rs12134932

chr1-15944661-C-A

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.1070+36G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 1,602,604 control chromosomes in the GnomAD database, including 5,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.098 (965 hom., cov: 33)
  • Exomes 𝑓: 0.078 (4913 hom.)
• Consequence: ZBTB17 NM_003443.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.590

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=-0.79).
• BP6: Variant 1-15944661-C-A is Benign according to our data. Variant chr1-15944661-C-A is described in ClinVar as [Benign]. Clinvar id is 1258996.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB17	NM_003443.3	c.1070+36G>T		intron_variant		ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9	c.1070+36G>T		intron_variant		1	NM_003443.3	P2
ZBTB17	ENST00000375733.6	c.1070+36G>T		intron_variant		1		A2
ZBTB17	ENST00000537142.5	c.824+36G>T		intron_variant		2
ZBTB17	ENST00000492834.1	n.779+36G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14861 AN: 152140 Hom.: 965 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0583

GnomAD3 exomes AF: 0.0673 AC: 15970 AN: 237272 Hom.: 738 AF XY: 0.0661 AC XY: 8595 AN XY: 130026

Gnomad AFR exome AF: 0.178

Gnomad AMR exome AF: 0.0339

Gnomad ASJ exome AF: 0.0932

Gnomad EAS exome AF: 0.000165

Gnomad SAS exome AF: 0.0345

Gnomad FIN exome AF: 0.0990

Gnomad NFE exome AF: 0.0761

Gnomad OTH exome AF: 0.0706

GnomAD4 exome AF: 0.0781 AC: 113217 AN: 1450346 Hom.: 4913 Cov.: 32 AF XY: 0.0764 AC XY: 55136 AN XY: 722052

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.0370

Gnomad4 ASJ exome AF: 0.0970

Gnomad4 EAS exome AF: 0.000328

Gnomad4 SAS exome AF: 0.0338

Gnomad4 FIN exome AF: 0.0958

Gnomad4 NFE exome AF: 0.0820

Gnomad4 OTH exome AF: 0.0743

GnomAD4 genome AF: 0.0977 AC: 14873 AN: 152258 Hom.: 965 Cov.: 33 AF XY: 0.0961 AC XY: 7154 AN XY: 74436

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0805 Hom.: 73

Bravo AF: 0.0989

Asia WGS AF: 0.0200 AC: 71 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 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.56
Dann	Benign	0.78

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: rs12134932; hg19: chr1-16271156;