rs1250003

chr10-79087057-C-T

Variant summary

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

The NM_020338.4(ZMIZ1):c.-337+17787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,258 control chromosomes in the GnomAD database, including 39,381 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 0.71 (39381 hom., cov: 34)
• Consequence: ZMIZ1 NM_020338.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

ZMIZ1 (HGNC:16493): (zinc finger MIZ-type containing 1) This gene encodes a member of the PIAS (protein inhibitor of activated STAT) family of proteins. The encoded protein regulates the activity of various transcription factors, including the androgen receptor, Smad3/4, and p53. The encoded protein may also play a role in sumoylation. A translocation between this locus on chromosome 10 and the protein tyrosine kinase ABL1 locus on chromosome 9 has been associated with acute lymphoblastic leukemia. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1	NM_020338.4	c.-337+17787C>T		intron_variant		ENST00000334512.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1	ENST00000334512.10	c.-337+17787C>T		intron_variant		5	NM_020338.4	P1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107580 AN: 152140 Hom.: 39323 Cov.: 34

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.707 AC: 107693 AN: 152258 Hom.: 39381 Cov.: 34 AF XY: 0.708 AC XY: 52672 AN XY: 74422

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.666

Alfa AF: 0.645 Hom.: 8922

Bravo AF: 0.706

Asia WGS AF: 0.668 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.0
Dann	Benign	0.50

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: rs1250003; hg19: chr10-80846814;