rs11113
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002953.4(RPS6KA1):c.*398C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 389,256 control chromosomes in the GnomAD database, including 70,859 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 0.61 ( 28100 hom., cov: 30)
Exomes 𝑓: 0.60 ( 42759 hom. )
Consequence
RPS6KA1
NM_002953.4 3_prime_UTR
NM_002953.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.548
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA1 | NM_002953.4 | c.*398C>T | 3_prime_UTR_variant | 22/22 | ENST00000374168.7 | ||
RPS6KA1 | NM_001006665.2 | c.*398C>T | 3_prime_UTR_variant | 21/21 | |||
RPS6KA1 | NM_001330441.2 | c.*398C>T | 3_prime_UTR_variant | 21/21 | |||
RPS6KA1 | XM_024448871.2 | c.*398C>T | 3_prime_UTR_variant | 22/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA1 | ENST00000374168.7 | c.*398C>T | 3_prime_UTR_variant | 22/22 | 1 | NM_002953.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.606 AC: 91968AN: 151706Hom.: 28086 Cov.: 30
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GnomAD4 exome AF: 0.596 AC: 141438AN: 237432Hom.: 42759 Cov.: 0 AF XY: 0.600 AC XY: 79780AN XY: 132988
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GnomAD4 genome ? AF: 0.606 AC: 92030AN: 151824Hom.: 28100 Cov.: 30 AF XY: 0.605 AC XY: 44872AN XY: 74162
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at