dbSNP rs746815273: CCNK:p.Pro482Pro (chr14-99510485-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_001099402.2(CCNK):c.1446G>A(p.Pro482Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P482P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000059 ( 0 hom. )

Consequence

CCNK
NM_001099402.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

0 publications found

Variant links:

Genes affected

CCNK (HGNC:1596): (cyclin K) The protein encoded by this gene is a member of the transcription cyclin family. These cyclins may regulate transcription through their association with and activation of cyclin-dependent kinases (CDK) that phosphorylate the C-terminal domain (CTD) of the large subunit of RNA polymerase II. This gene product may play a dual role in regulating CDK and RNA polymerase II activities. [provided by RefSeq, Jul 2008]

CCNK links:

CCDC85C (HGNC:35459): (coiled-coil domain containing 85C) Predicted to be involved in cerebral cortex development. Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]

CCDC85C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-1.07 with no splicing effect.

BS2

High AC in GnomAd4 at 15 Unknown,AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNK	NM_001099402.2 link	c.1446G>A	p.Pro482Pro	synonymous_variant	Exon 11 of 11	ENST00000389879.9	NP_001092872.1	O75909-3A0A024R6K1
CCDC85C	NM_001144995.2 link	c.*4761C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000380243.9	NP_001138467.1	A6NKD9
CCNK	XM_005268154.5 link	c.1446G>A	p.Pro482Pro	synonymous_variant	Exon 11 of 11		XP_005268211.1	O75909-3A0A024R6K1
CCNK	XM_047431839.1 link	c.1446G>A	p.Pro482Pro	synonymous_variant	Exon 12 of 12		XP_047287795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCNK	ENST00000389879.9 link	c.1446G>A	p.Pro482Pro	synonymous_variant	Exon 11 of 11	5	NM_001099402.2	ENSP00000374529.5	O75909-3
CCNK	ENST00000553865.1 link	n.4598G>A		non_coding_transcript_exon_variant	Exon 5 of 5	1
CCDC85C	ENST00000380243.9 link	c.*4761C>T		3_prime_UTR_variant	Exon 6 of 6	5	NM_001144995.2	ENSP00000369592.4	A6NKD9
CCNK	ENST00000555049.5 link	c.1117+3338G>A		intron_variant	Intron 10 of 10	1		ENSP00000452307.1	G3V5E1

Frequencies

GnomAD3 genomes

AF:

0.00107

AC:

AN:

13972

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0150

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000128

AC:

AN:

101400

AF XY:

0.000146

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000577

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000281

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000587

AC:

AN:

613054

Hom.:

Cov.:

AF XY:

0.0000551

AC XY:

AN XY:

308268

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

14394

American (AMR)

AF:

0.00116

AC:

AN:

22386

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10326

East Asian (EAS)

AF:

0.00

AC:

AN:

9482

South Asian (SAS)

AF:

0.00

AC:

AN:

42182

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17394

Middle Eastern (MID)

AF:

0.000623

AC:

AN:

1606

European-Non Finnish (NFE)

AF:

0.0000106

AC:

AN:

472094

Other (OTH)

AF:

0.000172

AC:

AN:

23190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00107

AC:

AN:

13978

Hom.:

Cov.:

AF XY:

0.00179

AC XY:

AN XY:

6704

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

3278

American (AMR)

AF:

0.0150

AC:

AN:

1002

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

406

East Asian (EAS)

AF:

0.00

AC:

AN:

388

South Asian (SAS)

AF:

0.00

AC:

AN:

438

European-Finnish (FIN)

AF:

0.00

AC:

AN:

656

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

7468

Other (OTH)

AF:

0.00

AC:

AN:

222

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

(source)

DANN

Benign

0.58

PhyloP100

-1.1

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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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rs746815273

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over