22-50578973-A-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

The NM_005198.5(CHKB):​c.*208T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 618,208 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.0047 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0040 ( 9 hom. )

Consequence

CHKB
NM_005198.5 3_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -0.100
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00466 (709/152252) while in subpopulation AFR AF= 0.0071 (295/41542). AF 95% confidence interval is 0.00643. There are 1 homozygotes in gnomad4. There are 335 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHKBNM_005198.5 linkuse as main transcriptc.*208T>G 3_prime_UTR_variant 11/11 ENST00000406938.3 NP_005189.2
CHKB-CPT1BNR_027928.2 linkuse as main transcriptn.1551+63T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHKBENST00000406938.3 linkuse as main transcriptc.*208T>G 3_prime_UTR_variant 11/111 NM_005198.5 ENSP00000384400 P1Q9Y259-1

Frequencies

GnomAD3 genomes
AF:
0.00466
AC:
709
AN:
152134
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00710
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00301
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00492
Gnomad OTH
AF:
0.00335
GnomAD4 exome
AF:
0.00400
AC:
1865
AN:
465956
Hom.:
9
Cov.:
4
AF XY:
0.00404
AC XY:
998
AN XY:
247332
show subpopulations
Gnomad4 AFR exome
AF:
0.0100
Gnomad4 AMR exome
AF:
0.00228
Gnomad4 ASJ exome
AF:
0.00139
Gnomad4 EAS exome
AF:
0.00156
Gnomad4 SAS exome
AF:
0.00481
Gnomad4 FIN exome
AF:
0.000294
Gnomad4 NFE exome
AF:
0.00461
Gnomad4 OTH exome
AF:
0.00381
GnomAD4 genome
AF:
0.00466
AC:
709
AN:
152252
Hom.:
1
Cov.:
33
AF XY:
0.00450
AC XY:
335
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.00710
Gnomad4 AMR
AF:
0.00301
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.00155
Gnomad4 SAS
AF:
0.00270
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00493
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00476
Hom.:
1
Bravo
AF:
0.00486
Asia WGS
AF:
0.00231
AC:
8
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Megaconial type congenital muscular dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
4.1
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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.

Other links and lift over

dbSNP: rs41281533; hg19: chr22-51017402; API