rs409161

Positions:

• chr6-166767040-G-A

Variant summary

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

The NM_001318936.2(RPS6KA2):​c.174+3823C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,028 control chromosomes in the GnomAD database, including 5,590 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 0.25 (5590 hom., cov: 33)
• Consequence: RPS6KA2 NM_001318936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

Genes affected

RPS6KA2 (HGNC:10431): (ribosomal protein S6 kinase A2) This gene encodes a member of the RSK (ribosomal S6 kinase) family of serine/threonine kinases. This kinase contains two non-identical kinase catalytic domains and phosphorylates various substrates, including members of the mitogen-activated kinase (MAPK) signalling pathway. The activity of this protein has been implicated in controlling cell growth and differentiation. Alternative splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KA2	NM_001006932.3	c.123+91160C>T		intron_variant
RPS6KA2	NM_001318936.2	c.174+3823C>T		intron_variant
RPS6KA2	NM_001318937.2	c.37+95068C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS6KA2	ENST00000503859.5	c.123+91160C>T		intron_variant		2
RPS6KA2	ENST00000506565.1	c.174+3823C>T		intron_variant		4
RPS6KA2	ENST00000510118.5	c.174+3823C>T		intron_variant		2
RPS6KA2	ENST00000512860.5	c.-169+139318C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37770 AN: 151910 Hom.: 5579 Cov.: 33

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.249 AC: 37790 AN: 152028 Hom.: 5590 Cov.: 33 AF XY: 0.251 AC XY: 18656 AN XY: 74312

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.278

Alfa AF: 0.289 Hom.: 9640

Bravo AF: 0.242

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs409161; hg19: chr6-167180528;