7-92615316-TATACA-T
Position:
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
NM_001145306.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.862
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]
Genome browser will be placed here
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 |
---|---|---|---|---|---|---|---|---|
CDK6 | NM_001145306.2 | c.835-35_835-31del | intron_variant | ENST00000424848.3 | NP_001138778.1 | |||
CDK6 | NM_001259.8 | c.835-35_835-31del | intron_variant | NP_001250.1 | ||||
CDK6 | XM_047419716.1 | c.835-35_835-31del | intron_variant | XP_047275672.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK6 | ENST00000424848.3 | c.835-35_835-31del | intron_variant | 1 | NM_001145306.2 | ENSP00000397087 | P1 | |||
CDK6 | ENST00000265734.8 | c.835-35_835-31del | intron_variant | 1 | ENSP00000265734 | P1 | ||||
CDK6 | ENST00000467166.1 | n.207-35_207-31del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.180 AC: 27294AN: 151956Hom.: 2999 Cov.: 27
GnomAD3 genomes
AF:
AC:
27294
AN:
151956
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.183 AC: 44981AN: 245744Hom.: 4844 AF XY: 0.186 AC XY: 24761AN XY: 133216
GnomAD3 exomes
AF:
AC:
44981
AN:
245744
Hom.:
AF XY:
AC XY:
24761
AN XY:
133216
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.217 AC: 298570AN: 1372928Hom.: 35362 AF XY: 0.215 AC XY: 148047AN XY: 688234
GnomAD4 exome
AF:
AC:
298570
AN:
1372928
Hom.:
AF XY:
AC XY:
148047
AN XY:
688234
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.179 AC: 27285AN: 152074Hom.: 2993 Cov.: 27 AF XY: 0.177 AC XY: 13187AN XY: 74354
GnomAD4 genome
AF:
AC:
27285
AN:
152074
Hom.:
Cov.:
27
AF XY:
AC XY:
13187
AN XY:
74354
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
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 submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at