Genetic Variant NM_005198.5:c.818+40T>C (chr22-50580150-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005198.5(CHKB):c.818+40T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,612,786 control chromosomes in the GnomAD database, including 177,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 12823 hom., cov: 33)

Exomes 𝑓: 0.47 ( 164367 hom. )

Consequence

CHKB
NM_005198.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.183

Variant links:

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]

CHKB links:

CHKB-CPT1B (HGNC:41998): (CHKB-CPT1B readthrough (NMD candidate)) The genes CHKB and CPT1B are adjacent on chromosome 22 and read-through transcripts are expressed that include exons from both loci. The read-through transcripts are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to express proteins. [provided by RefSeq, Jun 2009]

CHKB-CPT1B links:

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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=-0.91).

BP6

Variant 22-50580150-A-G is Benign according to our data. Variant chr22-50580150-A-G is described in ClinVar as [Benign]. Clinvar id is 1294337.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-50580150-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHKB	NM_005198.5 link	c.818+40T>C		intron_variant	Intron 7 of 10	ENST00000406938.3	NP_005189.2	Q9Y259-1A0A024R4X4
CHKB-CPT1B	NR_027928.2 link	n.1036+40T>C		intron_variant	Intron 7 of 29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHKB	ENST00000406938.3 link	c.818+40T>C		intron_variant	Intron 7 of 10	1	NM_005198.5	ENSP00000384400.3		Q9Y259-1

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58230

AN:

152062

Hom.:

12828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.434

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.482

Gnomad OTH

AF:

0.392

GnomAD3 exomes

AF:

0.444

AC:

110870

AN:

249564

Hom.:

25754

AF XY:

0.445

AC XY:

60124

AN XY:

135110

show subpopulations

Gnomad AFR exome

AF:

0.139

Gnomad AMR exome

AF:

0.464

Gnomad ASJ exome

AF:

0.450

Gnomad EAS exome

AF:

0.466

Gnomad SAS exome

AF:

0.362

Gnomad FIN exome

AF:

0.529

Gnomad NFE exome

AF:

0.484

Gnomad OTH exome

AF:

0.452

GnomAD4 exome

AF:

0.470

AC:

686023

AN:

1460604

Hom.:

164367

Cov.:

AF XY:

0.467

AC XY:

339141

AN XY:

726632

show subpopulations

Gnomad4 AFR exome

AF:

0.135

Gnomad4 AMR exome

AF:

0.463

Gnomad4 ASJ exome

AF:

0.442

Gnomad4 EAS exome

AF:

0.474

Gnomad4 SAS exome

AF:

0.368

Gnomad4 FIN exome

AF:

0.521

Gnomad4 NFE exome

AF:

0.488

Gnomad4 OTH exome

AF:

0.441

GnomAD4 genome

AF:

0.383

AC:

58231

AN:

152182

Hom.:

12823

Cov.:

AF XY:

0.386

AC XY:

28702

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.434

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.527

Gnomad4 NFE

AF:

0.482

Gnomad4 OTH

AF:

0.389

Alfa

AF:

0.460

Hom.:

20805

Bravo

AF:

0.372

Asia WGS

AF:

0.368

AC:

1280

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over