rs45518842
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000372938.10(CIZ1):c.683-7A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,611,328 control chromosomes in the GnomAD database, including 1,477 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000372938.10 splice_region, splice_polypyrimidine_tract, intron
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIZ1 | NM_001131016.2 | c.683-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000372938.10 | NP_001124488.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CIZ1 | ENST00000372938.10 | c.683-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001131016.2 | ENSP00000362029 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0537 AC: 8172AN: 152054Hom.: 707 Cov.: 31
GnomAD3 exomes AF: 0.0180 AC: 4530AN: 251194Hom.: 295 AF XY: 0.0160 AC XY: 2168AN XY: 135754
GnomAD4 exome AF: 0.00775 AC: 11303AN: 1459156Hom.: 772 Cov.: 29 AF XY: 0.00776 AC XY: 5637AN XY: 726078
GnomAD4 genome AF: 0.0538 AC: 8184AN: 152172Hom.: 705 Cov.: 31 AF XY: 0.0524 AC XY: 3899AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at