rs11120212

Variant names:

• chr1-213787711-T-A
• rs11120212
• ENST00000456240.1:n.144-6673T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000788945.1(ENSG00000225233):​n.439-6673T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,112 control chromosomes in the GnomAD database, including 2,106 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 0.15 (2106 hom., cov: 32)
• Consequence: ENSG00000225233 ENST00000788945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 publications found

Genes affected

ENSG00000225233 (HGNC:):

RPS6KC1 (HGNC:10439): (ribosomal protein S6 kinase C1) Sphingosine kinase catalyzes the formation of sphingosine 1 phosphate, a lipid cellular messenger. The protein encoded by this gene can bind to sphingosine kinase and to phosphatidylinositol 3-phosphate, suggesting a role in sphingosine 1 phophate signaling. The encoded protein can also bind to peroxiredoxin-3 and may help transport it to mitochondria. [provided by RefSeq, Mar 2017]

RPS6KC1 Gene-Disease associations (from GenCC):

• periventricular leukomalacia

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788945.1. 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
	ENSG00000225233	ENST00000456240.1	TSL:5	n.144-6673T>A		intron	N/A
	ENSG00000225233	ENST00000788945.1		n.439-6673T>A		intron	N/A
	ENSG00000225233	ENST00000788946.1		n.444-6673T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22439 AN: 151992 Hom.: 2092 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.148 AC: 22520 AN: 152112 Hom.: 2106 Cov.: 32 AF XY: 0.152 AC XY: 11286 AN XY: 74374

African (AFR) AF: 0.218 AC: 9042 AN: 41472

American (AMR) AF: 0.239 AC: 3650 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1188 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4816

European-Finnish (FIN) AF: 0.0411 AC: 436 AN: 10614

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0906 AC: 6159 AN: 67984

Other (OTH) AF: 0.153 AC: 323 AN: 2114

Alfa AF: 0.118 Hom.: 162

Bravo AF: 0.164

Asia WGS AF: 0.226 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		1.2

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: rs11120212;

hg19: chr1-213961054;