chr17-39461967-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016507.4(CDK12):c.-105C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.092 ( 46 hom., cov: 0)
Exomes 𝑓: 0.029 ( 317 hom. )
Consequence
CDK12
NM_016507.4 5_prime_UTR
NM_016507.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.01
Genes affected
CDK12 (HGNC:24224): (cyclin dependent kinase 12) Enables RNA polymerase II CTD heptapeptide repeat kinase activity and cyclin binding activity. Involved in phosphorylation of RNA polymerase II C-terminal domain; protein autophosphorylation; and regulation of MAP kinase activity. Located in nuclear speck. Part of cyclin K-CDK12 complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 17-39461967-C-T is Benign according to our data. Variant chr17-39461967-C-T is described in ClinVar as [Benign]. Clinvar id is 1252879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK12 | NM_016507.4 | c.-105C>T | 5_prime_UTR_variant | 1/14 | ENST00000447079.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK12 | ENST00000447079.6 | c.-105C>T | 5_prime_UTR_variant | 1/14 | 1 | NM_016507.4 | P4 | ||
CDK12 | ENST00000430627.6 | c.-105C>T | 5_prime_UTR_variant | 1/14 | 1 | A1 | |||
CDK12 | ENST00000584632.5 | c.-105C>T | 5_prime_UTR_variant | 1/13 | 5 | ||||
CDK12 | ENST00000559663.2 | c.-105C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/21 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0919 AC: 3194AN: 34768Hom.: 46 Cov.: 0
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GnomAD4 exome AF: 0.0290 AC: 19308AN: 665270Hom.: 317 Cov.: 10 AF XY: 0.0276 AC XY: 9461AN XY: 342570
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GnomAD4 genome AF: 0.0918 AC: 3194AN: 34804Hom.: 46 Cov.: 0 AF XY: 0.0906 AC XY: 1550AN XY: 17106
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2019 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at