dbSNP rs9661939: ZBTB17:p.Phe334Phe (chr1-15944765-G-A) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_003443.3(ZBTB17):c.1002C>T(p.Phe334Phe) variant causes a synonymous change. The variant allele was found at a frequency of 0.287 in 1,612,314 control chromosomes in the GnomAD database, including 71,173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5174 hom., cov: 33)

Exomes 𝑓: 0.29 ( 65999 hom. )

Consequence

ZBTB17
NM_003443.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.87

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 1-15944765-G-A is Benign according to our data. Variant chr1-15944765-G-A is described in ClinVar as [Benign]. Clinvar id is 1280656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB17	NM_003443.3 link	c.1002C>T	p.Phe334Phe	synonymous_variant	Exon 8 of 16	ENST00000375743.9	NP_003434.2	Q13105-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB17	ENST00000375743.9 link	c.1002C>T	p.Phe334Phe	synonymous_variant	Exon 8 of 16	1	NM_003443.3	ENSP00000364895.4		Q13105-1

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36276

AN:

152108

Hom.:

5166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.0156

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.285

AC:

69731

AN:

244386

Hom.:

11285

AF XY:

0.297

AC XY:

39320

AN XY:

132540

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.0164

Gnomad SAS exome

AF:

0.426

Gnomad FIN exome

AF:

0.230

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.303

GnomAD4 exome

AF:

0.292

AC:

426841

AN:

1460088

Hom.:

65999

Cov.:

AF XY:

0.298

AC XY:

216202

AN XY:

726294

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.325

Gnomad4 ASJ exome

AF:

0.362

Gnomad4 EAS exome

AF:

0.0107

Gnomad4 SAS exome

AF:

0.426

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.298

Gnomad4 OTH exome

AF:

0.283

GnomAD4 genome

AF:

0.239

AC:

36310

AN:

152226

Hom.:

5174

Cov.:

AF XY:

0.240

AC XY:

17893

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.0153

Gnomad4 SAS

AF:

0.422

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.301

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.280

Hom.:

3096

Bravo

AF:

0.233

Asia WGS

AF:

0.242

AC:

840

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.81

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