Variant chr10-78033930-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_033022.4(RPS24):c.3+26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 1,612,764 control chromosomes in the GnomAD database, including 283,526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 21687 hom., cov: 33)

Exomes 𝑓: 0.60 ( 261839 hom. )

Consequence

RPS24
NM_033022.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.641

Variant links:

Genes affected

RPS24 (HGNC:10411): (ribosomal protein S24) 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 S24E family of ribosomal proteins. It is located in the cytoplasm. Multiple transcript variants encoding different isoforms have been found for this gene. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Mutations in this gene result in Diamond-Blackfan anemia. [provided by RefSeq, Nov 2008]

RPS24 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-78033930-C-T is Benign according to our data. Variant chr10-78033930-C-T is described in ClinVar as [Benign]. Clinvar id is 1327973.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS24	NM_033022.4 linkuse as main transcript	c.3+26C>T		intron_variant		ENST00000372360.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS24	ENST00000372360.9 linkuse as main transcript	c.3+26C>T		intron_variant		1	NM_033022.4	P4	P62847-2

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78420

AN:

151996

Hom.:

21687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.657

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.527

GnomAD3 exomes

AF:

0.575

AC:

144612

AN:

251306

Hom.:

42839

AF XY:

0.573

AC XY:

77854

AN XY:

135838

show subpopulations

Gnomad AFR exome

AF:

0.302

Gnomad AMR exome

AF:

0.665

Gnomad ASJ exome

AF:

0.583

Gnomad EAS exome

AF:

0.472

Gnomad SAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.651

Gnomad NFE exome

AF:

0.607

Gnomad OTH exome

AF:

0.581

GnomAD4 exome

AF:

0.596

AC:

870100

AN:

1460650

Hom.:

261839

Cov.:

AF XY:

0.593

AC XY:

430780

AN XY:

726756

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.654

Gnomad4 ASJ exome

AF:

0.594

Gnomad4 EAS exome

AF:

0.482

Gnomad4 SAS exome

AF:

0.511

Gnomad4 FIN exome

AF:

0.649

Gnomad4 NFE exome

AF:

0.612

Gnomad4 OTH exome

AF:

0.569

GnomAD4 genome

AF:

0.516

AC:

78437

AN:

152114

Hom.:

21687

Cov.:

AF XY:

0.519

AC XY:

38561

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.304

Gnomad4 AMR

AF:

0.565

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.507

Gnomad4 FIN

AF:

0.657

Gnomad4 NFE

AF:

0.613

Gnomad4 OTH

AF:

0.523

Alfa

AF:

0.559

Hom.:

5065

Bravo

AF:

0.503

Asia WGS

AF:

0.482

AC:

1680

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Diamond-Blackfan anemia 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.78

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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