NM_002953.4:c.1591-2138A>G

Variant names:

• chr1-26569311-A-G
• rs282175
• NM_002953.4:c.1591-2138A>G

Variant summary

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

The NM_002953.4(RPS6KA1):​c.1591-2138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,996 control chromosomes in the GnomAD database, including 9,965 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 0.35 (9965 hom., cov: 32)
• Consequence: RPS6KA1 NM_002953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 6 publications found

Genes affected

RPS6KA1 (HGNC:10430): (ribosomal protein S6 kinase A1) This gene encodes a member of the RSK (ribosomal S6 kinase) family of serine/threonine kinases. This kinase contains 2 nonidentical 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. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002953.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS6KA1	NM_002953.4	MANE Select	c.1591-2138A>G		intron	N/A	NP_002944.2
	RPS6KA1	NM_001006665.2		c.1618-2138A>G		intron	N/A	NP_001006666.1
	RPS6KA1	NM_001330441.2		c.1543-2138A>G		intron	N/A	NP_001317370.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS6KA1	ENST00000374168.7	TSL:1 MANE Select	c.1591-2138A>G		intron	N/A	ENSP00000363283.2
	RPS6KA1	ENST00000531382.5	TSL:2	c.1618-2138A>G		intron	N/A	ENSP00000435412.1
	RPS6KA1	ENST00000374166.8	TSL:5	c.1558-2138A>G		intron	N/A	ENSP00000363281.4

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52500 AN: 151878 Hom.: 9962 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.346 AC: 52534 AN: 151996 Hom.: 9965 Cov.: 32 AF XY: 0.352 AC XY: 26181 AN XY: 74274

African (AFR) AF: 0.414 AC: 17155 AN: 41460

American (AMR) AF: 0.360 AC: 5488 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1053 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3901 AN: 5174

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4818

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10562

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18041 AN: 67954

Other (OTH) AF: 0.354 AC: 746 AN: 2106

Alfa AF: 0.296 Hom.: 1746

Bravo AF: 0.353

Asia WGS AF: 0.627 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		-0.17
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: rs282175; hg19: chr1-26895802;