rs1555933444
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004586.3(RPS6KA3):c.1000-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 21)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
RPS6KA3
NM_004586.3 splice_region, splice_polypyrimidine_tract, intron
NM_004586.3 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00001906
2
Clinical Significance
Conservation
PhyloP100: -0.0750
Genes affected
RPS6KA3 (HGNC:10432): (ribosomal protein S6 kinase A3) This gene encodes a member of the RSK (ribosomal S6 kinase) family of serine/threonine kinases. This kinase contains 2 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. Mutations in this gene have been associated with Coffin-Lowry syndrome (CLS). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-20176359-G-A is Benign according to our data. Variant chrX-20176359-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 459261.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA3 | NM_004586.3 | c.1000-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000379565.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA3 | ENST00000379565.9 | c.1000-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004586.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 107902Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 30916 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1036070Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 312138
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 107902Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 30916
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Coffin-Lowry syndrome;C0796225:Intellectual disability, X-linked 19 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at