rs140987045
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_004586.3(RPS6KA3):āc.139A>Gā(p.Ile47Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,131,301 control chromosomes in the GnomAD database, including 1 homozygotes. There are 394 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_004586.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA3 | NM_004586.3 | c.139A>G | p.Ile47Val | missense_variant | 3/22 | ENST00000379565.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA3 | ENST00000379565.9 | c.139A>G | p.Ile47Val | missense_variant | 3/22 | 1 | NM_004586.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00109 AC: 122AN: 112029Hom.: 0 Cov.: 23 AF XY: 0.000995 AC XY: 34AN XY: 34165
GnomAD3 exomes AF: 0.00158 AC: 290AN: 183013Hom.: 0 AF XY: 0.00150 AC XY: 101AN XY: 67545
GnomAD4 exome AF: 0.00124 AC: 1265AN: 1019218Hom.: 1 Cov.: 22 AF XY: 0.00121 AC XY: 360AN XY: 298516
GnomAD4 genome ? AF: 0.00109 AC: 122AN: 112083Hom.: 0 Cov.: 23 AF XY: 0.000993 AC XY: 34AN XY: 34229
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 23, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 28, 2017 | - - |
Coffin-Lowry syndrome;C0796225:Intellectual disability, X-linked 19 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at