14-96797538-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003384.3(VRK1):c.-6+91C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 151,864 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 64 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
VRK1
NM_003384.3 intron
NM_003384.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.19
Publications
0 publications found
Genes affected
VRK1 (HGNC:12718): (VRK serine/threonine kinase 1) This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. This gene is widely expressed in human tissues and has increased expression in actively dividing cells, such as those in testis, thymus, fetal liver, and carcinomas. Its protein localizes to the nucleus and has been shown to promote the stability and nuclear accumulation of a transcriptionally active p53 molecule and, in vitro, to phosphorylate Thr18 of p53 and reduce p53 ubiquitination. This gene, therefore, may regulate cell proliferation. This protein also phosphorylates histone, casein, and the transcription factors ATF2 (activating transcription factor 2) and c-JUN. [provided by RefSeq, Jul 2008]
VRK1 Gene-Disease associations (from GenCC):
- pontocerebellar hypoplasia type 1AInheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Ambry Genetics, Genomics England PanelApp
- microcephaly-complex motor and sensory axonal neuropathy syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- pontocerebellar hypoplasia type 1Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 14-96797538-C-T is Benign according to our data. Variant chr14-96797538-C-T is described in ClinVar as [Benign]. Clinvar id is 1272009.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0148 (2240/151864) while in subpopulation AFR AF = 0.051 (2115/41490). AF 95% confidence interval is 0.0492. There are 64 homozygotes in GnomAd4. There are 1080 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 64 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 2239AN: 151756Hom.: 64 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2239
AN:
151756
Hom.:
Cov.:
31
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 58Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 48
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
58
Hom.:
AF XY:
AC XY:
0
AN XY:
48
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AF:
AC:
0
AN:
8
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
48
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome AF: 0.0147 AC: 2240AN: 151864Hom.: 64 Cov.: 31 AF XY: 0.0145 AC XY: 1080AN XY: 74242 show subpopulations
GnomAD4 genome
AF:
AC:
2240
AN:
151864
Hom.:
Cov.:
31
AF XY:
AC XY:
1080
AN XY:
74242
show subpopulations
African (AFR)
AF:
AC:
2115
AN:
41490
American (AMR)
AF:
AC:
94
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5148
South Asian (SAS)
AF:
AC:
2
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10456
Middle Eastern (MID)
AF:
AC:
1
AN:
292
European-Non Finnish (NFE)
AF:
AC:
7
AN:
67904
Other (OTH)
AF:
AC:
21
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.494
Heterozygous variant carriers
0
107
214
322
429
536
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
17
AN:
3456
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 26, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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