Variant rs848217 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_003443.3(ZBTB17):c.621T>C(p.Ala207Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 1,605,680 control chromosomes in the GnomAD database, including 207,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19516 hom., cov: 32)

Exomes 𝑓: 0.51 ( 187960 hom. )

Consequence

ZBTB17
NM_003443.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.811

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:

ZBTB17 (HGNC:):

ZBTB17 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-15945755-A-G is Benign according to our data. Variant chr1-15945755-A-G is described in ClinVar as [Benign]. Clinvar id is 1264129.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.811 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB17	NM_003443.3 linkuse as main transcript	c.621T>C	p.Ala207Ala	synonymous_variant	6/16	ENST00000375743.9	NP_003434.2	Q13105-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB17	ENST00000375743.9 linkuse as main transcript	c.621T>C	p.Ala207Ala	synonymous_variant	6/16	1	NM_003443.3	ENSP00000364895.4		Q13105-1

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

76316

AN:

151820

Hom.:

19480

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.608

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.574

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.482

GnomAD3 exomes

AF:

0.530

AC:

128442

AN:

242426

Hom.:

35251

AF XY:

0.528

AC XY:

69776

AN XY:

132188

show subpopulations

Gnomad AFR exome

AF:

0.469

Gnomad AMR exome

AF:

0.700

Gnomad ASJ exome

AF:

0.584

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.582

Gnomad FIN exome

AF:

0.528

Gnomad NFE exome

AF:

0.500

Gnomad OTH exome

AF:

0.526

GnomAD4 exome

AF:

0.506

AC:

735040

AN:

1453742

Hom.:

187960

Cov.:

AF XY:

0.508

AC XY:

367455

AN XY:

723584

show subpopulations

Gnomad4 AFR exome

AF:

0.469

Gnomad4 AMR exome

AF:

0.688

Gnomad4 ASJ exome

AF:

0.580

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.581

Gnomad4 FIN exome

AF:

0.530

Gnomad4 NFE exome

AF:

0.498

Gnomad4 OTH exome

AF:

0.499

GnomAD4 genome

AF:

0.503

AC:

76406

AN:

151938

Hom.:

19516

Cov.:

AF XY:

0.509

AC XY:

37784

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.474

Gnomad4 AMR

AF:

0.609

Gnomad4 ASJ

AF:

0.589

Gnomad4 EAS

AF:

0.303

Gnomad4 SAS

AF:

0.575

Gnomad4 FIN

AF:

0.546

Gnomad4 NFE

AF:

0.496

Gnomad4 OTH

AF:

0.486

Alfa

AF:

0.505

Hom.:

7163

Bravo

AF:

0.505

Asia WGS

AF:

0.511

AC:

1776

AN:

3478

EpiCase

AF:

0.502

EpiControl

AF:

0.502

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.9

DANN

Benign

0.35

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