12-119805261-C-G

Position:

• chr12-119805261-C-G

Variant summary

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

The ENST00000392521.7(CIT):​c.1112-1872G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,028 control chromosomes in the GnomAD database, including 27,774 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 0.59 (27774 hom., cov: 32)
• Consequence: CIT ENST00000392521.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIT	NM_001206999.2	c.1112-1872G>C		intron_variant		ENST00000392521.7	NP_001193928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CIT	ENST00000392521.7	c.1112-1872G>C		intron_variant		1	NM_001206999.2	ENSP00000376306	P1
CIT	ENST00000261833.11	c.1112-1872G>C		intron_variant		1		ENSP00000261833
CIT	ENST00000536325.1	c.267+44913G>C		intron_variant		3		ENSP00000443199

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89878 AN: 151910 Hom.: 27762 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.591 AC: 89917 AN: 152028 Hom.: 27774 Cov.: 32 AF XY: 0.599 AC XY: 44528 AN XY: 74298

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.634

Alfa AF: 0.595 Hom.: 3413

Bravo AF: 0.590

Asia WGS AF: 0.771 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.76

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: rs10744743; hg19: chr12-120243065;