Variant chr5-69174772-C-CATTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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	MANE	Protein	UniProt
CCNB1	NM_031966.4 link	c.706-103_706-100dupTTAA	intron_variant	ENST00000256442.10	NP_114172.1	P14635-1
CCNB1	NM_001354844.2 link	c.706-103_706-100dupTTAA	intron_variant		NP_001341773.1
CCNB1	NM_001354845.2 link	c.547-103_547-100dupTTAA	intron_variant		NP_001341774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNB1	ENST00000256442.10 link	c.706-105_706-104insATTA		intron_variant		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

Gnomad4 AFR exome

AF:

0.695

Gnomad4 AMR exome

AF:

0.637

Gnomad4 ASJ exome

AF:

0.533

Gnomad4 EAS exome

AF:

0.569

Gnomad4 SAS exome

AF:

0.649

Gnomad4 FIN exome

AF:

0.573

Gnomad4 NFE exome

AF:

0.522

Gnomad4 OTH exome

AF:

0.558

GnomAD4 genome

AF:

0.595

AC:

89922

AN:

151236

Hom.:

27056

Cov.:

AF XY:

0.598

AC XY:

44112

AN XY:

73796

show subpopulations

Gnomad4 AFR

AF:

0.695

Gnomad4 AMR

AF:

0.632

Gnomad4 ASJ

AF:

0.529

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.646

Gnomad4 FIN

AF:

0.579

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.576

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

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over