Genetic Variant CDK10:c.160+171A>G (chr16-89689495-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052988.5(CDK10):c.160+171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 618,936 control chromosomes in the GnomAD database, including 232,131 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 0.85 ( 55487 hom., cov: 32)

Exomes 𝑓: 0.86 ( 176644 hom. )

Consequence

CDK10
NM_052988.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

104 publications found

Variant links:

Genes affected

CDK10 (HGNC:1770): (cyclin dependent kinase 10) The protein encoded by this gene belongs to the CDK subfamily of the Ser/Thr protein kinase family. The CDK subfamily members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and are known to be essential for cell cycle progression. This kinase has been shown to play a role in cellular proliferation and its function is limited to cell cycle G2-M phase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

CDK10 Gene-Disease associations (from GenCC):

Al Kaissi syndrome
Inheritance: AR Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

CDK10 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK10	NM_052988.5 link	c.160+171A>G		intron_variant	Intron 2 of 12	ENST00000353379.12	NP_443714.3	Q15131-1B7Z537

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK10	ENST00000353379.12 link	c.160+171A>G		intron_variant	Intron 2 of 12	1	NM_052988.5	ENSP00000338673.7		Q15131-1

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128966

AN:

152004

Hom.:

55469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.950

Gnomad AMR

AF:

0.851

Gnomad ASJ

AF:

0.906

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.905

Gnomad FIN

AF:

0.828

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.904

Gnomad OTH

AF:

0.876

GnomAD4 exome

AF:

0.860

AC:

401430

AN:

466812

Hom.:

176644

Cov.:

AF XY:

0.865

AC XY:

212032

AN XY:

245168

show subpopulations

African (AFR)

AF:

0.803

AC:

10407

AN:

12958

American (AMR)

AF:

0.839

AC:

17603

AN:

20982

Ashkenazi Jewish (ASJ)

AF:

0.913

AC:

12995

AN:

14226

East Asian (EAS)

AF:

0.398

AC:

12226

AN:

30702

South Asian (SAS)

AF:

0.920

AC:

43340

AN:

47090

European-Finnish (FIN)

AF:

0.831

AC:

35020

AN:

42158

Middle Eastern (MID)

AF:

0.950

AC:

1893

AN:

1992

European-Non Finnish (NFE)

AF:

0.907

AC:

245460

AN:

270508

Other (OTH)

AF:

0.858

AC:

22486

AN:

26196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2202

4404

6605

8807

11009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.848

AC:

129031

AN:

152124

Hom.:

55487

Cov.:

AF XY:

0.844

AC XY:

62724

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.802

AC:

33274

AN:

41490

American (AMR)

AF:

0.851

AC:

12975

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.906

AC:

3147

AN:

3472

East Asian (EAS)

AF:

0.394

AC:

2036

AN:

5164

South Asian (SAS)

AF:

0.905

AC:

4362

AN:

4822

European-Finnish (FIN)

AF:

0.828

AC:

8765

AN:

10582

Middle Eastern (MID)

AF:

0.959

AC:

282

AN:

294

European-Non Finnish (NFE)

AF:

0.904

AC:

61483

AN:

68024

Other (OTH)

AF:

0.873

AC:

1841

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

912

1824

2737

3649

4561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.882

Hom.:

255951

Bravo

AF:

0.842

Asia WGS

AF:

0.662

AC:

2306

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

7.6

(source)

DANN

Benign

0.36

PhyloP100

-0.079

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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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chr16-89689495-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over