chr10-79184473-T-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_020338.4(ZMIZ1):​c.-49-17111T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,064 control chromosomes in the GnomAD database, including 12,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.40 ( 12666 hom., cov: 32)

Consequence

ZMIZ1
NM_020338.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.06
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 10-79184473-T-G is Benign according to our data. Variant chr10-79184473-T-G is described in ClinVar as [Benign]. Clinvar id is 1281699.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZMIZ1NM_020338.4 linkuse as main transcriptc.-49-17111T>G intron_variant ENST00000334512.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZMIZ1ENST00000334512.10 linkuse as main transcriptc.-49-17111T>G intron_variant 5 NM_020338.4 P1Q9ULJ6-1

Frequencies

GnomAD3 genomes
AF:
0.398
AC:
60538
AN:
151946
Hom.:
12658
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.268
Gnomad AMI
AF:
0.406
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.407
Gnomad EAS
AF:
0.421
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.363
Gnomad NFE
AF:
0.459
Gnomad OTH
AF:
0.389
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.398
AC:
60555
AN:
152064
Hom.:
12666
Cov.:
32
AF XY:
0.400
AC XY:
29713
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.268
Gnomad4 AMR
AF:
0.433
Gnomad4 ASJ
AF:
0.407
Gnomad4 EAS
AF:
0.421
Gnomad4 SAS
AF:
0.363
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.459
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.440
Hom.:
7121
Bravo
AF:
0.390
Asia WGS
AF:
0.378
AC:
1315
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxFeb 18, 2020This variant is associated with the following publications: (PMID: 30181159) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
0.090
DANN
Benign
0.80

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs703977; hg19: chr10-80944230; API