rs2049956

Variant names:

• chr6-166438052-G-C
• rs2049956
• NM_021135.6:c.1333-5562C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-166438052-G-C
• chr6-166438052-G-T

Variant summary

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

The NM_021135.6(RPS6KA2):​c.1333-5562C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,138 control chromosomes in the GnomAD database, including 43,442 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 0.74 (43442 hom., cov: 32)
• Consequence: RPS6KA2 NM_021135.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021135.6. 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
	RPS6KA2	NM_021135.6	MANE Select	c.1333-5562C>G		intron	N/A	NP_066958.2
	RPS6KA2	NM_001318936.2		c.1408-5562C>G		intron	N/A	NP_001305865.2	F2Z2J1
	RPS6KA2	NM_001006932.3		c.1357-5562C>G		intron	N/A	NP_001006933.3	Q15349-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS6KA2	ENST00000265678.9	TSL:1 MANE Select	c.1333-5562C>G		intron	N/A	ENSP00000265678.4	Q15349-1
	RPS6KA2	ENST00000481261.6	TSL:1	c.1066-5562C>G		intron	N/A	ENSP00000422484.1	B7Z3B5
	RPS6KA2	ENST00000510118.5	TSL:2	c.1408-5562C>G		intron	N/A	ENSP00000422435.1	F2Z2J1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113170 AN: 152020 Hom.: 43433 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.744 AC: 113215 AN: 152138 Hom.: 43442 Cov.: 32 AF XY: 0.737 AC XY: 54835 AN XY: 74364

African (AFR) AF: 0.583 AC: 24180 AN: 41466

American (AMR) AF: 0.730 AC: 11158 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2814 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2681 AN: 5164

South Asian (SAS) AF: 0.612 AC: 2952 AN: 4822

European-Finnish (FIN) AF: 0.826 AC: 8751 AN: 10596

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58017 AN: 68010

Other (OTH) AF: 0.757 AC: 1598 AN: 2112

Alfa AF: 0.746 Hom.: 2408

Bravo AF: 0.732

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.46
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2049956; hg19: chr6-166851540;