Variant chr19-8321817-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001031.5(RPS28):c.87+114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 1,489,114 control chromosomes in the GnomAD database, including 113,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 17181 hom., cov: 32)

Exomes 𝑓: 0.37 ( 96608 hom. )

Consequence

RPS28
NM_001031.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.60

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 -16 ACMG points.

BP6

Variant 19-8321817-G-A is Benign according to our data. Variant chr19-8321817-G-A is described in ClinVar as [Benign]. Clinvar id is 1181154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS28	NM_001031.5 linkuse as main transcript	c.87+114G>A		intron_variant		ENST00000600659.3
RPS28	XM_047439201.1 linkuse as main transcript	c.87+114G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
RPS28	ENST00000600659.3 linkuse as main transcript	c.87+114G>A	intron_variant		1	NM_001031.5	P1
RPS28	ENST00000602140.1 linkuse as main transcript	n.237G>A	non_coding_transcript_exon_variant	2/2	1
RPS28	ENST00000449223.3 linkuse as main transcript	n.574G>A	non_coding_transcript_exon_variant	2/3	2
RPS28	ENST00000417088.2 linkuse as main transcript	n.70+114G>A	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67575

AN:

151892

Hom.:

17134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.700

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.406

GnomAD3 exomes

AF:

0.361

AC:

56763

AN:

157072

Hom.:

11174

AF XY:

0.370

AC XY:

31306

AN XY:

84560

show subpopulations

Gnomad AFR exome

AF:

0.711

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.261

Gnomad SAS exome

AF:

0.450

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.377

Gnomad OTH exome

AF:

0.350

GnomAD4 exome

AF:

0.372

AC:

497019

AN:

1337104

Hom.:

96608

Cov.:

AF XY:

0.373

AC XY:

246806

AN XY:

661192

show subpopulations

Gnomad4 AFR exome

AF:

0.712

Gnomad4 AMR exome

AF:

0.249

Gnomad4 ASJ exome

AF:

0.325

Gnomad4 EAS exome

AF:

0.239

Gnomad4 SAS exome

AF:

0.450

Gnomad4 FIN exome

AF:

0.274

Gnomad4 NFE exome

AF:

0.370

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.445

AC:

67669

AN:

152010

Hom.:

17181

Cov.:

AF XY:

0.441

AC XY:

32735

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.700

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.312

Gnomad4 EAS

AF:

0.251

Gnomad4 SAS

AF:

0.455

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.370

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.377

Hom.:

15941

Bravo

AF:

0.457

Asia WGS

AF:

0.382

AC:

1327

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.95

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.61

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.61

Position offset: 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