chr6-166772186-A-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001318936.2(RPS6KA2):​c.124-1273T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

RPS6KA2
NM_001318936.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPS6KA2NM_001006932.3 linkuse as main transcriptc.123+86014T>G intron_variant
RPS6KA2NM_001318936.2 linkuse as main transcriptc.124-1273T>G intron_variant
RPS6KA2NM_001318937.2 linkuse as main transcriptc.37+89922T>G intron_variant
RPS6KA2XM_047419235.1 linkuse as main transcriptc.-169+86014T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPS6KA2ENST00000503859.5 linkuse as main transcriptc.123+86014T>G intron_variant 2 Q15349-3
RPS6KA2ENST00000506565.1 linkuse as main transcriptc.124-1273T>G intron_variant 4
RPS6KA2ENST00000510118.5 linkuse as main transcriptc.124-1273T>G intron_variant 2
RPS6KA2ENST00000512860.5 linkuse as main transcriptc.-169+134172T>G intron_variant 4

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.10
DANN
Benign
0.43

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6456123; hg19: chr6-167185674; API