1-15943242-C-T

Position:

• chr1-15943242-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003443.3(ZBTB17):​c.1698-48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0765 in 1,613,216 control chromosomes in the GnomAD database, including 5,256 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.084 (630 hom., cov: 33)
  • Exomes 𝑓: 0.076 (4626 hom.)
• Consequence: ZBTB17 NM_003443.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.623

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 1-15943242-C-T is Benign according to our data. Variant chr1-15943242-C-T is described in ClinVar as [Benign]. Clinvar id is 1286770.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB17	NM_003443.3	c.1698-48G>A		intron_variant		ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9	c.1698-48G>A		intron_variant		1	NM_003443.3	P2

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12811 AN: 152104 Hom.: 630 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.0771

GnomAD3 exomes AF: 0.0654 AC: 16376 AN: 250210 Hom.: 694 AF XY: 0.0642 AC XY: 8690 AN XY: 135280

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.0356

Gnomad ASJ exome AF: 0.0211

Gnomad EAS exome AF: 0.00212

Gnomad SAS exome AF: 0.0419

Gnomad FIN exome AF: 0.102

Gnomad NFE exome AF: 0.0809

Gnomad OTH exome AF: 0.0660

GnomAD4 exome AF: 0.0757 AC: 110560 AN: 1460994 Hom.: 4626 Cov.: 33 AF XY: 0.0741 AC XY: 53837 AN XY: 726652

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.0381

Gnomad4 ASJ exome AF: 0.0244

Gnomad4 EAS exome AF: 0.00587

Gnomad4 SAS exome AF: 0.0417

Gnomad4 FIN exome AF: 0.0997

Gnomad4 NFE exome AF: 0.0812

Gnomad4 OTH exome AF: 0.0736

GnomAD4 genome AF: 0.0843 AC: 12832 AN: 152222 Hom.: 630 Cov.: 33 AF XY: 0.0815 AC XY: 6067 AN XY: 74432

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.0823

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0534 Hom.: 78

Bravo AF: 0.0820

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs4661672; hg19: chr1-16269737;