Variant 16-89561052-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000977.4(RPL13):c.93T>G(p.Arg31Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,605,014 control chromosomes in the GnomAD database, including 30,603 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3467 hom., cov: 34)

Exomes 𝑓: 0.19 ( 27136 hom. )

Consequence

RPL13
NM_000977.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.289

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 16-89561052-T-G is Benign according to our data. Variant chr16-89561052-T-G is described in ClinVar as [Benign]. Clinvar id is 1327970.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.289 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL13	NM_000977.4 link	c.93T>G	p.Arg31Arg	synonymous_variant	Exon 2 of 6	ENST00000311528.10	NP_000968.2	P26373-1A8K4C8
RPL13	NM_033251.2 link	c.93T>G	p.Arg31Arg	synonymous_variant	Exon 1 of 5		NP_150254.1	P26373-1A8K4C8
RPL13	NM_001243131.1 link	c.93T>G	p.Arg31Arg	synonymous_variant	Exon 2 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.93T>G	p.Arg31Arg	synonymous_variant	Exon 2 of 6	1	NM_000977.4	ENSP00000307889.5		P26373-1

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31302

AN:

152058

Hom.:

3444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.0883

Gnomad MID

AF:

0.197

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.215

GnomAD3 exomes

AF:

0.167

AC:

38475

AN:

229960

Hom.:

3487

AF XY:

0.168

AC XY:

21351

AN XY:

127012

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.155

Gnomad SAS exome

AF:

0.148

Gnomad FIN exome

AF:

0.0924

Gnomad NFE exome

AF:

0.192

Gnomad OTH exome

AF:

0.180

GnomAD4 exome

AF:

0.190

AC:

275719

AN:

1452848

Hom.:

27136

Cov.:

AF XY:

0.189

AC XY:

136324

AN XY:

722634

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.109

Gnomad4 ASJ exome

AF:

0.222

Gnomad4 EAS exome

AF:

0.134

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.0998

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.199

GnomAD4 genome

AF:

0.206

AC:

31358

AN:

152166

Hom.:

3467

Cov.:

AF XY:

0.199

AC XY:

14812

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.149

Gnomad4 ASJ

AF:

0.238

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.0883

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.194

Hom.:

1328

Bravo

AF:

0.215

Asia WGS

AF:

0.135

AC:

468

AN:

3470

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

-0.72

CADD

Benign

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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