4-39456250-T-TG

Position:

• chr4-39456250-T-TG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000661.5(RPL9):​c.391+155_391+156insC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.66 (33931 hom., cov: 0)
  • Exomes 𝑓: 0.69 (157301 hom.)
• Consequence: RPL9 NM_000661.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.87

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-39456250-T-TG is Benign according to our data. Variant chr4-39456250-T-TG is described in ClinVar as [Benign]. Clinvar id is 1268644.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPL9	NM_000661.5	c.391+155_391+156insC		intron_variant		ENST00000295955.14
RPL9	NM_001024921.4	c.391+155_391+156insC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL9	ENST00000295955.14	c.391+155_391+156insC		intron_variant		1	NM_000661.5	P1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100877 AN: 151978 Hom.: 33901 Cov.: 0

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.686

GnomAD3 exomes AF: 0.713 AC: 104167 AN: 146046 Hom.: 37509 AF XY: 0.715 AC XY: 55717 AN XY: 77960

Gnomad AFR exome AF: 0.533

Gnomad AMR exome AF: 0.793

Gnomad ASJ exome AF: 0.694

Gnomad EAS exome AF: 0.737

Gnomad SAS exome AF: 0.772

Gnomad FIN exome AF: 0.649

Gnomad NFE exome AF: 0.696

Gnomad OTH exome AF: 0.721

GnomAD4 exome AF: 0.694 AC: 449319 AN: 647172 Hom.: 157301 Cov.: 9 AF XY: 0.698 AC XY: 239873 AN XY: 343790

Gnomad4 AFR exome AF: 0.537

Gnomad4 AMR exome AF: 0.788

Gnomad4 ASJ exome AF: 0.700

Gnomad4 EAS exome AF: 0.728

Gnomad4 SAS exome AF: 0.764

Gnomad4 FIN exome AF: 0.650

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.681

GnomAD4 genome AF: 0.664 AC: 100963 AN: 152096 Hom.: 33931 Cov.: 0 AF XY: 0.664 AC XY: 49388 AN XY: 74336

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.691

Alfa AF: 0.624 Hom.: 3781

Bravo AF: 0.668

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3216720; hg19: chr4-39457870;