1-15944172-CTGGGTGAACAAGCTGA-C

Position:

• chr1-15944172-CTGGGTGAACAAGCTGA-C

Variant summary

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

The NM_003443.3(ZBTB17):​c.1371+112_1371+127del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,375,848 control chromosomes in the GnomAD database, including 513 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.034 (282 hom., cov: 33)
  • Exomes 𝑓: 0.0035 (231 hom.)
• Consequence: ZBTB17 NM_003443.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.23

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 1-15944172-CTGGGTGAACAAGCTGA-C is Benign according to our data. Variant chr1-15944172-CTGGGTGAACAAGCTGA-C is described in ClinVar as [Benign]. Clinvar id is 1262168.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.1371+112_1371+127del		intron_variant		ENST00000375743.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZBTB17	ENST00000375743.9	c.1371+112_1371+127del		intron_variant		1	NM_003443.3	P2

Frequencies

GnomAD3 genomes AF: 0.0340 AC: 5179 AN: 152170 Hom.: 282 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0234

GnomAD3 exomes AF: 0.00716 AC: 974 AN: 136122 Hom.: 50 AF XY: 0.00569 AC XY: 418 AN XY: 73458

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.00586

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000132

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000251

Gnomad OTH exome AF: 0.00433

GnomAD4 exome AF: 0.00351 AC: 4298 AN: 1223560 Hom.: 231 AF XY: 0.00299 AC XY: 1826 AN XY: 611154

Gnomad4 AFR exome AF: 0.119

Gnomad4 AMR exome AF: 0.00761

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000146

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000163

Gnomad4 OTH exome AF: 0.00845

GnomAD4 genome AF: 0.0340 AC: 5184 AN: 152288 Hom.: 282 Cov.: 33 AF XY: 0.0334 AC XY: 2491 AN XY: 74472

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0176 Hom.: 27

Bravo AF: 0.0384

Asia WGS AF: 0.00606 AC: 21 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 26, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs111756461; hg19: chr1-16270667;