7-92615316-TATACA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001145306.2(CDK6):​c.835-35_835-31del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,525,002 control chromosomes in the GnomAD database, including 38,355 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2993 hom., cov: 27)
Exomes 𝑓: 0.22 ( 35362 hom. )

Consequence

CDK6
NM_001145306.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.862
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 7-92615316-TATACA-T is Benign according to our data. Variant chr7-92615316-TATACA-T is described in ClinVar as [Benign]. Clinvar id is 1252462.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDK6NM_001145306.2 linkuse as main transcriptc.835-35_835-31del intron_variant ENST00000424848.3 NP_001138778.1
CDK6NM_001259.8 linkuse as main transcriptc.835-35_835-31del intron_variant NP_001250.1
CDK6XM_047419716.1 linkuse as main transcriptc.835-35_835-31del intron_variant XP_047275672.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDK6ENST00000424848.3 linkuse as main transcriptc.835-35_835-31del intron_variant 1 NM_001145306.2 ENSP00000397087 P1
CDK6ENST00000265734.8 linkuse as main transcriptc.835-35_835-31del intron_variant 1 ENSP00000265734 P1
CDK6ENST00000467166.1 linkuse as main transcriptn.207-35_207-31del intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27294
AN:
151956
Hom.:
2999
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.0722
Gnomad AMI
AF:
0.322
Gnomad AMR
AF:
0.165
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.0163
Gnomad SAS
AF:
0.104
Gnomad FIN
AF:
0.222
Gnomad MID
AF:
0.272
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.211
GnomAD3 exomes
AF:
0.183
AC:
44981
AN:
245744
Hom.:
4844
AF XY:
0.186
AC XY:
24761
AN XY:
133216
show subpopulations
Gnomad AFR exome
AF:
0.0681
Gnomad AMR exome
AF:
0.124
Gnomad ASJ exome
AF:
0.282
Gnomad EAS exome
AF:
0.0135
Gnomad SAS exome
AF:
0.117
Gnomad FIN exome
AF:
0.230
Gnomad NFE exome
AF:
0.245
Gnomad OTH exome
AF:
0.215
GnomAD4 exome
AF:
0.217
AC:
298570
AN:
1372928
Hom.:
35362
AF XY:
0.215
AC XY:
148047
AN XY:
688234
show subpopulations
Gnomad4 AFR exome
AF:
0.0628
Gnomad4 AMR exome
AF:
0.130
Gnomad4 ASJ exome
AF:
0.280
Gnomad4 EAS exome
AF:
0.0157
Gnomad4 SAS exome
AF:
0.114
Gnomad4 FIN exome
AF:
0.231
Gnomad4 NFE exome
AF:
0.240
Gnomad4 OTH exome
AF:
0.213
GnomAD4 genome
AF:
0.179
AC:
27285
AN:
152074
Hom.:
2993
Cov.:
27
AF XY:
0.177
AC XY:
13187
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0721
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.0164
Gnomad4 SAS
AF:
0.104
Gnomad4 FIN
AF:
0.222
Gnomad4 NFE
AF:
0.251
Gnomad4 OTH
AF:
0.209
Alfa
AF:
0.226
Hom.:
750
Bravo
AF:
0.173
Asia WGS
AF:
0.0810
AC:
282
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1610912; hg19: chr7-92244630; API