rs258322

chr16-89689495-A-Gchr16-89689495-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CDK10	NM_052988.5	c.160+171A>G		intron_variant		ENST00000353379.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK10	ENST00000353379.12	c.160+171A>G		intron_variant		1	NM_052988.5	P1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128966 AN: 152004 Hom.: 55469 Cov.: 32

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.: 5 AF XY: 0.865 AC XY: 212032 AN XY: 245168

Gnomad4 AFR exome AF: 0.803

Gnomad4 AMR exome AF: 0.839

Gnomad4 ASJ exome AF: 0.913

Gnomad4 EAS exome AF: 0.398

Gnomad4 SAS exome AF: 0.920

Gnomad4 FIN exome AF: 0.831

Gnomad4 NFE exome AF: 0.907

Gnomad4 OTH exome AF: 0.858

GnomAD4 genome AF: 0.848 AC: 129031 AN: 152124 Hom.: 55487 Cov.: 32 AF XY: 0.844 AC XY: 62724 AN XY: 74356

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.873

Alfa AF: 0.891 Hom.: 108473

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
Dann	Benign	0.36

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

LitVar

Other links and lift over

dbSNP: rs258322; hg19: chr16-89755903;