chr10-79176690-T-C

Position:

• chr10-79176690-T-C

Variant summary

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

The NM_020338.4(ZMIZ1):​c.-50+14557T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 150,310 control chromosomes in the GnomAD database, including 13,196 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 0.35 (13196 hom., cov: 33)
• Consequence: ZMIZ1 NM_020338.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1	NM_020338.4	c.-50+14557T>C		intron_variant		ENST00000334512.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1	ENST00000334512.10	c.-50+14557T>C		intron_variant		5	NM_020338.4	P1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 52574 AN: 150192 Hom.: 13155 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.350 AC: 52674 AN: 150310 Hom.: 13196 Cov.: 33 AF XY: 0.358 AC XY: 26255 AN XY: 73362

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.342

Alfa AF: 0.200 Hom.: 4675

Bravo AF: 0.370

Asia WGS AF: 0.544 AC: 1885 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.45

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: rs3862511; hg19: chr10-80936447;