15-59107350-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004701.4(CCNB2):ā€‹c.53C>Gā€‹(p.Thr18Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

CCNB2
NM_004701.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.521
Variant links:
Genes affected
CCNB2 (HGNC:1580): (cyclin B2) Cyclin B2 is a member of the cyclin family, specifically the B-type cyclins. The B-type cyclins, B1 and B2, associate with p34cdc2 and are essential components of the cell cycle regulatory machinery. B1 and B2 differ in their subcellular localization. Cyclin B1 co-localizes with microtubules, whereas cyclin B2 is primarily associated with the Golgi region. Cyclin B2 also binds to transforming growth factor beta RII and thus cyclin B2/cdc2 may play a key role in transforming growth factor beta-mediated cell cycle control. [provided by RefSeq, Jul 2008]

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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;
BP4
Computational evidence support a benign effect (MetaRNN=0.07867816).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCNB2NM_004701.4 linkc.53C>G p.Thr18Arg missense_variant Exon 2 of 9 ENST00000288207.7 NP_004692.1 O95067

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCNB2ENST00000288207.7 linkc.53C>G p.Thr18Arg missense_variant Exon 2 of 9 1 NM_004701.4 ENSP00000288207.2 O95067
CCNB2ENST00000621385.1 linkc.53C>G p.Thr18Arg missense_variant Exon 2 of 8 1 ENSP00000480809.1 H1UBN3
CCNB2ENST00000559622.5 linkc.24+2058C>G intron_variant Intron 1 of 5 5 ENSP00000453685.1 H0YMP3
CCNB2ENST00000561077.1 linkn.196C>G non_coding_transcript_exon_variant Exon 2 of 3 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000400
AC:
1
AN:
249990
Hom.:
0
AF XY:
0.00000739
AC XY:
1
AN XY:
135258
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000328
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000138
AC:
2
AN:
1453460
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
723160
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000233
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.061
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
2.3
DANN
Benign
0.25
DEOGEN2
Benign
0.055
T;.
Eigen
Benign
-0.98
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.44
T;T
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.079
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
L;.
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-0.21
N;.
REVEL
Benign
0.053
Sift
Benign
0.63
T;.
Sift4G
Benign
0.54
T;T
Polyphen
0.0
B;.
Vest4
0.20
MutPred
0.39
Gain of MoRF binding (P = 0.0087);Gain of MoRF binding (P = 0.0087);
MVP
0.32
MPC
0.12
ClinPred
0.022
T
GERP RS
0.017
Varity_R
0.028
gMVP
0.30

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: rs768589001; hg19: chr15-59399549; API