chr7-92671549-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001145306.2(CDK6):c.538-14G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0312 in 1,512,180 control chromosomes in the GnomAD database, including 2,722 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.036 ( 354 hom., cov: 32)
Exomes 𝑓: 0.031 ( 2368 hom. )
Consequence
CDK6
NM_001145306.2 splice_polypyrimidine_tract, intron
NM_001145306.2 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.84
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 7-92671549-C-T is Benign according to our data. Variant chr7-92671549-C-T is described in ClinVar as [Benign]. Clinvar id is 1291635.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK6 | NM_001145306.2 | c.538-14G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000424848.3 | |||
CDK6 | NM_001259.8 | c.538-14G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
CDK6 | XM_047419716.1 | c.538-14G>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK6 | ENST00000424848.3 | c.538-14G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001145306.2 | P1 | |||
CDK6 | ENST00000265734.8 | c.538-14G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
CDK6 | ENST00000473078.1 | n.86-14G>A | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0357 AC: 5427AN: 152168Hom.: 356 Cov.: 32
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GnomAD3 exomes AF: 0.0543 AC: 10536AN: 193982Hom.: 1019 AF XY: 0.0516 AC XY: 5435AN XY: 105386
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GnomAD4 exome AF: 0.0307 AC: 41733AN: 1359894Hom.: 2368 Cov.: 22 AF XY: 0.0310 AC XY: 20945AN XY: 676170
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GnomAD4 genome ? AF: 0.0356 AC: 5427AN: 152286Hom.: 354 Cov.: 32 AF XY: 0.0376 AC XY: 2803AN XY: 74458
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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 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at