9-128179037-C-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001131016.2(CIZ1):c.1170G>T(p.Gln390His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 1,613,994 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001131016.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIZ1 | NM_001131016.2 | c.1170G>T | p.Gln390His | missense_variant | 8/17 | ENST00000372938.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIZ1 | ENST00000372938.10 | c.1170G>T | p.Gln390His | missense_variant | 8/17 | 1 | NM_001131016.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00516 AC: 785AN: 152224Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00428 AC: 1064AN: 248812Hom.: 0 AF XY: 0.00431 AC XY: 580AN XY: 134722
GnomAD4 exome AF: 0.00712 AC: 10402AN: 1461652Hom.: 34 Cov.: 34 AF XY: 0.00697 AC XY: 5068AN XY: 727116
GnomAD4 genome AF: 0.00515 AC: 785AN: 152342Hom.: 2 Cov.: 33 AF XY: 0.00477 AC XY: 355AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | CIZ1: BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
CIZ1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at