chr12-119688269-A-AAGG
Variant summary
Our verdict is Benign. The variant received -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 was made for transcript
Our verdict: Benign. The variant received -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 show subpopulations
GnomAD3 genomes
AF:
AC:
59786
AN:
151896
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.311 AC: 78159AN: 251202 AF XY: 0.312 show subpopulations
GnomAD2 exomes
AF:
AC:
78159
AN:
251202
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.349 AC: 509200AN: 1458162Hom.: 93554 Cov.: 31 AF XY: 0.347 AC XY: 251829AN XY: 725606 show subpopulations
GnomAD4 exome
AF:
AC:
509200
AN:
1458162
Hom.:
Cov.:
31
AF XY:
AC XY:
251829
AN XY:
725606
show subpopulations
African (AFR)
AF:
AC:
18795
AN:
33382
American (AMR)
AF:
AC:
10465
AN:
44714
Ashkenazi Jewish (ASJ)
AF:
AC:
7800
AN:
26118
East Asian (EAS)
AF:
AC:
2237
AN:
39700
South Asian (SAS)
AF:
AC:
21664
AN:
86192
European-Finnish (FIN)
AF:
AC:
15632
AN:
53410
Middle Eastern (MID)
AF:
AC:
2190
AN:
5752
European-Non Finnish (NFE)
AF:
AC:
409589
AN:
1108612
Other (OTH)
AF:
AC:
20828
AN:
60282
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.471
Heterozygous variant carriers
0
14773
29546
44318
59091
73864
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.394 AC: 59849AN: 152014Hom.: 12872 Cov.: 0 AF XY: 0.384 AC XY: 28540AN XY: 74322 show subpopulations
GnomAD4 genome
AF:
AC:
59849
AN:
152014
Hom.:
Cov.:
0
AF XY:
AC XY:
28540
AN XY:
74322
show subpopulations
African (AFR)
AF:
AC:
23149
AN:
41416
American (AMR)
AF:
AC:
4789
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1076
AN:
3468
East Asian (EAS)
AF:
AC:
212
AN:
5192
South Asian (SAS)
AF:
AC:
1122
AN:
4824
European-Finnish (FIN)
AF:
AC:
3076
AN:
10580
Middle Eastern (MID)
AF:
AC:
114
AN:
294
European-Non Finnish (NFE)
AF:
AC:
25282
AN:
67932
Other (OTH)
AF:
AC:
803
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1801
3602
5403
7204
9005
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
592
AN:
3478
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
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at