6-166459460-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021135.6(RPS6KA2):c.1064G>A(p.Arg355Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000178 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021135.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA2 | NM_021135.6 | c.1064G>A | p.Arg355Gln | missense_variant | 12/21 | ENST00000265678.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA2 | ENST00000265678.9 | c.1064G>A | p.Arg355Gln | missense_variant | 12/21 | 1 | NM_021135.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000108 AC: 27AN: 250726Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135532
GnomAD4 exome AF: 0.000183 AC: 268AN: 1460986Hom.: 0 Cov.: 29 AF XY: 0.000176 AC XY: 128AN XY: 726876
GnomAD4 genome AF: 0.000125 AC: 19AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.1088G>A (p.R363Q) alteration is located in exon 13 (coding exon 13) of the RPS6KA2 gene. This alteration results from a G to A substitution at nucleotide position 1088, causing the arginine (R) at amino acid position 363 to be replaced by a glutamine (Q). 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