rs11666543

Variant names:

• chr19-54208113-A-G
• rs11666543
• ENST00000448962.5:n.220+6504A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448962.5(RPS9):​n.220+6504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,158 control chromosomes in the GnomAD database, including 47,998 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47998 hom., cov: 33)
• Consequence: RPS9 ENST00000448962.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

RPS9 (HGNC:10442): (ribosomal protein S9) 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 40S subunit. The protein belongs to the S4P family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, multiple processed pseudogenes derived from this gene are dispersed through the genome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS9	ENST00000448962.5	n.220+6504A>G		intron_variant	Intron 3 of 4	2		ENSP00000399623.1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119416 AN: 152040 Hom.: 47936 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.809

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.786 AC: 119536 AN: 152158 Hom.: 47998 Cov.: 33 AF XY: 0.788 AC XY: 58577 AN XY: 74382

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.812

Alfa AF: 0.721 Hom.: 58874

Bravo AF: 0.807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11666543; hg19: chr19-54711981;