rs749927570
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207391.3(RGS9BP):c.365C>G(p.Ser122Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,530,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. S122S) has been classified as Likely benign.
Frequency
Consequence
NM_207391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS9BP | NM_207391.3 | c.365C>G | p.Ser122Cys | missense_variant | 1/1 | ENST00000334176.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS9BP | ENST00000334176.4 | c.365C>G | p.Ser122Cys | missense_variant | 1/1 | NM_207391.3 | P1 | ||
ANKRD27 | ENST00000590519.2 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151994Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000795 AC: 10AN: 125808Hom.: 0 AF XY: 0.000116 AC XY: 8AN XY: 68872
GnomAD4 exome AF: 0.0000363 AC: 50AN: 1378492Hom.: 0 Cov.: 39 AF XY: 0.0000544 AC XY: 37AN XY: 679748
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 122 of the RGS9BP protein (p.Ser122Cys). This variant is present in population databases (rs749927570, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with RGS9BP-related conditions. ClinVar contains an entry for this variant (Variation ID: 522947). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Bradyopsia Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 05, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | May 03, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at