chr12-119690382-C-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001206999.2(CIT):c.5955G>T(p.Pro1985=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000968 in 1,596,536 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0051 ( 3 hom., cov: 31)
Exomes 𝑓: 0.00054 ( 6 hom. )
Consequence
CIT
NM_001206999.2 synonymous
NM_001206999.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.47
Genes affected
CIT (HGNC:1985): (citron rho-interacting serine/threonine kinase) This gene encodes a serine/threonine-protein kinase that functions in cell division. Together with the kinesin KIF14, this protein localizes to the central spindle and midbody, and functions to promote efficient cytokinesis. This protein is involved in central nervous system development. Polymorphisms in this gene are associated with bipolar disorder and risk for schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 12-119690382-C-A is Benign according to our data. Variant chr12-119690382-C-A is described in ClinVar as [Benign]. Clinvar id is 786235.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.47 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00507 (772/152270) while in subpopulation AFR AF= 0.0174 (722/41576). AF 95% confidence interval is 0.0163. There are 3 homozygotes in gnomad4. There are 376 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIT | NM_001206999.2 | c.5955G>T | p.Pro1985= | synonymous_variant | 47/48 | ENST00000392521.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIT | ENST00000392521.7 | c.5955G>T | p.Pro1985= | synonymous_variant | 47/48 | 1 | NM_001206999.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00506 AC: 770AN: 152152Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.00131 AC: 293AN: 223676Hom.: 0 AF XY: 0.00105 AC XY: 129AN XY: 122868
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GnomAD4 exome AF: 0.000535 AC: 773AN: 1444266Hom.: 6 Cov.: 31 AF XY: 0.000484 AC XY: 348AN XY: 718770
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 08, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 18, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at