Variant 16-89561263-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_000977.4(RPL13):c.141C>T(p.Ala47Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,553,686 control chromosomes in the GnomAD database, including 28,959 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2289 hom., cov: 34)

Exomes 𝑓: 0.19 ( 26670 hom. )

Consequence

RPL13
NM_000977.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0930

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

BP6

Variant 16-89561263-C-T is Benign according to our data. Variant chr16-89561263-C-T is described in ClinVar as [Benign]. Clinvar id is 1327971.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.093 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL13	NM_000977.4 link	c.141C>T	p.Ala47Ala	synonymous_variant	Exon 3 of 6	ENST00000311528.10	NP_000968.2	P26373-1A8K4C8
RPL13	NM_033251.2 link	c.141C>T	p.Ala47Ala	synonymous_variant	Exon 2 of 5		NP_150254.1	P26373-1A8K4C8
RPL13	NM_001243131.1 link	c.141C>T	p.Ala47Ala	synonymous_variant	Exon 3 of 7		NP_001230060.1	P26373-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL13	ENST00000311528.10 link	c.141C>T	p.Ala47Ala	synonymous_variant	Exon 3 of 6	1	NM_000977.4	ENSP00000307889.5		P26373-1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25426

AN:

152106

Hom.:

2284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.0893

Gnomad MID

AF:

0.182

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.193

GnomAD3 exomes

AF:

0.164

AC:

25264

AN:

153978

Hom.:

2279

AF XY:

0.167

AC XY:

14243

AN XY:

85444

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.238

Gnomad EAS exome

AF:

0.144

Gnomad SAS exome

AF:

0.147

Gnomad FIN exome

AF:

0.0952

Gnomad NFE exome

AF:

0.201

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.192

AC:

269238

AN:

1401460

Hom.:

26670

Cov.:

AF XY:

0.191

AC XY:

132561

AN XY:

693542

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.111

Gnomad4 ASJ exome

AF:

0.240

Gnomad4 EAS exome

AF:

0.125

Gnomad4 SAS exome

AF:

0.151

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.204

Gnomad4 OTH exome

AF:

0.196

GnomAD4 genome

AF:

0.167

AC:

25450

AN:

152226

Hom.:

2289

Cov.:

AF XY:

0.162

AC XY:

12063

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.153

Gnomad4 FIN

AF:

0.0893

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.121

Hom.:

338

Bravo

AF:

0.171

Asia WGS

AF:

0.117

AC:

408

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Spondyloepimetaphyseal dysplasia, Isidor-Toutain type

Benign:1

Nov 07, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Uncertain

0.98

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

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