rs11666543

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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]

ENSG00000300077 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448962.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS9	ENST00000448962.5	TSL:2	n.220+6504A>G		intron	N/A	ENSP00000399623.1	F2Z3C0
	ENSG00000300077	ENST00000768692.1		n.-79T>C		upstream_gene	N/A

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

African (AFR) AF: 0.927 AC: 38494 AN: 41536

American (AMR) AF: 0.841 AC: 12857 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2159 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4797 AN: 5156

South Asian (SAS) AF: 0.836 AC: 4034 AN: 4824

European-Finnish (FIN) AF: 0.664 AC: 7028 AN: 10580

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47560 AN: 67988

Other (OTH) AF: 0.812 AC: 1713 AN: 2110

Alfa AF: 0.739 Hom.: 116398

Bravo AF: 0.807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
PhyloP100		-0.056

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11666543; hg19: chr19-54711981;