rs10927875

Positions:

• chr1-15972817-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375743.9(ZBTB17):​c.-3+222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,104 control chromosomes in the GnomAD database, including 6,580 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6580 hom., cov: 32)
• Consequence: ZBTB17 ENST00000375743.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB17	NM_003443.3	c.-3+222G>A		intron_variant		ENST00000375743.9	NP_003434.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZBTB17	ENST00000375743.9	c.-3+222G>A		intron_variant		1	NM_003443.3	ENSP00000364895	P2
ZBTB17	ENST00000375733.6	c.-3+222G>A		intron_variant		1		ENSP00000364885	A2
ZBTB17	ENST00000537142.5	c.-64+222G>A		intron_variant		2		ENSP00000438529
ZBTB17	ENST00000479282.5	n.209+222G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43067 AN: 151986 Hom.: 6572 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.283 AC: 43110 AN: 152104 Hom.: 6580 Cov.: 32 AF XY: 0.285 AC XY: 21202 AN XY: 74372

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.00829

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.272

Alfa AF: 0.316 Hom.: 18173

Bravo AF: 0.279

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.41

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: rs10927875; hg19: chr1-16299312;