10-119430387-C-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_005308.3(GRK5):āc.546C>Gā(p.Thr182Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000175 in 1,613,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.00093 ( 0 hom., cov: 31)
Exomes š: 0.000096 ( 0 hom. )
Consequence
GRK5
NM_005308.3 synonymous
NM_005308.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.245
Genes affected
GRK5 (HGNC:4544): (G protein-coupled receptor kinase 5) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor kinase subfamily of the Ser/Thr protein kinase family. The protein phosphorylates the activated forms of G protein-coupled receptors thus initiating their deactivation. It has also been shown to play a role in regulating the motility of polymorphonuclear leukocytes (PMNs). [provided by RefSeq, Jul 2008]
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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=-0.45).
BP6
Variant 10-119430387-C-G is Benign according to our data. Variant chr10-119430387-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3050818.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.245 with no splicing effect.
BS2
High AC in GnomAd4 at 142 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRK5 | NM_005308.3 | c.546C>G | p.Thr182Thr | synonymous_variant | 7/16 | ENST00000392870.3 | NP_005299.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRK5 | ENST00000392870.3 | c.546C>G | p.Thr182Thr | synonymous_variant | 7/16 | 1 | NM_005308.3 | ENSP00000376609.2 |
Frequencies
GnomAD3 genomes AF: 0.000933 AC: 142AN: 152126Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000220 AC: 55AN: 250360Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135338
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GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461310Hom.: 0 Cov.: 30 AF XY: 0.0000839 AC XY: 61AN XY: 726966
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GnomAD4 genome AF: 0.000933 AC: 142AN: 152244Hom.: 0 Cov.: 31 AF XY: 0.000846 AC XY: 63AN XY: 74434
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GRK5-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 07, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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