Variant 1-53214202-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_017887.3(CZIB):c.*457C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00936 in 165,186 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0094 ( 10 hom., cov: 33)

Exomes 𝑓: 0.0086 ( 1 hom. )

Consequence

CZIB
NM_017887.3 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.431

Variant links:

Genes affected

CZIB (HGNC:26059): (CXXC motif containing zinc binding protein) Enables zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

CZIB links:

CPT2 (HGNC:2330): (carnitine palmitoyltransferase 2) The protein encoded by this gene is a nuclear protein which is transported to the mitochondrial inner membrane. Together with carnitine palmitoyltransferase I, the encoded protein oxidizes long-chain fatty acids in the mitochondria. Defects in this gene are associated with mitochondrial long-chain fatty-acid (LCFA) oxidation disorders. [provided by RefSeq, Jul 2008]

CPT2 links:

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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=-0.84).

BP6

Variant 1-53214202-G-T is Benign according to our data. Variant chr1-53214202-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 368875.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00942 (1435/152290) while in subpopulation SAS AF= 0.0363 (175/4826). AF 95% confidence interval is 0.0319. There are 10 homozygotes in gnomad4. There are 731 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CZIB	NM_017887.3 linkuse as main transcript	c.*457C>A		3_prime_UTR_variant	8/8	ENST00000294360.5	NP_060357.1
CPT2	NM_000098.3 linkuse as main transcript			downstream_gene_variant		ENST00000371486.4	NP_000089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CZIB	ENST00000294360.5 linkuse as main transcript	c.*457C>A		3_prime_UTR_variant	8/8	1	NM_017887.3	ENSP00000294360	P1
CPT2	ENST00000371486.4 linkuse as main transcript			downstream_gene_variant		1	NM_000098.3	ENSP00000360541	P1

Frequencies

GnomAD3 genomes

AF:

0.00944

AC:

1436

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00244

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00753

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00943

Gnomad SAS

AF:

0.0364

Gnomad FIN

AF:

0.0190

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0111

Gnomad OTH

AF:

0.00766

GnomAD4 exome

AF:

0.00861

AC:

111

AN:

12896

Hom.:

Cov.:

AF XY:

0.00953

AC XY:

AN XY:

6718

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.0133

Gnomad4 EAS exome

AF:

0.00568

Gnomad4 SAS exome

AF:

0.0244

Gnomad4 FIN exome

AF:

0.00394

Gnomad4 NFE exome

AF:

0.00877

Gnomad4 OTH exome

AF:

0.00482

GnomAD4 genome

AF:

0.00942

AC:

1435

AN:

152290

Hom.:

Cov.:

AF XY:

0.00982

AC XY:

731

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00243

Gnomad4 AMR

AF:

0.00752

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00946

Gnomad4 SAS

AF:

0.0363

Gnomad4 FIN

AF:

0.0190

Gnomad4 NFE

AF:

0.0111

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00708

Hom.:

Bravo

AF:

0.00671

Asia WGS

AF:

0.0330

AC:

113

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Carnitine palmitoyltransferase II deficiency

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.78

DANN

Benign

0.56

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.

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