1-1707458-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024011.4(CDK11A):āc.1196T>Cā(p.Leu399Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00283 in 148,598 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0028 ( 2 hom., cov: 28)
Exomes š: 0.00019 ( 22 hom. )
Failed GnomAD Quality Control
Consequence
CDK11A
NM_024011.4 missense
NM_024011.4 missense
Scores
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.41
Genes affected
CDK11A (HGNC:1730): (cyclin dependent kinase 11A) This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently deleted or altered in neuroblastoma. The protein kinase encoded by this gene can be cleaved by caspases and may play a role in cell apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005014986).
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK11A | NM_024011.4 | c.1196T>C | p.Leu399Ser | missense_variant | 11/20 | ENST00000404249.8 | NP_076916.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK11A | ENST00000404249.8 | c.1196T>C | p.Leu399Ser | missense_variant | 11/20 | 1 | NM_024011.4 | ENSP00000384442.3 |
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 420AN: 148488Hom.: 2 Cov.: 28
GnomAD3 genomes
AF:
AC:
420
AN:
148488
Hom.:
Cov.:
28
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: 0.00348 AC: 849AN: 244268Hom.: 37 AF XY: 0.00328 AC XY: 435AN XY: 132584
GnomAD3 exomes
AF:
AC:
849
AN:
244268
Hom.:
AF XY:
AC XY:
435
AN XY:
132584
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 Data not reliable, filtered out with message: AS_VQSR AF: 0.000192 AC: 279AN: 1455460Hom.: 22 Cov.: 31 AF XY: 0.000171 AC XY: 124AN XY: 723980
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
279
AN:
1455460
Hom.:
Cov.:
31
AF XY:
AC XY:
124
AN XY:
723980
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: 0.00283 AC: 421AN: 148598Hom.: 2 Cov.: 28 AF XY: 0.00266 AC XY: 193AN XY: 72622
GnomAD4 genome
AF:
AC:
421
AN:
148598
Hom.:
Cov.:
28
AF XY:
AC XY:
193
AN XY:
72622
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.:
ExAC
AF:
AC:
1102
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;.;.;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;.;.;.;N
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.0
.;.;B;.;B;.
Vest4
MVP
MPC
0.27
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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