chr17-39462785-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_016507.4(CDK12):c.714G>A(p.Ser238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00971 in 1,614,046 control chromosomes in the GnomAD database, including 1,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.052 ( 665 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 618 hom. )
Consequence
CDK12
NM_016507.4 synonymous
NM_016507.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.03
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 17-39462785-G-A is Benign according to our data. Variant chr17-39462785-G-A is described in ClinVar as [Benign]. Clinvar id is 1250047.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.03 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK12 | NM_016507.4 | c.714G>A | p.Ser238= | synonymous_variant | 1/14 | ENST00000447079.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK12 | ENST00000447079.6 | c.714G>A | p.Ser238= | synonymous_variant | 1/14 | 1 | NM_016507.4 | P4 | |
CDK12 | ENST00000430627.6 | c.714G>A | p.Ser238= | synonymous_variant | 1/14 | 1 | A1 | ||
CDK12 | ENST00000584632.5 | c.714G>A | p.Ser238= | synonymous_variant | 1/13 | 5 | |||
CDK12 | ENST00000559663.2 | c.714G>A | p.Ser238= | synonymous_variant, NMD_transcript_variant | 1/21 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0518 AC: 7878AN: 152058Hom.: 665 Cov.: 32
GnomAD3 genomes
AF:
AC:
7878
AN:
152058
Hom.:
Cov.:
32
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: 0.0141 AC: 3531AN: 251180Hom.: 268 AF XY: 0.0101 AC XY: 1367AN XY: 135838
GnomAD3 exomes
AF:
AC:
3531
AN:
251180
Hom.:
AF XY:
AC XY:
1367
AN XY:
135838
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: 0.00531 AC: 7767AN: 1461870Hom.: 618 Cov.: 32 AF XY: 0.00445 AC XY: 3238AN XY: 727232
GnomAD4 exome
AF:
AC:
7767
AN:
1461870
Hom.:
Cov.:
32
AF XY:
AC XY:
3238
AN XY:
727232
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: 0.0519 AC: 7898AN: 152176Hom.: 665 Cov.: 32 AF XY: 0.0505 AC XY: 3761AN XY: 74406
GnomAD4 genome
AF:
AC:
7898
AN:
152176
Hom.:
Cov.:
32
AF XY:
AC XY:
3761
AN XY:
74406
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:
70
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:4
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 15, 2019 | - - |
CDK12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary breast ovarian cancer syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | National Health Laboratory Service, Universitas Academic Hospital and University of the Free State | Apr 19, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at