Genetic Variant RPL9:c.258+175A>G (chr4-39457411-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000661.5(RPL9):c.258+175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 562,526 control chromosomes in the GnomAD database, including 9,546 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2240 hom., cov: 32)

Exomes 𝑓: 0.18 ( 7306 hom. )

Consequence

RPL9
NM_000661.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.500

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=-0.85).

BP6

Variant 4-39457411-T-C is Benign according to our data. Variant chr4-39457411-T-C is described in ClinVar as [Benign]. Clinvar id is 1291998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL9	NM_000661.5 link	c.258+175A>G		intron_variant	Intron 4 of 7	ENST00000295955.14	NP_000652.2	P32969Q53Z07
RPL9	NM_001024921.4 link	c.258+175A>G		intron_variant	Intron 4 of 7		NP_001020092.1	P32969Q53Z07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL9	ENST00000295955.14 link	c.258+175A>G		intron_variant	Intron 4 of 7	1	NM_000661.5	ENSP00000346022.7		P32969

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24113

AN:

151646

Hom.:

2238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0726

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.202

GnomAD4 exome

AF:

0.181

AC:

74333

AN:

410772

Hom.:

7306

Cov.:

AF XY:

0.182

AC XY:

39534

AN XY:

217624

show subpopulations

Gnomad4 AFR exome

AF:

0.0733

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.245

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.172

Gnomad4 FIN exome

AF:

0.156

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.188

GnomAD4 genome

AF:

0.159

AC:

24109

AN:

151754

Hom.:

2240

Cov.:

AF XY:

0.157

AC XY:

11655

AN XY:

74124

show subpopulations

Gnomad4 AFR

AF:

0.0724

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.190

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.168

Hom.:

313

Bravo

AF:

0.161

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 15, 2021

GeneDx

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

-0.85

CADD

Benign

6.8

DANN

Benign

0.56

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