chr1-15942289-C-T

Position:

• chr1-15942289-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.2129-37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0176 in 1,613,672 control chromosomes in the GnomAD database, including 3,066 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.081 (1563 hom., cov: 33)
  • Exomes 𝑓: 0.011 (1503 hom.)
• Consequence: ZBTB17 NM_003443.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.321

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=-0.83).
• BP6: Variant 1-15942289-C-T is Benign according to our data. Variant chr1-15942289-C-T is described in ClinVar as [Benign]. Clinvar id is 1272499.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB17	NM_003443.3	c.2129-37G>A		intron_variant		ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9	c.2129-37G>A		intron_variant		1	NM_003443.3	P2

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12255 AN: 152200 Hom.: 1558 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00370

Gnomad OTH AF: 0.0716

GnomAD3 exomes AF: 0.0240 AC: 6010 AN: 250676 Hom.: 665 AF XY: 0.0188 AC XY: 2550 AN XY: 135550

Gnomad AFR exome AF: 0.280

Gnomad AMR exome AF: 0.0179

Gnomad ASJ exome AF: 0.0125

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00523

Gnomad FIN exome AF: 0.0000926

Gnomad NFE exome AF: 0.00396

Gnomad OTH exome AF: 0.0203

GnomAD4 exome AF: 0.0111 AC: 16154 AN: 1461354 Hom.: 1503 Cov.: 32 AF XY: 0.00996 AC XY: 7237 AN XY: 726954

Gnomad4 AFR exome AF: 0.287

Gnomad4 AMR exome AF: 0.0204

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00568

Gnomad4 FIN exome AF: 0.0000941

Gnomad4 NFE exome AF: 0.00288

Gnomad4 OTH exome AF: 0.0232

GnomAD4 genome AF: 0.0807 AC: 12288 AN: 152318 Hom.: 1563 Cov.: 33 AF XY: 0.0780 AC XY: 5808 AN XY: 74492

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00579

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.00369

Gnomad4 OTH AF: 0.0709

Alfa AF: 0.0407 Hom.: 134

Bravo AF: 0.0932

Asia WGS AF: 0.0200 AC: 70 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 25, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs72885816; hg19: chr1-16268784;