rs42235

chr7-92618762-C-T

Variant summary

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

The NM_001145306.2(CDK6):c.699-555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,066 control chromosomes in the GnomAD database, including 7,817 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 0.31 (7817 hom., cov: 32)
• Consequence: CDK6 NM_001145306.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

CDK6 (HGNC:1777): (cyclin dependent kinase 6) The protein encoded by this gene is a member of the CMGC family of serine/threonine protein kinases. This kinase is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression and G1/S transition. The activity of this kinase first appears in mid-G1 phase, which is controlled by the regulatory subunits including D-type cyclins and members of INK4 family of CDK inhibitors. This kinase, as well as CDK4, has been shown to phosphorylate, and thus regulate the activity of, tumor suppressor protein Rb. Altered expression of this gene has been observed in multiple human cancers. A mutation in this gene resulting in reduced cell proliferation, and impaired cell motility and polarity, and has been identified in patients with primary microcephaly. [provided by RefSeq, Aug 2017]

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 (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK6	NM_001145306.2	c.699-555G>A		intron_variant		ENST00000424848.3
CDK6	NM_001259.8	c.699-555G>A		intron_variant
CDK6	XM_047419716.1	c.699-555G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK6	ENST00000424848.3	c.699-555G>A		intron_variant		1	NM_001145306.2	P1
CDK6	ENST00000265734.8	c.699-555G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46999 AN: 151948 Hom.: 7809 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.309 AC: 47050 AN: 152066 Hom.: 7817 Cov.: 32 AF XY: 0.304 AC XY: 22593 AN XY: 74332

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.0260

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.303

Alfa AF: 0.302 Hom.: 10082

Bravo AF: 0.311

Asia WGS AF: 0.133 AC: 465 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	0.36
Dann	Benign	0.33

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

LitVar

Other links and lift over

dbSNP: rs42235; hg19: chr7-92248076;