15-59123268-G-C

Position:

• chr15-59123268-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004701.4(CCNB2):​c.976-249G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,920 control chromosomes in the GnomAD database, including 13,435 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 0.40 (13435 hom., cov: 31)
• Consequence: CCNB2 NM_004701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCNB2	NM_004701.4	c.976-249G>C		intron_variant		ENST00000288207.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNB2	ENST00000288207.7	c.976-249G>C		intron_variant		1	NM_004701.4	P1
	ENST00000559026.1	n.532+1703G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60917 AN: 151802 Hom.: 13398 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.399

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.402 AC: 60999 AN: 151920 Hom.: 13435 Cov.: 31 AF XY: 0.401 AC XY: 29755 AN XY: 74252

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.398

Alfa AF: 0.185 Hom.: 324

Bravo AF: 0.423

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.070
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486878; hg19: chr15-59415467;