Variant 19-8321483-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The ENST00000449223.3(RPS28):n.326C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 1,549,990 control chromosomes in the GnomAD database, including 7,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.092 ( 701 hom., cov: 32)

Exomes 𝑓: 0.098 ( 7003 hom. )

Consequence

RPS28
ENST00000449223.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.56

Variant links:

Genes affected

RPS28 (HGNC:10418): (ribosomal protein S28) 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 S28E 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]

RPS28 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 19-8321483-C-T is Benign according to our data. Variant chr19-8321483-C-T is described in ClinVar as [Benign]. Clinvar id is 1257584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS28	NM_001031.5 linkuse as main transcript			upstream_gene_variant		ENST00000600659.3	NP_001022.1
RPS28	XM_047439201.1 linkuse as main transcript			upstream_gene_variant			XP_047295157.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
RPS28	ENST00000449223.3 linkuse as main transcript	n.326C>T	non_coding_transcript_exon_variant	1/3	2
RPS28	ENST00000600659.3 linkuse as main transcript		upstream_gene_variant		1	NM_001031.5	ENSP00000472469	P1
RPS28	ENST00000602140.1 linkuse as main transcript		upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0922

AC:

14020

AN:

152096

Hom.:

701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0873

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.0686

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.0822

Gnomad FIN

AF:

0.0861

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0946

Gnomad OTH

AF:

0.0981

GnomAD3 exomes

AF:

0.0911

AC:

14911

AN:

163744

Hom.:

804

AF XY:

0.0927

AC XY:

8159

AN XY:

87986

show subpopulations

Gnomad AFR exome

AF:

0.0893

Gnomad AMR exome

AF:

0.0458

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.138

Gnomad SAS exome

AF:

0.0798

Gnomad FIN exome

AF:

0.0902

Gnomad NFE exome

AF:

0.0954

Gnomad OTH exome

AF:

0.0934

GnomAD4 exome

AF:

0.0977

AC:

136573

AN:

1397776

Hom.:

7003

Cov.:

AF XY:

0.0975

AC XY:

67222

AN XY:

689280

show subpopulations

Gnomad4 AFR exome

AF:

0.0925

Gnomad4 AMR exome

AF:

0.0486

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.140

Gnomad4 SAS exome

AF:

0.0777

Gnomad4 FIN exome

AF:

0.0911

Gnomad4 NFE exome

AF:

0.0982

Gnomad4 OTH exome

AF:

0.102

GnomAD4 genome

AF:

0.0922

AC:

14030

AN:

152214

Hom.:

701

Cov.:

AF XY:

0.0905

AC XY:

6735

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0873

Gnomad4 AMR

AF:

0.0684

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.0827

Gnomad4 FIN

AF:

0.0861

Gnomad4 NFE

AF:

0.0946

Gnomad4 OTH

AF:

0.0980

Alfa

AF:

0.0930

Hom.:

1010

Bravo

AF:

0.0909

Asia WGS

AF:

0.0980

AC:

340

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 27, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

0.25

DANN

Benign

0.80

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