chr7-92650049-T-C

Variant names:

• chr7-92650049-T-C
• rs2282983
• NM_001145306.2:c.647+21377A>G

Variant summary

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

The NM_001145306.2(CDK6):​c.647+21377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,048 control chromosomes in the GnomAD database, including 14,933 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.43 (14933 hom., cov: 32)
• Consequence: CDK6 NM_001145306.2 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.03
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145306.2. 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+21377A>G		intron	N/A	NP_001138778.1	Q00534
	CDK6	NM_001259.8		c.647+21377A>G		intron	N/A	NP_001250.1	Q00534

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK6	ENST00000424848.3	TSL:1 MANE Select	c.647+21377A>G		intron	N/A	ENSP00000397087.3	Q00534
	CDK6	ENST00000265734.8	TSL:1	c.647+21377A>G		intron	N/A	ENSP00000265734.4	Q00534
	CDK6	ENST00000906280.1		c.647+21377A>G		intron	N/A	ENSP00000576339.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65731 AN: 151932 Hom.: 14909 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.433 AC: 65815 AN: 152048 Hom.: 14933 Cov.: 32 AF XY: 0.436 AC XY: 32360 AN XY: 74300

African (AFR) AF: 0.578 AC: 23970 AN: 41470

American (AMR) AF: 0.436 AC: 6664 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5172

South Asian (SAS) AF: 0.385 AC: 1857 AN: 4824

European-Finnish (FIN) AF: 0.381 AC: 4027 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24862 AN: 67958

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.394 Hom.: 34643

Bravo AF: 0.443

Asia WGS AF: 0.404 AC: 1405 AN: 3476

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Behcet disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2282983; hg19: chr7-92279363;