Genetic Variant CHKB-DT:n.182_189dupGGCGGCGG (chr22-50583192-C-CCGGCGGGG) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000380711.3(CHKB-DT):n.182_189dupGGCGGCGG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 176,082 control chromosomes in the GnomAD database, including 297 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 296 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 1 hom. )

Consequence

CHKB-DT
ENST00000380711.3 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.251

Publications

0 publications found

Variant links:

Genes affected

CHKB-DT (HGNC:40146): (CHKB divergent transcript)

CHKB-DT links:

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 22-50583192-C-CCGGCGGGG is Benign according to our data. Variant chr22-50583192-C-CCGGCGGGG is described in ClinVar as Benign. ClinVar VariationId is 1259647.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380711.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
CHKB-DT	NR_021492.2	n.182_189dupGGCGGCGG	non_coding_transcript_exon	Exon 1 of 2
CHKB-DT	NR_110536.1	n.182_189dupGGCGGCGG	non_coding_transcript_exon	Exon 1 of 4
CHKB-CPT1B	NR_027928.2	n.-201_-194dupCCCCGCCG	upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CHKB-DT	ENST00000380711.3	TSL:2	n.182_189dupGGCGGCGG	non_coding_transcript_exon	Exon 1 of 2
CHKB-DT	ENST00000648558.1		n.52_59dupGGCGGCGG	non_coding_transcript_exon	Exon 1 of 4
CHKB-DT	ENST00000656328.1		n.88_95dupGGCGGCGG	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

5313

AN:

152070

Hom.:

295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0162

Gnomad ASJ

AF:

0.00433

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00140

Gnomad OTH

AF:

0.0287

GnomAD4 exome

AF:

0.00167

AC:

AN:

23902

Hom.:

Cov.:

AF XY:

0.00162

AC XY:

AN XY:

12310

show subpopulations

African (AFR)

AF:

0.0300

AC:

AN:

700

American (AMR)

AF:

0.00408

AC:

AN:

490

Ashkenazi Jewish (ASJ)

AF:

0.00365

AC:

AN:

822

East Asian (EAS)

AF:

0.00

AC:

AN:

1300

South Asian (SAS)

AF:

0.00

AC:

AN:

2148

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1060

Middle Eastern (MID)

AF:

0.00

AC:

AN:

138

European-Non Finnish (NFE)

AF:

0.000512

AC:

AN:

15628

Other (OTH)

AF:

0.00371

AC:

AN:

1616

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0350

AC:

5331

AN:

152180

Hom.:

296

Cov.:

AF XY:

0.0338

AC XY:

2516

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.118

AC:

4891

AN:

41498

American (AMR)

AF:

0.0161

AC:

247

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00433

AC:

AN:

3468

East Asian (EAS)

AF:

0.00117

AC:

AN:

5148

South Asian (SAS)

AF:

0.00145

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.000471

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00140

AC:

AN:

68000

Other (OTH)

AF:

0.0284

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

235

470

706

941

1176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000560

Hom.:

Asia WGS

AF:

0.00751

AC:

AN:

3474

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.25

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over