rs201214475
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM2PP2BP4_ModerateBP6
The NM_001206999.2(CIT):c.4012C>T(p.Arg1338Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000176 in 1,611,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00018 ( 1 hom. )
Consequence
CIT
NM_001206999.2 missense
NM_001206999.2 missense
Scores
1
5
11
Clinical Significance
Conservation
PhyloP100: 5.01
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, CIT
BP4
?
Computational evidence support a benign effect (MetaRNN=0.15229696).
BP6
?
Variant 12-119718401-G-A is Benign according to our data. Variant chr12-119718401-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 521138.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIT | NM_001206999.2 | c.4012C>T | p.Arg1338Cys | missense_variant | 32/48 | ENST00000392521.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIT | ENST00000392521.7 | c.4012C>T | p.Arg1338Cys | missense_variant | 32/48 | 1 | NM_001206999.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152162Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000210 AC: 52AN: 248204Hom.: 0 AF XY: 0.000171 AC XY: 23AN XY: 134160
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GnomAD4 exome AF: 0.000183 AC: 267AN: 1459652Hom.: 1 Cov.: 32 AF XY: 0.000182 AC XY: 132AN XY: 725970
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GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152280Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74444
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.98
.;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at