NM_001020.6:c.15C>T

Variant names:

• chr19-39435881-G-A
• rs17626
• NM_001020.6:c.15C>T

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.15C>T​(p.Gly5Gly) 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
• Publications: 29 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=-0.64).
• 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS16	NM_001020.6	MANE Select	c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 5	NP_001011.1	P62249
	RPS16	NM_001363860.2		c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 4	NP_001350789.1	Q6IPX4
	RPS16	NM_001321111.2		c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 5	NP_001308040.1	M0R210

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS16	ENST00000251453.8	TSL:1 MANE Select	c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 5	ENSP00000251453.2	P62249
	RPS16	ENST00000339471.8	TSL:1	c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 4	ENSP00000367806.2	Q6IPX4
	RPS16	ENST00000601655.5	TSL:1	c.15C>T	p.Gly5Gly	synonymous	Exon 1 of 5	ENSP00000472231.1	M0R210

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

GnomAD2 exomes AF: 0.391 AC: 95926 AN: 245482 AF XY: 0.386

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 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

African (AFR) AF: 0.660 AC: 22103 AN: 33468

American (AMR) AF: 0.341 AC: 15228 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 10318 AN: 26130

East Asian (EAS) AF: 0.507 AC: 20126 AN: 39684

South Asian (SAS) AF: 0.385 AC: 33191 AN: 86252

European-Finnish (FIN) AF: 0.389 AC: 18088 AN: 46498

Middle Eastern (MID) AF: 0.420 AC: 2424 AN: 5766

European-Non Finnish (NFE) AF: 0.344 AC: 382481 AN: 1111622

Other (OTH) AF: 0.390 AC: 23524 AN: 60328

GnomAD4 genome AF: 0.445 AC: 67618 AN: 152064 Hom.: 16477 Cov.: 33 AF XY: 0.445 AC XY: 33051 AN XY: 74336

African (AFR) AF: 0.649 AC: 26905 AN: 41446

American (AMR) AF: 0.370 AC: 5653 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2674 AN: 5172

South Asian (SAS) AF: 0.400 AC: 1928 AN: 4824

European-Finnish (FIN) AF: 0.402 AC: 4258 AN: 10590

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

European-Non Finnish (NFE) AF: 0.346 AC: 23542 AN: 67968

Other (OTH) AF: 0.448 AC: 946 AN: 2110

Alfa AF: 0.357 Hom.: 4686

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.9
DANN	Benign	0.93
PhyloP100		-3.9
PromoterAI		-0.024	Neutral
RBP_binding_hub_radar		0.97
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: rs17626; hg19: chr19-39926521; COSMIC: COSV52238668; COSMIC: COSV52238668;