rs17628

Variant names:

• chr19-39435869-A-C
• rs17628
• NM_001020.6:c.27T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001020.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS16	NM_001020.6	MANE Select	c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 5	NP_001011.1
	RPS16	NM_001363860.2		c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 4	NP_001350789.1
	RPS16	NM_001321111.2		c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 5	NP_001308040.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS16	ENST00000251453.8	TSL:1 MANE Select	c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 5	ENSP00000251453.2
	RPS16	ENST00000339471.8	TSL:1	c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 4	ENSP00000367806.2
	RPS16	ENST00000601655.5	TSL:1	c.27T>G	p.Ser9Ser	synonymous	Exon 1 of 5	ENSP00000472231.1

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

GnomAD2 exomes AF: 0.391 AC: 96413 AN: 246842 AF XY: 0.386

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 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

African (AFR) AF: 0.660 AC: 22100 AN: 33462

American (AMR) AF: 0.340 AC: 15195 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 10319 AN: 26132

East Asian (EAS) AF: 0.507 AC: 20129 AN: 39692

South Asian (SAS) AF: 0.385 AC: 33183 AN: 86238

European-Finnish (FIN) AF: 0.389 AC: 18665 AN: 47950

Middle Eastern (MID) AF: 0.420 AC: 2424 AN: 5768

European-Non Finnish (NFE) AF: 0.344 AC: 382389 AN: 1111388

Other (OTH) AF: 0.390 AC: 23523 AN: 60322

GnomAD4 genome AF: 0.445 AC: 67644 AN: 152044 Hom.: 16482 Cov.: 33 AF XY: 0.445 AC XY: 33065 AN XY: 74314

African (AFR) AF: 0.649 AC: 26922 AN: 41466

American (AMR) AF: 0.370 AC: 5655 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1323 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2670 AN: 5160

South Asian (SAS) AF: 0.400 AC: 1931 AN: 4826

European-Finnish (FIN) AF: 0.402 AC: 4249 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23556 AN: 67962

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.387 Hom.: 25574

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		-0.38
PromoterAI		0.0072	Neutral
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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