rs1782644

Positions:

• chr10-79241418-A-G

Variant summary

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

The NM_020338.4(ZMIZ1):​c.280+25144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,052 control chromosomes in the GnomAD database, including 3,189 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 0.16 (3189 hom., cov: 32)
• Consequence: ZMIZ1 NM_020338.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMIZ1	NM_020338.4	c.280+25144A>G		intron_variant		ENST00000334512.10	NP_065071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMIZ1	ENST00000334512.10	c.280+25144A>G		intron_variant		5	NM_020338.4	ENSP00000334474	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24416 AN: 151934 Hom.: 3175 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0638

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.161 AC: 24469 AN: 152052 Hom.: 3189 Cov.: 32 AF XY: 0.156 AC XY: 11593 AN XY: 74336

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0638

Gnomad4 EAS AF: 0.0501

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0853

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0932 Hom.: 1340

Bravo AF: 0.177

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.53

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: rs1782644; hg19: chr10-81001175;