rs202984

Positions:

• chr12-119747149-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001206999.2(CIT):​c.2905-4685T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,172 control chromosomes in the GnomAD database, including 45,499 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45499 hom., cov: 32)
• Consequence: CIT NM_001206999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIT	NM_001206999.2	c.2905-4685T>C		intron_variant		ENST00000392521.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIT	ENST00000392521.7	c.2905-4685T>C		intron_variant		1	NM_001206999.2	P1

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117260 AN: 152054 Hom.: 45461 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.771 AC: 117353 AN: 152172 Hom.: 45499 Cov.: 32 AF XY: 0.769 AC XY: 57207 AN XY: 74398

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.795

Alfa AF: 0.783 Hom.: 5803

Bravo AF: 0.772

Asia WGS AF: 0.671 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.37

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: rs202984; hg19: chr12-120184954;