Variant rs9930567 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000977.4(RPL13):c.334G>A(p.Ala112Thr) variant causes a missense change. The variant allele was found at a frequency of 0.19 in 1,613,752 control chromosomes in the GnomAD database, including 32,280 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.15 ( 2354 hom., cov: 33)

Exomes 𝑓: 0.19 ( 29926 hom. )

Consequence

RPL13
NM_000977.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.82

Variant links:

Genes affected

RPL13 (HGNC:10303): (ribosomal protein L13) 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 60S subunit. The protein belongs to the L13E family of ribosomal proteins. It is located in the cytoplasm. This gene is expressed at significantly higher levels in benign breast lesions than in breast carcinomas. Alternatively spliced transcript variants encoding distinct 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. [provided by RefSeq, Jul 2011]

RPL13 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 (MetaRNN=0.0022824407).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RPL13	NM_000977.4 linkuse as main transcript	c.334G>A	p.Ala112Thr	missense_variant	4/6	ENST00000311528.10
RPL13	NM_033251.2 linkuse as main transcript	c.334G>A	p.Ala112Thr	missense_variant	3/5
RPL13	NM_001243131.1 linkuse as main transcript	c.267+67G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL13	ENST00000311528.10 linkuse as main transcript	c.334G>A	p.Ala112Thr	missense_variant	4/6	1	NM_000977.4	P1	P26373-1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23435

AN:

152110

Hom.:

2353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0405

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0911

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.212

GnomAD3 exomes

AF:

0.163

AC:

40893

AN:

250942

Hom.:

4162

AF XY:

0.167

AC XY:

22714

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.0372

Gnomad AMR exome

AF:

0.126

Gnomad ASJ exome

AF:

0.210

Gnomad EAS exome

AF:

0.000816

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.226

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.194

AC:

283638

AN:

1461524

Hom.:

29926

Cov.:

AF XY:

0.193

AC XY:

140637

AN XY:

727040

show subpopulations

Gnomad4 AFR exome

AF:

0.0360

Gnomad4 AMR exome

AF:

0.134

Gnomad4 ASJ exome

AF:

0.205

Gnomad4 EAS exome

AF:

0.000504

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.182

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.184

GnomAD4 genome

AF:

0.154

AC:

23426

AN:

152228

Hom.:

2354

Cov.:

AF XY:

0.149

AC XY:

11100

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0404

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.193

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.0916

Gnomad4 FIN

AF:

0.171

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.209

Alfa

AF:

0.196

Hom.:

1728

Bravo

AF:

0.152

TwinsUK

AF:

0.199

AC:

739

ALSPAC

AF:

0.210

AC:

809

ESP6500AA

AF:

0.0494

AC:

217

ESP6500EA

AF:

0.210

AC:

1810

ExAC

AF:

0.161

AC:

19594

EpiCase

AF:

0.238

EpiControl

AF:

0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.033

T;T;.;T

Eigen

Benign

-0.024

Eigen_PC

Benign

0.13

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.92

.;.;D;D

MetaRNN

Benign

0.0023

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.4

L;L;.;L

MutationTaster

Benign

2.1e-8

P;P;P;P

PrimateAI

Uncertain

0.71

PROVEAN

Benign

-0.81

N;N;.;N

REVEL

Benign

0.069

Sift

Benign

0.24

T;T;.;T

Sift4G

Benign

0.30

T;T;T;T

Polyphen

0.0030

B;B;.;B

Vest4

0.21

MPC

0.26

ClinPred

0.024

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.9

Varity_R

0.16

gMVP

0.53

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over