rs7311975

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001206999.2(CIT):c.4307-40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 1,603,300 control chromosomes in the GnomAD database, including 5,915 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 2616 hom., cov: 33)

Exomes 𝑓: 0.044 ( 3299 hom. )

Consequence

CIT
NM_001206999.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.54

Publications

16 publications found

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:

MIR1178 (HGNC:35259): (microRNA 1178) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1178 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 12-119713688-T-C is Benign according to our data. Variant chr12-119713688-T-C is described in ClinVar as Benign. ClinVar VariationId is 1279215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001206999.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CIT	NM_001206999.2	MANE Select	c.4307-40A>G	intron	N/A	NP_001193928.1	O14578-4
CIT	NM_007174.3		c.4181-40A>G	intron	N/A	NP_009105.1	O14578-1
MIR1178	NR_031589.1		n.37A>G	non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CIT	ENST00000392521.7	TSL:1 MANE Select	c.4307-40A>G	intron	N/A	ENSP00000376306.2	O14578-4
CIT	ENST00000261833.11	TSL:1	c.4181-40A>G	intron	N/A	ENSP00000261833.7	O14578-1
CIT	ENST00000928243.1		c.4307-40A>G	intron	N/A	ENSP00000598302.1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18809

AN:

152150

Hom.:

2604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0678

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.0265

Gnomad SAS

AF:

0.0339

Gnomad FIN

AF:

0.0359

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0370

Gnomad OTH

AF:

0.0966

GnomAD2 exomes

AF:

0.0551

AC:

13688

AN:

248324

AF XY:

0.0491

show subpopulations

Gnomad AFR exome

AF:

0.351

Gnomad AMR exome

AF:

0.0406

Gnomad ASJ exome

AF:

0.0136

Gnomad EAS exome

AF:

0.0224

Gnomad FIN exome

AF:

0.0331

Gnomad NFE exome

AF:

0.0362

Gnomad OTH exome

AF:

0.0428

GnomAD4 exome

AF:

0.0440

AC:

63895

AN:

1451032

Hom.:

3299

Cov.:

AF XY:

0.0427

AC XY:

30886

AN XY:

722578

show subpopulations

African (AFR)

AF:

0.356

AC:

11864

AN:

33286

American (AMR)

AF:

0.0422

AC:

1884

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.0124

AC:

323

AN:

26064

East Asian (EAS)

AF:

0.0384

AC:

1521

AN:

39658

South Asian (SAS)

AF:

0.0350

AC:

3009

AN:

85956

European-Finnish (FIN)

AF:

0.0306

AC:

1632

AN:

53362

Middle Eastern (MID)

AF:

0.0486

AC:

279

AN:

5744

European-Non Finnish (NFE)

AF:

0.0364

AC:

40114

AN:

1102220

Other (OTH)

AF:

0.0544

AC:

3269

AN:

60048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3125

6250

9375

12500

15625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1644

3288

4932

6576

8220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.124

AC:

18862

AN:

152268

Hom.:

2616

Cov.:

AF XY:

0.122

AC XY:

9050

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.345

AC:

14347

AN:

41526

American (AMR)

AF:

0.0677

AC:

1035

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

AN:

3468

East Asian (EAS)

AF:

0.0266

AC:

138

AN:

5186

South Asian (SAS)

AF:

0.0337

AC:

163

AN:

4830

European-Finnish (FIN)

AF:

0.0359

AC:

382

AN:

10626

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0370

AC:

2516

AN:

68014

Other (OTH)

AF:

0.0956

AC:

202

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

685

1371

2056

2742

3427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0268

Hom.:

Bravo

AF:

0.140

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.023

(source)

DANN

Benign

0.41

PhyloP100

-3.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over