Variant rs2294714 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000983.4(RPL22):c.13-10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,563,072 control chromosomes in the GnomAD database, including 65,572 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 0.33 ( 8589 hom., cov: 33)

Exomes 𝑓: 0.28 ( 56983 hom. )

Consequence

RPL22
NM_000983.4 intron

Scores

Splicing: ADA: 0.00003427

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Variant links:

Genes affected

RPL22 (HGNC:10315): (ribosomal protein L22) 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 cytoplasmic ribosomal protein that is a component of the 60S subunit. The protein belongs to the L22E family of ribosomal proteins. Its initiating methionine residue is post-translationally removed. The protein can bind specifically to Epstein-Barr virus-encoded RNAs (EBERs) 1 and 2. The mouse protein has been shown to be capable of binding to heparin. Transcript variants utilizing alternative polyA signals exist. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. It was previously thought that this gene mapped to 3q26 and that it was fused to the acute myeloid leukemia 1 (AML1) gene located at 21q22 in some therapy-related myelodysplastic syndrome patients with 3;21 translocations; however, these fusions actually involve a ribosomal protein L22 pseudogene located at 3q26, and this gene actually maps to 1p36.3-p36.2. [provided by RefSeq, Jul 2008]

RPL22 links:

RPL22 (HGNC:):

RPL22 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL22	NM_000983.4 linkuse as main transcript	c.13-10A>G		intron_variant		ENST00000234875.9	NP_000974.1	P35268

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL22	ENST00000234875.9 linkuse as main transcript	c.13-10A>G		intron_variant		1	NM_000983.4	ENSP00000346088.3		P35268
ENSG00000285629	ENST00000484532.6 linkuse as main transcript	n.-97A>G		upstream_gene_variant		2		ENSP00000465763.1		K7EKS7

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49468

AN:

151898

Hom.:

8563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.454

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.310

GnomAD3 exomes

AF:

0.312

AC:

77373

AN:

248234

Hom.:

12828

AF XY:

0.304

AC XY:

40856

AN XY:

134236

show subpopulations

Gnomad AFR exome

AF:

0.436

Gnomad AMR exome

AF:

0.362

Gnomad ASJ exome

AF:

0.214

Gnomad EAS exome

AF:

0.464

Gnomad SAS exome

AF:

0.296

Gnomad FIN exome

AF:

0.376

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.279

GnomAD4 exome

AF:

0.281

AC:

396087

AN:

1411056

Hom.:

56983

Cov.:

AF XY:

0.280

AC XY:

197061

AN XY:

704438

show subpopulations

Gnomad4 AFR exome

AF:

0.439

Gnomad4 AMR exome

AF:

0.355

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.436

Gnomad4 SAS exome

AF:

0.298

Gnomad4 FIN exome

AF:

0.371

Gnomad4 NFE exome

AF:

0.262

Gnomad4 OTH exome

AF:

0.284

GnomAD4 genome

AF:

0.326

AC:

49547

AN:

152016

Hom.:

8589

Cov.:

AF XY:

0.332

AC XY:

24659

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.424

Gnomad4 AMR

AF:

0.320

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.270

Hom.:

1567

Bravo

AF:

0.326

Asia WGS

AF:

0.345

AC:

1201

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.84

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000034

dbscSNV1_RF

Benign

0.0040

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over