rs2278978

chr1-26546754-A-G

Variant summary

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

The NM_002953.4(RPS6KA1):c.109-113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 749,456 control chromosomes in the GnomAD database, including 205,097 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 0.77 (45634 hom., cov: 32)
  • Exomes 𝑓: 0.73 (159463 hom.)
• Consequence: RPS6KA1 NM_002953.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS6KA1	NM_002953.4	c.109-113A>G		intron_variant		ENST00000374168.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS6KA1	ENST00000374168.7	c.109-113A>G		intron_variant		1	NM_002953.4	P1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117071 AN: 152044 Hom.: 45598 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.729 AC: 435237 AN: 597294 Hom.: 159463 AF XY: 0.723 AC XY: 228721 AN XY: 316336

Gnomad4 AFR exome AF: 0.891

Gnomad4 AMR exome AF: 0.666

Gnomad4 ASJ exome AF: 0.664

Gnomad4 EAS exome AF: 0.769

Gnomad4 SAS exome AF: 0.662

Gnomad4 FIN exome AF: 0.751

Gnomad4 NFE exome AF: 0.734

Gnomad4 OTH exome AF: 0.736

GnomAD4 genome AF: 0.770 AC: 117162 AN: 152162 Hom.: 45634 Cov.: 32 AF XY: 0.766 AC XY: 56931 AN XY: 74368

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.761

Alfa AF: 0.734 Hom.: 84486

Bravo AF: 0.773

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4
Dann	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278978; hg19: chr1-26873245; COSMIC: COSV64809871; COSMIC: COSV64809871;