Genetic Variant CCNF:c.279-142_279-129delCACATATATATATA (chr16-2435662-CACACATATATATAT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001761.3(CCNF):c.279-142_279-129delCACATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 16 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CCNF
NM_001761.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.181

Variant links:

Genes affected

CCNF (HGNC:1591): (cyclin F) This gene encodes a member of the cyclin family. Cyclins are important regulators of cell cycle transitions through their ability to bind and activate cyclin-dependent protein kinases. This member also belongs to the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class and it was one of the first proteins in which the F-box motif was identified. [provided by RefSeq, Jul 2008]

CCNF links:

ENSG00000285970 (HGNC:):

ENSG00000285970 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 16-2435662-CACACATATATATAT-C is Benign according to our data. Variant chr16-2435662-CACACATATATATAT-C is described in ClinVar as [Benign]. Clinvar id is 1249938.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNF	NM_001761.3 link	c.279-142_279-129delCACATATATATATA		intron_variant	Intron 3 of 16	ENST00000397066.9	NP_001752.2	P41002Q59HD0
CCNF	NM_001323538.2 link	c.-646-142_-646-129delCACATATATATATA		intron_variant	Intron 2 of 15		NP_001310467.1	Q59HD0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCNF	ENST00000397066.9 link	c.279-143_279-130delACACATATATATAT	intron_variant	Intron 3 of 16	1	NM_001761.3	ENSP00000380256.4	P41002
CCNF	ENST00000293968.11 link	n.172-143_172-130delACACATATATATAT	intron_variant	Intron 2 of 15	1		ENSP00000293968.7	H0Y2P7
CCNF	ENST00000569093.1 link	n.312-143_312-130delACACATATATATAT	intron_variant	Intron 3 of 3	2
ENSG00000285970	ENST00000648756.1 link	n.372+182_372+195delATATATATATGTGT	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0293

AC:

786

AN:

26792

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0689

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000270

Gnomad OTH

AF:

0.0276

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

36092

Hom.:

AF XY:

0.00

AC XY:

AN XY:

20564

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0293

AC:

787

AN:

26842

Hom.:

Cov.:

AF XY:

0.0273

AC XY:

337

AN XY:

12348

show subpopulations

Gnomad4 AFR

AF:

0.0687

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000270

Gnomad4 OTH

AF:

0.0276

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 03, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over