rs3213716
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031464.5(RPS6KL1):c.532-102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,356,996 control chromosomes in the GnomAD database, including 101,146 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 0.30 ( 8714 hom., cov: 31)
Exomes 𝑓: 0.39 ( 92432 hom. )
Consequence
RPS6KL1
NM_031464.5 intron
NM_031464.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.711
Genes affected
RPS6KL1 (HGNC:20222): (ribosomal protein S6 kinase like 1) Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be located in ribosome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KL1 | NM_031464.5 | c.532-102C>T | intron_variant | ENST00000557413.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KL1 | ENST00000557413.6 | c.532-102C>T | intron_variant | 5 | NM_031464.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.305 AC: 46288AN: 151916Hom.: 8714 Cov.: 31
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GnomAD4 exome AF: 0.385 AC: 464214AN: 1204962Hom.: 92432 Cov.: 16 AF XY: 0.383 AC XY: 229019AN XY: 598358
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GnomAD4 genome ? AF: 0.304 AC: 46291AN: 152034Hom.: 8714 Cov.: 31 AF XY: 0.302 AC XY: 22473AN XY: 74316
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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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at