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

RPS16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-0.377 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RPS16	NM_001020.6 linkuse as main transcript	c.27T>G	p.Ser9=	synonymous_variant	1/5	ENST00000251453.8
RPS16	NM_001363860.2 linkuse as main transcript	c.27T>G	p.Ser9=	synonymous_variant	1/4
RPS16	NM_001321111.2 linkuse as main transcript	c.27T>G	p.Ser9=	synonymous_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS16	ENST00000251453.8 linkuse as main transcript	c.27T>G	p.Ser9=	synonymous_variant	1/5	1	NM_001020.6	P1

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67569

AN:

151928

Hom.:

16451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.446

GnomAD3 exomes

AF:

0.391

AC:

96413

AN:

246842

Hom.:

19925

AF XY:

0.386

AC XY:

51752

AN XY:

133918

show subpopulations

Gnomad AFR exome

AF:

0.656

Gnomad AMR exome

AF:

0.334

Gnomad ASJ exome

AF:

0.399

Gnomad EAS exome

AF:

0.535

Gnomad SAS exome

AF:

0.389

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.346

Gnomad OTH exome

AF:

0.379

GnomAD4 exome

AF:

0.363

AC:

527927

AN:

1455660

Hom.:

98533

Cov.:

AF XY:

0.364

AC XY:

263609

AN XY:

724570

show subpopulations

Gnomad4 AFR exome

AF:

0.660

Gnomad4 AMR exome

AF:

0.340

Gnomad4 ASJ exome

AF:

0.395

Gnomad4 EAS exome

AF:

0.507

Gnomad4 SAS exome

AF:

0.385

Gnomad4 FIN exome

AF:

0.389

Gnomad4 NFE exome

AF:

0.344

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.445

AC:

67644

AN:

152044

Hom.:

16482

Cov.:

AF XY:

0.445

AC XY:

33065

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.649

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.517

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.402

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.370

Hom.:

13844

Bravo

AF:

0.449

Asia WGS

AF:

0.519

AC:

1807

AN:

3478

EpiCase

AF:

0.352

EpiControl

AF:

0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.1

DANN

Benign

0.75

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over