Genetic Variant CCNB1:c.706-103_706-100dupTTAA (chr5-69174772-C-CATTA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_031966.4(CCNB1):c.706-103_706-100dupTTAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 835,410 control chromosomes in the GnomAD database, including 133,431 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 27056 hom., cov: 0)

Exomes 𝑓: 0.55 ( 106375 hom. )

Consequence

CCNB1
NM_031966.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Publications

2 publications found

Variant links:

Genes affected

CCNB1 (HGNC:1579): (cyclin B1) The protein encoded by this gene is a regulatory protein involved in mitosis. The gene product complexes with p34(cdc2) to form the maturation-promoting factor (MPF). The encoded protein is necessary for proper control of the G2/M transition phase of the cell cycle. [provided by RefSeq, Aug 2017]

CCNB1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031966.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCNB1	NM_031966.4	MANE Select	c.706-103_706-100dupTTAA	intron	N/A	NP_114172.1
CCNB1	NM_001354844.2		c.706-103_706-100dupTTAA	intron	N/A	NP_001341773.1
CCNB1	NM_001354845.2		c.547-103_547-100dupTTAA	intron	N/A	NP_001341774.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCNB1	ENST00000256442.10	TSL:1 MANE Select	c.706-105_706-104insATTA	intron	N/A	ENSP00000256442.5
CCNB1	ENST00000506572.5	TSL:1	c.706-105_706-104insATTA	intron	N/A	ENSP00000423387.1
CCNB1	ENST00000505500.5	TSL:1	c.706-105_706-104insATTA	intron	N/A	ENSP00000424588.1

Frequencies

GnomAD3 genomes

AF:

0.594

AC:

89838

AN:

151116

Hom.:

27025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.695

Gnomad AMI

AF:

0.655

Gnomad AMR

AF:

0.632

Gnomad ASJ

AF:

0.529

Gnomad EAS

AF:

0.501

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.579

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.576

GnomAD4 exome

AF:

0.550

AC:

376634

AN:

684174

Hom.:

106375

AF XY:

0.554

AC XY:

199573

AN XY:

360308

show subpopulations

African (AFR)

AF:

0.695

AC:

12050

AN:

17326

American (AMR)

AF:

0.637

AC:

19846

AN:

31166

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

8897

AN:

16698

East Asian (EAS)

AF:

0.569

AC:

20531

AN:

36054

South Asian (SAS)

AF:

0.649

AC:

37822

AN:

58248

European-Finnish (FIN)

AF:

0.573

AC:

26394

AN:

46044

Middle Eastern (MID)

AF:

0.554

AC:

2242

AN:

4044

European-Non Finnish (NFE)

AF:

0.522

AC:

229765

AN:

440418

Other (OTH)

AF:

0.558

AC:

19087

AN:

34176

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

8311

16622

24934

33245

41556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3408

6816

10224

13632

17040

<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:

0.595

AC:

89922

AN:

151236

Hom.:

27056

Cov.:

AF XY:

0.598

AC XY:

44112

AN XY:

73796

show subpopulations

African (AFR)

AF:

0.695

AC:

28566

AN:

41112

American (AMR)

AF:

0.632

AC:

9588

AN:

15180

Ashkenazi Jewish (ASJ)

AF:

0.529

AC:

1835

AN:

3468

East Asian (EAS)

AF:

0.500

AC:

2574

AN:

5144

South Asian (SAS)

AF:

0.646

AC:

3107

AN:

4808

European-Finnish (FIN)

AF:

0.579

AC:

6033

AN:

10416

Middle Eastern (MID)

AF:

0.582

AC:

171

AN:

294

European-Non Finnish (NFE)

AF:

0.535

AC:

36245

AN:

67808

Other (OTH)

AF:

0.576

AC:

1210

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1820

3640

5460

7280

9100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.569

Hom.:

2658

Asia WGS

AF:

0.586

AC:

2042

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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5-69174772-CATTA-CATTAATTA

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