rs17626

chr19-39435881-G-Achr19-39435881-G-Cchr19-39435881-G-T

Variant summary

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

The NM_001020.6(RPS16):c.15C>T(p.Gly5=) 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 1,606,520 control chromosomes in the GnomAD database, including 114,877 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 (16477 hom., cov: 33)
  • Exomes 𝑓: 0.36 (98400 hom.)
• Consequence: RPS16 NM_001020.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.92

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP7: Synonymous conserved (PhyloP=-3.92 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	UniProt
RPS16	NM_001020.6	c.15C>T	p.Gly5=	synonymous_variant	1/5	ENST00000251453.8
RPS16	NM_001363860.2	c.15C>T	p.Gly5=	synonymous_variant	1/4
RPS16	NM_001321111.2	c.15C>T	p.Gly5=	synonymous_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS16	ENST00000251453.8	c.15C>T	p.Gly5=	synonymous_variant	1/5	1	NM_001020.6	P1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67541 AN: 151944 Hom.: 16445 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.445

GnomAD3 exomes AF: 0.391 AC: 95926 AN: 245482 Hom.: 19811 AF XY: 0.386 AC XY: 51514 AN XY: 133286

Gnomad AFR exome AF: 0.656

Gnomad AMR exome AF: 0.335

Gnomad ASJ exome AF: 0.399

Gnomad EAS exome AF: 0.535

Gnomad SAS exome AF: 0.389

Gnomad FIN exome AF: 0.395

Gnomad NFE exome AF: 0.346

Gnomad OTH exome AF: 0.380

GnomAD4 exome AF: 0.363 AC: 527483 AN: 1454456 Hom.: 98400 Cov.: 44 AF XY: 0.364 AC XY: 263420 AN XY: 724018

Gnomad4 AFR exome AF: 0.660

Gnomad4 AMR exome AF: 0.341

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: 67618 AN: 152064 Hom.: 16477 Cov.: 33 AF XY: 0.445 AC XY: 33051 AN XY: 74336

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.448

Alfa AF: 0.344 Hom.: 3587

Bravo AF: 0.449

Asia WGS AF: 0.519 AC: 1806 AN: 3476

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	-0.64
Cadd	Benign	3.9
Dann	Benign	0.93
RBP_binding_hub_radar		0.97
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: rs17626; hg19: chr19-39926521; COSMIC: COSV52238668; COSMIC: COSV52238668;