Genetic Variant CIT:c.6187-17_6187-15dupCCT (chr12-119688269-A-AAGG) – ACMG Classification: Benign (-16 pts)

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

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]

CIT links:

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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

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIT	NM_001206999.2 link	c.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
CIT	ENST00000392521.7 link	c.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.:

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

GnomAD3 exomes

AF:

0.311

AC:

78159

AN:

251202

Hom.:

13969

AF XY:

0.312

AC XY:

42429

AN XY:

135774

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 SAS exome

AF:

0.246

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.:

AF XY:

0.347

AC XY:

251829

AN XY:

725606

show subpopulations

Gnomad4 AFR exome

AF:

0.563

Gnomad4 AMR exome

AF:

0.234

Gnomad4 ASJ exome

AF:

0.299

Gnomad4 EAS exome

AF:

0.0563

Gnomad4 SAS exome

AF:

0.251

Gnomad4 FIN exome

AF:

0.293

Gnomad4 NFE exome

AF:

0.369

Gnomad4 OTH exome

AF:

0.346

GnomAD4 genome

AF:

0.394

AC:

59849

AN:

152014

Hom.:

12872

Cov.:

AF XY:

0.384

AC XY:

28540

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.0408

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.380

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

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. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over