7-92647412-C-T

Variant names:

• chr7-92647412-C-T
• rs2282981
• NM_001145306.2:c.647+24014G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001259.8(CDK6):​c.647+24014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 152,208 control chromosomes in the GnomAD database, including 462 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 0.059 (462 hom., cov: 32)
• Consequence: CDK6 NM_001259.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 publications found

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]

CDK6 Gene-Disease associations (from GenCC):

• autosomal recessive primary microcephaly

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• microcephaly 12, primary, autosomal recessive

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

LOC112268009 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001259.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK6	NM_001145306.2	MANE Select	c.647+24014G>A		intron	N/A	NP_001138778.1
	CDK6	NM_001259.8		c.647+24014G>A		intron	N/A	NP_001250.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK6	ENST00000424848.3	TSL:1 MANE Select	c.647+24014G>A		intron	N/A	ENSP00000397087.3
	CDK6	ENST00000265734.8	TSL:1	c.647+24014G>A		intron	N/A	ENSP00000265734.4
	CDK6	ENST00000906280.1		c.647+24014G>A		intron	N/A	ENSP00000576339.1

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9034 AN: 152088 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0594 AC: 9044 AN: 152208 Hom.: 462 Cov.: 32 AF XY: 0.0653 AC XY: 4859 AN XY: 74418

African (AFR) AF: 0.100 AC: 4155 AN: 41530

American (AMR) AF: 0.0313 AC: 478 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3472

East Asian (EAS) AF: 0.160 AC: 826 AN: 5166

South Asian (SAS) AF: 0.202 AC: 974 AN: 4810

European-Finnish (FIN) AF: 0.0824 AC: 873 AN: 10600

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0217 AC: 1479 AN: 68012

Other (OTH) AF: 0.0624 AC: 132 AN: 2116

Alfa AF: 0.0362 Hom.: 307

Bravo AF: 0.0551

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.55
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2282981; hg19: chr7-92276726;