chr8-53881024-G-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000276500.4(RGS20):āc.9G>Cā(p.Thr3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,589,470 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0025 ( 2 hom., cov: 32)
Exomes š: 0.0030 ( 13 hom. )
Consequence
RGS20
ENST00000276500.4 synonymous
ENST00000276500.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0490
Genes affected
RGS20 (HGNC:14600): (regulator of G protein signaling 20) The protein encoded by this gene belongs to the family of regulator of G protein signaling (RGS) proteins, which are regulatory and structural components of G protein-coupled receptor complexes. RGS proteins inhibit signal transduction by increasing the GTPase activity of G protein alpha subunits, thereby driving them into their inactive GDP-bound forms. This protein selectively binds to G(z)-alpha and G(alpha)-i2 subunits, and regulates their signaling activities. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 8-53881024-G-C is Benign according to our data. Variant chr8-53881024-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2658601.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 385 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS20 | NM_170587.4 | c.510+1422G>C | intron_variant | ENST00000297313.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS20 | ENST00000297313.8 | c.510+1422G>C | intron_variant | 1 | NM_170587.4 |
Frequencies
GnomAD3 genomes AF: 0.00253 AC: 385AN: 152014Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00192 AC: 401AN: 208452Hom.: 0 AF XY: 0.00202 AC XY: 235AN XY: 116170
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GnomAD4 exome AF: 0.00305 AC: 4382AN: 1437346Hom.: 13 Cov.: 31 AF XY: 0.00296 AC XY: 2116AN XY: 714232
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GnomAD4 genome AF: 0.00253 AC: 385AN: 152124Hom.: 2 Cov.: 32 AF XY: 0.00272 AC XY: 202AN XY: 74366
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | RGS20: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at