1-15941940-TTAAA-T

Position:

• chr1-15941940-TTAAA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003443.3(ZBTB17):​c.*25_*28del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00295 in 1,574,684 control chromosomes in the GnomAD database, including 207 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0060 (39 hom., cov: 33)
  • Exomes 𝑓: 0.0026 (168 hom.)
• Consequence: ZBTB17 NM_003443.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.47

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 -10 ACMG points.

• BP6: Variant 1-15941940-TTAAA-T is Benign according to our data. Variant chr1-15941940-TTAAA-T is described in ClinVar as [Benign]. Clinvar id is 1238751.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZBTB17	NM_003443.3	c.*25_*28del		3_prime_UTR_variant	16/16	ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9	c.*25_*28del		3_prime_UTR_variant	16/16	1	NM_003443.3	P2

Frequencies

GnomAD3 genomes AF: 0.00599 AC: 912 AN: 152174 Hom.: 39 Cov.: 33

Gnomad AFR AF: 0.00195

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.00526

GnomAD3 exomes AF: 0.0131 AC: 2894 AN: 220750 Hom.: 143 AF XY: 0.00961 AC XY: 1166 AN XY: 121290

Gnomad AFR exome AF: 0.00243

Gnomad AMR exome AF: 0.0850

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000509

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000135

Gnomad OTH exome AF: 0.00488

GnomAD4 exome AF: 0.00262 AC: 3727 AN: 1422392 Hom.: 168 AF XY: 0.00221 AC XY: 1554 AN XY: 704086

Gnomad4 AFR exome AF: 0.00103

Gnomad4 AMR exome AF: 0.0786

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000509

Gnomad4 SAS exome AF: 0.000600

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000139

Gnomad4 OTH exome AF: 0.00171

GnomAD4 genome AF: 0.00601 AC: 916 AN: 152292 Hom.: 39 Cov.: 33 AF XY: 0.00709 AC XY: 528 AN XY: 74470

Gnomad4 AFR AF: 0.00195

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000397

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.00347 Hom.: 1

Bravo AF: 0.00977

Asia WGS AF: 0.00260 AC: 9 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 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs199620366; hg19: chr1-16268435;