rs203332

chr12-119772533-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001206999.2(CIT):c.2082+237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,082 control chromosomes in the GnomAD database, including 20,017 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.51 (20017 hom., cov: 32)
• Consequence: CIT NM_001206999.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.829

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 12-119772533-G-A is Benign according to our data. Variant chr12-119772533-G-A is described in ClinVar as [Benign]. Clinvar id is 1240491.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIT	NM_001206999.2	c.2082+237C>T		intron_variant		ENST00000392521.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIT	ENST00000392521.7	c.2082+237C>T		intron_variant		1	NM_001206999.2	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77444 AN: 151964 Hom.: 20001 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.510 AC: 77505 AN: 152082 Hom.: 20017 Cov.: 32 AF XY: 0.510 AC XY: 37890 AN XY: 74322

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.528

Alfa AF: 0.506 Hom.: 3355

Bravo AF: 0.516

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.73
Cadd	Benign	15
Dann	Benign	0.63

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

Other links and lift over

dbSNP: rs203332; hg19: chr12-120210337;