rs549586410

Variant summary

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

The NM_004701.4(CCNB2):​c.25G>A​(p.Val9Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,532,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

CCNB2
NM_004701.4 missense, splice_region

Scores

3
16
Splicing: ADA: 0.005687
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.58
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]

Genome browser will be placed here

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=0.08073327).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCNB2NM_004701.4 linkc.25G>A p.Val9Met missense_variant, splice_region_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.25G>A p.Val9Met missense_variant, splice_region_variant Exon 2 of 9 1 NM_004701.4 ENSP00000288207.2 O95067
CCNB2ENST00000621385.1 linkc.25G>A p.Val9Met missense_variant, splice_region_variant Exon 2 of 8 1 ENSP00000480809.1 H1UBN3
CCNB2ENST00000559622.5 linkc.24+2030G>A intron_variant Intron 1 of 5 5 ENSP00000453685.1 H0YMP3
CCNB2ENST00000561077.1 linkn.168G>A splice_region_variant, non_coding_transcript_exon_variant Exon 2 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.0000416
AC:
6
AN:
144360
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000780
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000429
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000150
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000281
AC:
6
AN:
213566
Hom.:
0
AF XY:
0.0000258
AC XY:
3
AN XY:
116428
show subpopulations
Gnomad AFR exome
AF:
0.0000676
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000636
Gnomad SAS exome
AF:
0.000167
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000108
AC:
15
AN:
1387934
Hom.:
0
Cov.:
32
AF XY:
0.0000174
AC XY:
12
AN XY:
688014
show subpopulations
Gnomad4 AFR exome
AF:
0.0000334
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000260
Gnomad4 SAS exome
AF:
0.000159
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000176
GnomAD4 genome
AF:
0.0000415
AC:
6
AN:
144452
Hom.:
0
Cov.:
32
AF XY:
0.0000573
AC XY:
4
AN XY:
69854
show subpopulations
Gnomad4 AFR
AF:
0.0000778
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000430
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000150
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000330
AC:
4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
20
DANN
Uncertain
1.0
DEOGEN2
Benign
0.045
T;.
Eigen
Benign
-0.14
Eigen_PC
Benign
-0.11
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.80
T;T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.081
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
2.0
M;.
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
0.28
N;.
REVEL
Benign
0.039
Sift
Benign
0.21
T;.
Sift4G
Benign
0.19
T;T
Polyphen
0.68
P;.
Vest4
0.36
MutPred
0.23
Gain of disorder (P = 0.045);Gain of disorder (P = 0.045);
MVP
0.67
MPC
0.46
ClinPred
0.052
T
GERP RS
3.1
Varity_R
0.033
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0057
dbscSNV1_RF
Benign
0.12
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: rs549586410; hg19: chr15-59399521; API