rs17628

Positions:

• chr19-39435869-A-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001020.6(RPS16):​c.27T>G​(p.Ser9Ser) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

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 (HGNC:):

ACMG classification

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	Protein	UniProt
RPS16	NM_001020.6	c.27T>G	p.Ser9Ser	synonymous_variant	1/5	ENST00000251453.8	NP_001011.1
RPS16	NM_001363860.2	c.27T>G	p.Ser9Ser	synonymous_variant	1/4		NP_001350789.1
RPS16	NM_001321111.2	c.27T>G	p.Ser9Ser	synonymous_variant	1/5		NP_001308040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS16	ENST00000251453.8	c.27T>G	p.Ser9Ser	synonymous_variant	1/5	1	NM_001020.6	ENSP00000251453.2

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67569 AN: 151928 Hom.: 16451 Cov.: 33

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

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.: 41 AF XY: 0.364 AC XY: 263609 AN XY: 724570

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.: 33 AF XY: 0.445 AC XY: 33065 AN XY: 74314

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

Other links and lift over

dbSNP: rs17628; hg19: chr19-39926509; COSMIC: COSV52238647; COSMIC: COSV52238647;