dbSNP rs164390: CCNB1:c.-76G>T (chr5-69167187-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031966.4(CCNB1):c.-76G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 1,311,346 control chromosomes in the GnomAD database, including 116,800 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14034 hom., cov: 33)

Exomes 𝑓: 0.42 ( 102766 hom. )

Consequence

CCNB1
NM_031966.4 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.946

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:

ENSG00000248664 (HGNC:):

ENSG00000248664 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNB1	NM_031966.4 link	c.-76G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 9	ENST00000256442.10	NP_114172.1	P14635-1
CCNB1	NM_031966.4 link	c.-76G>T		5_prime_UTR_variant	Exon 1 of 9	ENST00000256442.10	NP_114172.1	P14635-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNB1	ENST00000256442.10 link	c.-76G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 9	1	NM_031966.4	ENSP00000256442.5		P14635-1
CCNB1	ENST00000256442.10 link	c.-76G>T		5_prime_UTR_variant	Exon 1 of 9	1	NM_031966.4	ENSP00000256442.5		P14635-1

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65161

AN:

152006

Hom.:

14020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.407

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.418

AC:

484824

AN:

1159222

Hom.:

102766

Cov.:

AF XY:

0.421

AC XY:

242807

AN XY:

576556

show subpopulations

African (AFR)

AF:

0.459

AC:

11615

AN:

25306

American (AMR)

AF:

0.445

AC:

12227

AN:

27474

Ashkenazi Jewish (ASJ)

AF:

0.374

AC:

6971

AN:

18636

East Asian (EAS)

AF:

0.514

AC:

17446

AN:

33912

South Asian (SAS)

AF:

0.542

AC:

35559

AN:

65588

European-Finnish (FIN)

AF:

0.394

AC:

17899

AN:

45422

Middle Eastern (MID)

AF:

0.409

AC:

1352

AN:

3306

European-Non Finnish (NFE)

AF:

0.406

AC:

361344

AN:

890666

Other (OTH)

AF:

0.417

AC:

20411

AN:

48912

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13961

27921

41882

55842

69803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.429

AC:

65202

AN:

152124

Hom.:

14034

Cov.:

AF XY:

0.430

AC XY:

32007

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.452

AC:

18777

AN:

41500

American (AMR)

AF:

0.449

AC:

6867

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.367

AC:

1272

AN:

3466

East Asian (EAS)

AF:

0.458

AC:

2367

AN:

5164

South Asian (SAS)

AF:

0.550

AC:

2652

AN:

4822

European-Finnish (FIN)

AF:

0.381

AC:

4030

AN:

10580

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.407

AC:

27652

AN:

67986

Other (OTH)

AF:

0.413

AC:

869

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2032

4064

6097

8129

10161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.411

Hom.:

15897

Bravo

AF:

0.431

Asia WGS

AF:

0.519

AC:

1803

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.4

(source)

DANN

Benign

0.60

PhyloP100

-0.95

PromoterAI

-0.020

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

Details are displayed if max score is > 0.2

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

Publications

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rs164390

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over