rs1250541

chr10-79275156-G-Cchr10-79275156-G-T

Variant summary

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

The NM_020338.4(ZMIZ1):c.281-2025G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,186 control chromosomes in the GnomAD database, including 25,054 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 0.56 (25054 hom., cov: 34)
• Consequence: ZMIZ1 NM_020338.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1	NM_020338.4	c.281-2025G>C		intron_variant		ENST00000334512.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1	ENST00000334512.10	c.281-2025G>C		intron_variant		5	NM_020338.4	P1
ZMIZ1	ENST00000472035.5	n.71-2025G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85449 AN: 152068 Hom.: 25001 Cov.: 34

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.562 AC: 85558 AN: 152186 Hom.: 25054 Cov.: 34 AF XY: 0.564 AC XY: 41974 AN XY: 74400

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.528

Alfa AF: 0.353 Hom.: 815

Bravo AF: 0.568

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.52
Dann	Benign	0.33

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: rs1250541; hg19: chr10-81034913;