rs13198549

chr6-166760209-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+10654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,058 control chromosomes in the GnomAD database, including 24,801 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 0.56 (24801 hom., cov: 33)
• Consequence: RPS6KA2 NM_001318936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KA2	NM_001006932.3	c.123+97991C>T		intron_variant
RPS6KA2	NM_001318936.2	c.174+10654C>T		intron_variant
RPS6KA2	NM_001318937.2	c.37+101899C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS6KA2	ENST00000503859.5	c.123+97991C>T		intron_variant		2
RPS6KA2	ENST00000506565.1	c.174+10654C>T		intron_variant		4
RPS6KA2	ENST00000510118.5	c.174+10654C>T		intron_variant		2
RPS6KA2	ENST00000512860.5	c.-169+146149C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.559 AC: 85003 AN: 151940 Hom.: 24790 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.559 AC: 85064 AN: 152058 Hom.: 24801 Cov.: 33 AF XY: 0.561 AC XY: 41668 AN XY: 74298

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.581

Alfa AF: 0.599 Hom.: 5630

Bravo AF: 0.549

Asia WGS AF: 0.617 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.9
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13198549; hg19: chr6-167173697; COSMIC: COSV72313029; COSMIC: COSV72313029;