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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.78
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CITNM_001206999.2 linkc.6187-17_6187-15dupCCT intron_variant Intron 47 of 47 ENST00000392521.7 NP_001193928.1 O14578-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CITENST00000392521.7 linkc.6187-15_6187-14insCCT intron_variant Intron 47 of 47 1 NM_001206999.2 ENSP00000376306.2 O14578-4

Frequencies

GnomAD3 genomes
AF:
0.394
AC:
59786
AN:
151896
Hom.:
12854
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.559
Gnomad AMI
AF:
0.248
Gnomad AMR
AF:
0.313
Gnomad ASJ
AF:
0.310
Gnomad EAS
AF:
0.0407
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.291
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.372
Gnomad OTH
AF:
0.386
GnomAD2 exomes
AF:
0.311
AC:
78159
AN:
251202
AF XY:
0.312
show subpopulations
Gnomad AFR exome
AF:
0.558
Gnomad AMR exome
AF:
0.225
Gnomad ASJ exome
AF:
0.308
Gnomad EAS exome
AF:
0.0352
Gnomad FIN exome
AF:
0.294
Gnomad NFE exome
AF:
0.367
Gnomad OTH exome
AF:
0.336
GnomAD4 exome
AF:
0.349
AC:
509200
AN:
1458162
Hom.:
93554
Cov.:
31
AF XY:
0.347
AC XY:
251829
AN XY:
725606
show subpopulations
African (AFR)
AF:
0.563
AC:
18795
AN:
33382
American (AMR)
AF:
0.234
AC:
10465
AN:
44714
Ashkenazi Jewish (ASJ)
AF:
0.299
AC:
7800
AN:
26118
East Asian (EAS)
AF:
0.0563
AC:
2237
AN:
39700
South Asian (SAS)
AF:
0.251
AC:
21664
AN:
86192
European-Finnish (FIN)
AF:
0.293
AC:
15632
AN:
53410
Middle Eastern (MID)
AF:
0.381
AC:
2190
AN:
5752
European-Non Finnish (NFE)
AF:
0.369
AC:
409589
AN:
1108612
Other (OTH)
AF:
0.346
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

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
12628
25256
37884
50512
63140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.394
AC:
59849
AN:
152014
Hom.:
12872
Cov.:
0
AF XY:
0.384
AC XY:
28540
AN XY:
74322
show subpopulations
African (AFR)
AF:
0.559
AC:
23149
AN:
41416
American (AMR)
AF:
0.313
AC:
4789
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.310
AC:
1076
AN:
3468
East Asian (EAS)
AF:
0.0408
AC:
212
AN:
5192
South Asian (SAS)
AF:
0.233
AC:
1122
AN:
4824
European-Finnish (FIN)
AF:
0.291
AC:
3076
AN:
10580
Middle Eastern (MID)
AF:
0.388
AC:
114
AN:
294
European-Non Finnish (NFE)
AF:
0.372
AC:
25282
AN:
67932
Other (OTH)
AF:
0.380
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
540
1080
1620
2160
2700
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.300
Hom.:
1329
Asia WGS
AF:
0.169
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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar for variant 12:119688269 A>AAGG . It may be empty.

Other links and lift over

dbSNP: rs10669112; hg19: chr12-120126074; API