rs767703623
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001131016.2(CIZ1):c.26_49del(p.Gln9_Gln16del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,541,198 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. Q9Q) has been classified as Likely benign.
Frequency
Consequence
NM_001131016.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIZ1 | NM_001131016.2 | c.26_49del | p.Gln9_Gln16del | inframe_deletion | 2/17 | ENST00000372938.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIZ1 | ENST00000372938.10 | c.26_49del | p.Gln9_Gln16del | inframe_deletion | 2/17 | 1 | NM_001131016.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00105 AC: 160AN: 151858Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000501 AC: 74AN: 147838Hom.: 0 AF XY: 0.000421 AC XY: 33AN XY: 78380
GnomAD4 exome AF: 0.00113 AC: 1576AN: 1389222Hom.: 0 AF XY: 0.00109 AC XY: 749AN XY: 685614
GnomAD4 genome ? AF: 0.00105 AC: 160AN: 151976Hom.: 0 Cov.: 31 AF XY: 0.00133 AC XY: 99AN XY: 74264
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 08, 2022 | - - |
Dystonic disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 455982). This variant has not been reported in the literature in individuals affected with CIZ1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant, c.26_49del, results in the deletion of 8 amino acid(s) of the CIZ1 protein (p.Gln9_Gln16del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at