chr15-59107670-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_004701.4(CCNB2):c.267G>A(p.Lys89Lys) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.00903 in 1,611,998 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0062 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0093 ( 78 hom. )
Consequence
CCNB2
NM_004701.4 splice_region, synonymous
NM_004701.4 splice_region, synonymous
Scores
2
Splicing: ADA: 0.9996
2
Clinical Significance
Conservation
PhyloP100: 5.69
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP6
Variant 15-59107670-G-A is Benign according to our data. Variant chr15-59107670-G-A is described in ClinVar as [Benign]. Clinvar id is 777248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 4 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNB2 | ENST00000288207.7 | c.267G>A | p.Lys89Lys | splice_region_variant, synonymous_variant | Exon 3 of 9 | 1 | NM_004701.4 | ENSP00000288207.2 | ||
CCNB2 | ENST00000621385.1 | c.267G>A | p.Lys89Lys | splice_region_variant, synonymous_variant | Exon 3 of 8 | 1 | ENSP00000480809.1 | |||
CCNB2 | ENST00000559622.5 | c.24+2378G>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000453685.1 | ||||
CCNB2 | ENST00000561077.1 | n.516G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00618 AC: 941AN: 152184Hom.: 4 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
941
AN:
152184
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.00572 AC: 1430AN: 250176 AF XY: 0.00580 show subpopulations
GnomAD2 exomes
AF:
AC:
1430
AN:
250176
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00933 AC: 13612AN: 1459696Hom.: 78 Cov.: 32 AF XY: 0.00919 AC XY: 6676AN XY: 726236 show subpopulations
GnomAD4 exome
AF:
AC:
13612
AN:
1459696
Hom.:
Cov.:
32
AF XY:
AC XY:
6676
AN XY:
726236
Gnomad4 AFR exome
AF:
AC:
49
AN:
33386
Gnomad4 AMR exome
AF:
AC:
93
AN:
44480
Gnomad4 ASJ exome
AF:
AC:
11
AN:
26104
Gnomad4 EAS exome
AF:
AC:
0
AN:
39690
Gnomad4 SAS exome
AF:
AC:
47
AN:
86104
Gnomad4 FIN exome
AF:
AC:
194
AN:
53314
Gnomad4 NFE exome
AF:
AC:
12779
AN:
1110542
Gnomad4 Remaining exome
AF:
AC:
434
AN:
60314
Heterozygous variant carriers
0
678
1357
2035
2714
3392
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
472
944
1416
1888
2360
<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: 0.00619 AC: 942AN: 152302Hom.: 4 Cov.: 32 AF XY: 0.00555 AC XY: 413AN XY: 74478 show subpopulations
GnomAD4 genome
AF:
AC:
942
AN:
152302
Hom.:
Cov.:
32
AF XY:
AC XY:
413
AN XY:
74478
Gnomad4 AFR
AF:
AC:
0.00190087
AN:
0.00190087
Gnomad4 AMR
AF:
AC:
0.00470404
AN:
0.00470404
Gnomad4 ASJ
AF:
AC:
0.000576701
AN:
0.000576701
Gnomad4 EAS
AF:
AC:
0
AN:
0
Gnomad4 SAS
AF:
AC:
0.000829187
AN:
0.000829187
Gnomad4 FIN
AF:
AC:
0.00235538
AN:
0.00235538
Gnomad4 NFE
AF:
AC:
0.0110115
AN:
0.0110115
Gnomad4 OTH
AF:
AC:
0.00520341
AN:
0.00520341
Heterozygous variant carriers
0
48
96
144
192
240
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
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100
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Jun 26, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Mutation Taster
=14/86
disease causing
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 36
DS_DL_spliceai
Position offset: 0
Find out detailed SpliceAI scores and Pangolin per-transcript scores at