X-47224638-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_006201.5(CDK16):ā€‹c.357A>Gā€‹(p.Ser119Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,209,531 control chromosomes in the GnomAD database, including 1,397 homozygotes. There are 4,473 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: š‘“ 0.072 ( 724 hom., 2132 hem., cov: 22)
Exomes š‘“: 0.0078 ( 673 hom. 2341 hem. )

Consequence

CDK16
NM_006201.5 synonymous

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.28
Variant links:
Genes affected
CDK16 (HGNC:8749): (cyclin dependent kinase 16) The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It may play a role in signal transduction cascades in terminally differentiated cells; in exocytosis; and in transport of secretory cargo from the endoplasmic reticulum. This gene is thought to escape X inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant X-47224638-A-G is Benign according to our data. Variant chrX-47224638-A-G is described in ClinVar as [Benign]. Clinvar id is 3059606.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-3.28 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDK16NM_006201.5 linkuse as main transcriptc.357A>G p.Ser119Ser synonymous_variant 4/16 ENST00000357227.9 NP_006192.1 Q00536-1A0A140VK97Q9BRL4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDK16ENST00000357227.9 linkuse as main transcriptc.357A>G p.Ser119Ser synonymous_variant 4/161 NM_006201.5 ENSP00000349762.4 Q00536-1

Frequencies

GnomAD3 genomes
AF:
0.0716
AC:
7969
AN:
111351
Hom.:
718
Cov.:
22
AF XY:
0.0631
AC XY:
2116
AN XY:
33549
show subpopulations
Gnomad AFR
AF:
0.247
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0285
Gnomad ASJ
AF:
0.00303
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000750
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0168
Gnomad NFE
AF:
0.000924
Gnomad OTH
AF:
0.0544
GnomAD3 exomes
AF:
0.0206
AC:
3748
AN:
181925
Hom.:
363
AF XY:
0.0134
AC XY:
900
AN XY:
66955
show subpopulations
Gnomad AFR exome
AF:
0.251
Gnomad AMR exome
AF:
0.0125
Gnomad ASJ exome
AF:
0.00188
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000578
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000731
Gnomad OTH exome
AF:
0.00888
GnomAD4 exome
AF:
0.00777
AC:
8528
AN:
1098128
Hom.:
673
Cov.:
32
AF XY:
0.00644
AC XY:
2341
AN XY:
363504
show subpopulations
Gnomad4 AFR exome
AF:
0.253
Gnomad4 AMR exome
AF:
0.0144
Gnomad4 ASJ exome
AF:
0.00175
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000923
Gnomad4 FIN exome
AF:
0.0000247
Gnomad4 NFE exome
AF:
0.000331
Gnomad4 OTH exome
AF:
0.0198
GnomAD4 genome
AF:
0.0718
AC:
8001
AN:
111403
Hom.:
724
Cov.:
22
AF XY:
0.0634
AC XY:
2132
AN XY:
33611
show subpopulations
Gnomad4 AFR
AF:
0.248
Gnomad4 AMR
AF:
0.0284
Gnomad4 ASJ
AF:
0.00303
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000752
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000924
Gnomad4 OTH
AF:
0.0537
Alfa
AF:
0.0354
Hom.:
354
Bravo
AF:
0.0837
EpiCase
AF:
0.000327
EpiControl
AF:
0.00113

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

CDK16-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJun 11, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.15
DANN
Benign
0.48
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: rs5952422; hg19: chrX-47084037; API