Variant 12-119782478-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001206999.2(CIT):c.1665+40T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,602,542 control chromosomes in the GnomAD database, including 177,630 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.45 ( 15600 hom., cov: 31)

Exomes 𝑓: 0.47 ( 162030 hom. )

Consequence

CIT
NM_001206999.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.91

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BP6

Variant 12-119782478-A-G is Benign according to our data. Variant chr12-119782478-A-G is described in ClinVar as [Benign]. Clinvar id is 1247335.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIT	NM_001206999.2 linkuse as main transcript	c.1665+40T>C		intron_variant		ENST00000392521.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIT	ENST00000392521.7 linkuse as main transcript	c.1665+40T>C		intron_variant		1	NM_001206999.2	P1	O14578-4

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67614

AN:

151642

Hom.:

15597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.561

Gnomad ASJ

AF:

0.548

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.479

GnomAD3 exomes

AF:

0.478

AC:

117789

AN:

246292

Hom.:

28738

AF XY:

0.475

AC XY:

63375

AN XY:

133322

show subpopulations

Gnomad AFR exome

AF:

0.347

Gnomad AMR exome

AF:

0.595

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.390

Gnomad SAS exome

AF:

0.467

Gnomad FIN exome

AF:

0.496

Gnomad NFE exome

AF:

0.469

Gnomad OTH exome

AF:

0.506

GnomAD4 exome

AF:

0.470

AC:

682233

AN:

1450782

Hom.:

162030

Cov.:

AF XY:

0.470

AC XY:

339036

AN XY:

721032

show subpopulations

Gnomad4 AFR exome

AF:

0.349

Gnomad4 AMR exome

AF:

0.588

Gnomad4 ASJ exome

AF:

0.549

Gnomad4 EAS exome

AF:

0.398

Gnomad4 SAS exome

AF:

0.460

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.474

GnomAD4 genome

AF:

0.446

AC:

67642

AN:

151760

Hom.:

15600

Cov.:

AF XY:

0.446

AC XY:

33101

AN XY:

74140

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.561

Gnomad4 ASJ

AF:

0.548

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.459

Gnomad4 FIN

AF:

0.504

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.476

Alfa

AF:

0.411

Hom.:

2568

Bravo

AF:

0.449

Asia WGS

AF:

0.466

AC:

1621

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.11

DANN

Benign

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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