chr7-39950791-A-ACCGCCGCCGCCC
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP5_ModerateBS2
The NM_003718.5(CDK13):c.159_170dup(p.Pro54_Pro57dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,463,408 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000038 ( 0 hom. )
Consequence
CDK13
NM_003718.5 inframe_insertion
NM_003718.5 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.483
Genes affected
CDK13 (HGNC:1733): (cyclin dependent kinase 13) The protein encoded by this gene is a member of the cyclin-dependent serine/threonine protein kinase family. Members of this family are well known for their essential roles as master switches in cell cycle control. The exact function of this protein has not yet been determined, but it may play a role in mRNA processing and may be involved in regulation of hematopoiesis. Alternatively spliced transcript variants have been described.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PP5
Variant 7-39950791-A-ACCGCCGCCGCCC is Pathogenic according to our data. Variant chr7-39950791-A-ACCGCCGCCGCCC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1723513.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK13 | NM_003718.5 | c.159_170dup | p.Pro54_Pro57dup | inframe_insertion | 1/14 | ENST00000181839.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK13 | ENST00000181839.10 | c.159_170dup | p.Pro54_Pro57dup | inframe_insertion | 1/14 | 1 | NM_003718.5 | P3 | |
CDK13 | ENST00000340829.10 | c.159_170dup | p.Pro54_Pro57dup | inframe_insertion | 1/14 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 151054Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000381 AC: 5AN: 1312354Hom.: 0 Cov.: 33 AF XY: 0.00000464 AC XY: 3AN XY: 646928
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GnomAD4 genome AF: 0.0000199 AC: 3AN: 151054Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73792
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In-frame insertion of 4 amino acids in a non-repeat region; Has not been previously published as pathogenic or benign to our knowledge - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at