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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCNB1	NM_031966.4 link	c.706-103_706-100dupTTAA	intron_variant	Intron 5 of 8	ENST00000256442.10	NP_114172.1	P14635-1
CCNB1	NM_001354844.2 link	c.706-103_706-100dupTTAA	intron_variant	Intron 5 of 7		NP_001341773.1
CCNB1	NM_001354845.2 link	c.547-103_547-100dupTTAA	intron_variant	Intron 4 of 7		NP_001341774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNB1	ENST00000256442.10 link	c.706-105_706-104insATTA		intron_variant	Intron 5 of 8	1	NM_031966.4	ENSP00000256442.5		P14635-1

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

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

Alfa

AF:

0.569

Hom.:

2658

Asia WGS

AF:

0.586

AC:

2042

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over