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12-119689930-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001206999.2(CIT):c.6186+221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 152,262 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.026 ( 74 hom., cov: 31)

Consequence

CIT
NM_001206999.2 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.212
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]

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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=-0.91).
BP6
Variant 12-119689930-C-T is Benign according to our data. Variant chr12-119689930-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1202291.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0261 (3976/152262) while in subpopulation AFR AF= 0.0409 (1702/41566). AF 95% confidence interval is 0.0393. There are 74 homozygotes in gnomad4. There are 1904 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd at 73 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CITNM_001206999.2 linkuse as main transcriptc.6186+221G>A intron_variant ENST00000392521.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CITENST00000392521.7 linkuse as main transcriptc.6186+221G>A intron_variant 1 NM_001206999.2 P1O14578-4

Frequencies

GnomAD3 genomes
AF:
0.0261
AC:
3964
AN:
152144
Hom.:
73
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0407
Gnomad AMI
AF:
0.00220
Gnomad AMR
AF:
0.0248
Gnomad ASJ
AF:
0.00749
Gnomad EAS
AF:
0.0222
Gnomad SAS
AF:
0.0143
Gnomad FIN
AF:
0.0203
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0209
Gnomad OTH
AF:
0.0240
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0261
AC:
3976
AN:
152262
Hom.:
74
Cov.:
31
AF XY:
0.0256
AC XY:
1904
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0409
Gnomad4 AMR
AF:
0.0247
Gnomad4 ASJ
AF:
0.00749
Gnomad4 EAS
AF:
0.0223
Gnomad4 SAS
AF:
0.0141
Gnomad4 FIN
AF:
0.0203
Gnomad4 NFE
AF:
0.0209
Gnomad4 OTH
AF:
0.0233
Alfa
AF:
0.0130
Hom.:
4
Bravo
AF:
0.0259
Asia WGS
AF:
0.0180
AC:
62
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJul 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
2.2
Dann
Benign
0.83

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.

Other links and lift over

dbSNP: rs111356250; hg19: chr12-120127735; API