chr10-119423275-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005308.3(GRK5):c.440+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,594,878 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0072 ( 18 hom., cov: 33)
Exomes 𝑓: 0.00078 ( 18 hom. )
Consequence
GRK5
NM_005308.3 intron
NM_005308.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.340
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 10-119423275-C-T is Benign according to our data. Variant chr10-119423275-C-T is described in ClinVar as [Benign]. Clinvar id is 709987.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0072 (1097/152270) while in subpopulation AFR AF= 0.0254 (1055/41544). AF 95% confidence interval is 0.0241. There are 18 homozygotes in gnomad4. There are 500 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1097 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRK5 | NM_005308.3 | c.440+9C>T | intron_variant | ENST00000392870.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRK5 | ENST00000392870.3 | c.440+9C>T | intron_variant | 1 | NM_005308.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00721 AC: 1097AN: 152152Hom.: 18 Cov.: 33
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GnomAD3 exomes AF: 0.00180 AC: 453AN: 251306Hom.: 5 AF XY: 0.00147 AC XY: 199AN XY: 135824
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GnomAD4 exome AF: 0.000780 AC: 1125AN: 1442608Hom.: 18 Cov.: 27 AF XY: 0.000701 AC XY: 504AN XY: 719104
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GnomAD4 genome ? AF: 0.00720 AC: 1097AN: 152270Hom.: 18 Cov.: 33 AF XY: 0.00672 AC XY: 500AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at