12-119688269-A-AAGG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001206999.2(CIT):c.6187-17_6187-15dupCCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,610,176 control chromosomes in the GnomAD database, including 106,426 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.39 ( 12872 hom., cov: 0)
Exomes 𝑓: 0.35 ( 93554 hom. )
Consequence
CIT
NM_001206999.2 intron
NM_001206999.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.78
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 -16 ACMG points.
BP6
Variant 12-119688269-A-AAGG is Benign according to our data. Variant chr12-119688269-A-AAGG is described in ClinVar as [Benign]. Clinvar id is 1264110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.394 AC: 59786AN: 151896Hom.: 12854 Cov.: 0
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GnomAD3 exomes AF: 0.311 AC: 78159AN: 251202Hom.: 13969 AF XY: 0.312 AC XY: 42429AN XY: 135774
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GnomAD4 exome AF: 0.349 AC: 509200AN: 1458162Hom.: 93554 Cov.: 31 AF XY: 0.347 AC XY: 251829AN XY: 725606
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GnomAD4 genome AF: 0.394 AC: 59849AN: 152014Hom.: 12872 Cov.: 0 AF XY: 0.384 AC XY: 28540AN XY: 74322
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Jul 07, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at