11-67433430-C-G
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 1P and 4B. PP3BS2
The NM_003952.3(RPS6KB2):c.889C>G(p.Arg297Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003952.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS6KB2 | NM_003952.3 | c.889C>G | p.Arg297Gly | missense_variant | Exon 10 of 15 | ENST00000312629.10 | NP_003943.2 | |
RPS6KB2 | XM_006718656.4 | c.289C>G | p.Arg97Gly | missense_variant | Exon 6 of 11 | XP_006718719.1 | ||
RPS6KB2 | XM_047427395.1 | c.867C>G | p.Pro289Pro | synonymous_variant | Exon 10 of 11 | XP_047283351.1 | ||
RPS6KB2 | XM_047427396.1 | c.798C>G | p.Pro266Pro | synonymous_variant | Exon 9 of 10 | XP_047283352.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152172Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000481 AC: 12AN: 249364 AF XY: 0.0000296 show subpopulations
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460558Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 726686 show subpopulations
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74342 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.889C>G (p.R297G) alteration is located in exon 10 (coding exon 10) of the RPS6KB2 gene. This alteration results from a C to G substitution at nucleotide position 889, causing the arginine (R) at amino acid position 297 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at