chr1-15972817-C-T

Variant names:

• chr1-15972817-C-T
• rs10927875
• NM_003443.3:c.-3+222G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003443.3(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 NM_003443.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 48 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB17	NM_003443.3	MANE Select	c.-3+222G>A		intron	N/A	NP_003434.2	Q13105-1
	ZBTB17	NM_001287603.2		c.-3+222G>A		intron	N/A	NP_001274532.1	Q13105-2
	ZBTB17	NM_001324138.2		c.-3+222G>A		intron	N/A	NP_001311067.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZBTB17	ENST00000375743.9	TSL:1 MANE Select	c.-3+222G>A		intron	N/A	ENSP00000364895.4	Q13105-1
	ZBTB17	ENST00000375733.6	TSL:1	c.-3+222G>A		intron	N/A	ENSP00000364885.2	Q13105-2
	ZBTB17	ENST00000894624.1		c.-3+3166G>A		intron	N/A	ENSP00000564683.1

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

African (AFR) AF: 0.224 AC: 9292 AN: 41476

American (AMR) AF: 0.286 AC: 4374 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3470

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5188

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4822

European-Finnish (FIN) AF: 0.317 AC: 3343 AN: 10562

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21951 AN: 67998

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.312 Hom.: 35807

Bravo AF: 0.279

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.41
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10927875; hg19: chr1-16299312;