Variant 19-1438866-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The ENST00000592588.7(RPS15):c.63C>T(p.Asp21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 1,590,574 control chromosomes in the GnomAD database, including 2,450 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 258 hom., cov: 32)

Exomes 𝑓: 0.052 ( 2192 hom. )

Consequence

RPS15
ENST00000592588.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.251

Variant links:

Genes affected

RPS15 (HGNC:10388): (ribosomal protein S15) 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 S19P family of ribosomal proteins. It is located in the cytoplasm. This gene has been found to be activated in various tumors, such as insulinomas, esophageal cancers, and colon cancers. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

RPS15 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 19-1438866-C-T is Benign according to our data. Variant chr19-1438866-C-T is described in ClinVar as [Benign]. Clinvar id is 440243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.251 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS15	NM_001018.5 linkuse as main transcript	c.63C>T	p.Asp21=	synonymous_variant	2/4	ENST00000592588.7	NP_001009.1
RPS15	NM_001308226.2 linkuse as main transcript	c.84C>T	p.Asp28=	synonymous_variant	2/4		NP_001295155.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS15	ENST00000592588.7 linkuse as main transcript	c.63C>T	p.Asp21=	synonymous_variant	2/4	1	NM_001018.5	ENSP00000467466	P1

Frequencies

GnomAD3 genomes

AF:

0.0538

AC:

8190

AN:

152170

Hom.:

254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0483

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0428

Gnomad ASJ

AF:

0.0853

Gnomad EAS

AF:

0.0358

Gnomad SAS

AF:

0.0704

Gnomad FIN

AF:

0.0782

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0539

Gnomad OTH

AF:

0.0735

GnomAD3 exomes

AF:

0.0526

AC:

11189

AN:

212584

Hom.:

346

AF XY:

0.0551

AC XY:

6362

AN XY:

115492

show subpopulations

Gnomad AFR exome

AF:

0.0464

Gnomad AMR exome

AF:

0.0230

Gnomad ASJ exome

AF:

0.0837

Gnomad EAS exome

AF:

0.0387

Gnomad SAS exome

AF:

0.0776

Gnomad FIN exome

AF:

0.0779

Gnomad NFE exome

AF:

0.0510

Gnomad OTH exome

AF:

0.0470

GnomAD4 exome

AF:

0.0517

AC:

74306

AN:

1438288

Hom.:

2192

Cov.:

AF XY:

0.0530

AC XY:

37822

AN XY:

713588

show subpopulations

Gnomad4 AFR exome

AF:

0.0455

Gnomad4 AMR exome

AF:

0.0246

Gnomad4 ASJ exome

AF:

0.0848

Gnomad4 EAS exome

AF:

0.0287

Gnomad4 SAS exome

AF:

0.0767

Gnomad4 FIN exome

AF:

0.0752

Gnomad4 NFE exome

AF:

0.0497

Gnomad4 OTH exome

AF:

0.0539

GnomAD4 genome

AF:

0.0539

AC:

8212

AN:

152286

Hom.:

258

Cov.:

AF XY:

0.0558

AC XY:

4152

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0487

Gnomad4 AMR

AF:

0.0427

Gnomad4 ASJ

AF:

0.0853

Gnomad4 EAS

AF:

0.0357

Gnomad4 SAS

AF:

0.0694

Gnomad4 FIN

AF:

0.0782

Gnomad4 NFE

AF:

0.0539

Gnomad4 OTH

AF:

0.0761

Alfa

AF:

0.0530

Hom.:

158

Bravo

AF:

0.0495

Asia WGS

AF:

0.0820

AC:

284

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Feb 07, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over