rs56218010
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000379565.9(RPS6KA3):āc.113T>Gā(p.Ile38Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0217 in 1,191,596 control chromosomes in the GnomAD database, including 218 homozygotes. There are 7,832 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
ENST00000379565.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS6KA3 | NM_004586.3 | c.113T>G | p.Ile38Ser | missense_variant | 2/22 | ENST00000379565.9 | NP_004577.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS6KA3 | ENST00000379565.9 | c.113T>G | p.Ile38Ser | missense_variant | 2/22 | 1 | NM_004586.3 | ENSP00000368884 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 1782AN: 110777Hom.: 13 Cov.: 23 AF XY: 0.0147 AC XY: 485AN XY: 32993
GnomAD3 exomes AF: 0.0161 AC: 2948AN: 183231Hom.: 22 AF XY: 0.0164 AC XY: 1113AN XY: 67727
GnomAD4 exome AF: 0.0223 AC: 24111AN: 1080767Hom.: 205 Cov.: 27 AF XY: 0.0211 AC XY: 7348AN XY: 349055
GnomAD4 genome AF: 0.0161 AC: 1781AN: 110829Hom.: 13 Cov.: 23 AF XY: 0.0146 AC XY: 484AN XY: 33055
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 12, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 10, 2013 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 26, 2018 | - - |
Coffin-Lowry syndrome;C0796225:Intellectual disability, X-linked 19 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at