rs12334
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001131016.2(CIZ1):c.1733C>T(p.Ser578Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00475 in 1,591,550 control chromosomes in the GnomAD database, including 286 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S578S) has been classified as Likely benign.
Frequency
Consequence
NM_001131016.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIZ1 | NM_001131016.2 | c.1733C>T | p.Ser578Phe | missense_variant | 10/17 | ENST00000372938.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIZ1 | ENST00000372938.10 | c.1733C>T | p.Ser578Phe | missense_variant | 10/17 | 1 | NM_001131016.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0248 AC: 3772AN: 152138Hom.: 152 Cov.: 32
GnomAD3 exomes AF: 0.00668 AC: 1414AN: 211726Hom.: 49 AF XY: 0.00487 AC XY: 556AN XY: 114116
GnomAD4 exome AF: 0.00263 AC: 3783AN: 1439294Hom.: 132 Cov.: 34 AF XY: 0.00231 AC XY: 1648AN XY: 713814
GnomAD4 genome ? AF: 0.0248 AC: 3782AN: 152256Hom.: 154 Cov.: 32 AF XY: 0.0239 AC XY: 1776AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at