Variant 4-39455015-T-C 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 ENST00000295955.14(RPL9):c.392-71A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,438,862 control chromosomes in the GnomAD database, including 25,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3712 hom., cov: 32)

Exomes 𝑓: 0.18 ( 21671 hom. )

Consequence

RPL9
ENST00000295955.14 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.221

Variant links:

Genes affected

RPL9 (HGNC:10369): (ribosomal protein L9) 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 L6P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

RPL9 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=-0.8).

BP6

Variant 4-39455015-T-C is Benign according to our data. Variant chr4-39455015-T-C is described in ClinVar as [Benign]. Clinvar id is 1273476.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL9	NM_000661.5 linkuse as main transcript	c.392-71A>G		intron_variant		ENST00000295955.14	NP_000652.2
RPL9	NM_001024921.4 linkuse as main transcript	c.392-71A>G		intron_variant			NP_001020092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL9	ENST00000295955.14 linkuse as main transcript	c.392-71A>G		intron_variant		1	NM_000661.5	ENSP00000346022	P1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31686

AN:

152072

Hom.:

3701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.205

GnomAD4 exome

AF:

0.180

AC:

231622

AN:

1286672

Hom.:

21671

Cov.:

AF XY:

0.180

AC XY:

115732

AN XY:

644264

show subpopulations

Gnomad4 AFR exome

AF:

0.313

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.157

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.119

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.209

AC:

31742

AN:

152190

Hom.:

3712

Cov.:

AF XY:

0.203

AC XY:

15127

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.307

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.186

Hom.:

870

Bravo

AF:

0.220

Asia WGS

AF:

0.158

AC:

549

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.0

DANN

Benign

0.62

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