rs17518299

Positions:

• chr6-166763909-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+6954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,172 control chromosomes in the GnomAD database, including 3,014 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 0.19 (3014 hom., cov: 33)
• Consequence: RPS6KA2 NM_001318936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS6KA2	NM_001318936.2	c.174+6954C>T		intron_variant			NP_001305865.2
RPS6KA2	NM_001006932.3	c.123+94291C>T		intron_variant			NP_001006933.3
RPS6KA2	NM_001318937.2	c.37+98199C>T		intron_variant			NP_001305866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS6KA2	ENST00000510118.5	c.174+6954C>T		intron_variant		2		ENSP00000422435.1
RPS6KA2	ENST00000503859.5	c.123+94291C>T		intron_variant		2		ENSP00000427015.1
RPS6KA2	ENST00000506565.1	c.174+6954C>T		intron_variant		4		ENSP00000425148.1
RPS6KA2	ENST00000512860.5	c.-169+142449C>T		intron_variant		4		ENSP00000427605.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29474 AN: 152054 Hom.: 3012 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.194 AC: 29489 AN: 152172 Hom.: 3014 Cov.: 33 AF XY: 0.193 AC XY: 14335 AN XY: 74396

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.188

Alfa AF: 0.204 Hom.: 424

Bravo AF: 0.186

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17518299; hg19: chr6-167177397;