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GeneBe

1-1704238-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_024011.4(CDK11A):c.1671C>T(p.His557=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,608,518 control chromosomes in the GnomAD database, including 215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 16 hom., cov: 31)
Exomes 𝑓: 0.0029 ( 199 hom. )

Consequence

CDK11A
NM_024011.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.233
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-1704238-G-A is Benign according to our data. Variant chr1-1704238-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638057.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.233 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 16 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDK11ANM_024011.4 linkuse as main transcriptc.1671C>T p.His557= synonymous_variant 15/20 ENST00000404249.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDK11AENST00000404249.8 linkuse as main transcriptc.1671C>T p.His557= synonymous_variant 15/201 NM_024011.4 P1Q9UQ88-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00180
AC:
272
AN:
150958
Hom.:
16
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000683
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00172
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000851
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00309
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00153
AC:
380
AN:
248096
Hom.:
13
AF XY:
0.00139
AC XY:
187
AN XY:
134666
show subpopulations
Gnomad AFR exome
AF:
0.000454
Gnomad AMR exome
AF:
0.000552
Gnomad ASJ exome
AF:
0.000300
Gnomad EAS exome
AF:
0.000111
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000791
Gnomad NFE exome
AF:
0.00287
Gnomad OTH exome
AF:
0.00166
GnomAD4 exome
AF:
0.00291
AC:
4235
AN:
1457450
Hom.:
199
Cov.:
77
AF XY:
0.00276
AC XY:
2003
AN XY:
725034
show subpopulations
Gnomad4 AFR exome
AF:
0.000629
Gnomad4 AMR exome
AF:
0.000560
Gnomad4 ASJ exome
AF:
0.000422
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00113
Gnomad4 NFE exome
AF:
0.00364
Gnomad4 OTH exome
AF:
0.00141
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00180
AC:
272
AN:
151068
Hom.:
16
Cov.:
31
AF XY:
0.00156
AC XY:
115
AN XY:
73818
show subpopulations
Gnomad4 AFR
AF:
0.000681
Gnomad4 AMR
AF:
0.00172
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000851
Gnomad4 NFE
AF:
0.00309
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00218
Hom.:
7
Bravo
AF:
0.00180
EpiCase
AF:
0.00262
EpiControl
AF:
0.00250

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023CDK11A: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
Cadd
Benign
3.6
Dann
Benign
0.94
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs186584733; hg19: chr1-1635677; API