Variant 1-15942982-T-TG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003443.3(ZBTB17):c.1828+81_1828+82insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.094 in 1,574,690 control chromosomes in the GnomAD database, including 11,025 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 3533 hom., cov: 31)

Exomes 𝑓: 0.087 ( 7492 hom. )

Consequence

ZBTB17
NM_003443.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.137

Variant links:

Genes affected

ZBTB17 (HGNC:12936): (zinc finger and BTB domain containing 17) This gene encodes a zinc finger protein involved in the regulation of c-myc. The symbol MIZ1 has also been associated with PIAS2 which is a different gene located on chromosome 18. [provided by RefSeq, Jul 2008]

ZBTB17 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-15942982-T-TG is Benign according to our data. Variant chr1-15942982-T-TG is described in ClinVar as [Benign]. Clinvar id is 1183759.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB17	NM_003443.3 linkuse as main transcript	c.1828+81_1828+82insC		intron_variant		ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9 linkuse as main transcript	c.1828+81_1828+82insC		intron_variant		1	NM_003443.3	P2	Q13105-1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24852

AN:

151850

Hom.:

3524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0945

Gnomad ASJ

AF:

0.0380

Gnomad EAS

AF:

0.00347

Gnomad SAS

AF:

0.0479

Gnomad FIN

AF:

0.0930

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0865

Gnomad OTH

AF:

0.147

GnomAD4 exome

AF:

0.0865

AC:

123089

AN:

1422722

Hom.:

7492

Cov.:

AF XY:

0.0837

AC XY:

58914

AN XY:

703726

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.0590

Gnomad4 ASJ exome

AF:

0.0369

Gnomad4 EAS exome

AF:

0.00576

Gnomad4 SAS exome

AF:

0.0468

Gnomad4 FIN exome

AF:

0.0985

Gnomad4 NFE exome

AF:

0.0839

Gnomad4 OTH exome

AF:

0.0960

GnomAD4 genome

AF:

0.164

AC:

24899

AN:

151968

Hom.:

3533

Cov.:

AF XY:

0.158

AC XY:

11761

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.383

Gnomad4 AMR

AF:

0.0943

Gnomad4 ASJ

AF:

0.0380

Gnomad4 EAS

AF:

0.00348

Gnomad4 SAS

AF:

0.0480

Gnomad4 FIN

AF:

0.0930

Gnomad4 NFE

AF:

0.0865

Gnomad4 OTH

AF:

0.145

Alfa

AF:

0.0603

Hom.:

100

Bravo

AF:

0.173

Asia WGS

AF:

0.0490

AC:

171

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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