22-50579365-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005198.5(CHKB):c.1113+61T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,584,834 control chromosomes in the GnomAD database, including 8,205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.10 ( 1188 hom., cov: 32)
Exomes 𝑓: 0.074 ( 7017 hom. )
Consequence
CHKB
NM_005198.5 intron
NM_005198.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.528
Genes affected
CHKB (HGNC:1938): (choline kinase beta) Choline kinase (CK) and ethanolamine kinase (EK) catalyze the phosphorylation of choline/ethanolamine to phosphocholine/phosphoethanolamine. This is the first enzyme in the biosynthesis of phosphatidylcholine/phosphatidylethanolamine in all animal cells. The highly purified CKs from mammalian sources and their recombinant gene products have been shown to have EK activity also, indicating that both activities reside on the same protein. The choline kinase-like protein encoded by CHKL belongs to the choline/ethanolamine kinase family; however, its exact function is not known. Read-through transcripts are expressed from this locus that include exons from the downstream CPT1B locus. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 22-50579365-A-G is Benign according to our data. Variant chr22-50579365-A-G is described in ClinVar as [Benign]. Clinvar id is 1284104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-50579365-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHKB | NM_005198.5 | c.1113+61T>C | intron_variant | ENST00000406938.3 | NP_005189.2 | |||
CHKB-CPT1B | NR_027928.2 | n.1331+61T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHKB | ENST00000406938.3 | c.1113+61T>C | intron_variant | 1 | NM_005198.5 | ENSP00000384400 | P1 |
Frequencies
GnomAD3 genomes AF: 0.101 AC: 15370AN: 151992Hom.: 1185 Cov.: 32
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GnomAD4 exome AF: 0.0744 AC: 106549AN: 1432724Hom.: 7017 Cov.: 27 AF XY: 0.0758 AC XY: 54001AN XY: 712162
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GnomAD4 genome AF: 0.101 AC: 15405AN: 152110Hom.: 1188 Cov.: 32 AF XY: 0.106 AC XY: 7855AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 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