ENST00000513868.6:n.541-3663T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000513868.6(PVT1):n.541-3663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,928 control chromosomes in the GnomAD database, including 18,346 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.47 ( 18346 hom., cov: 31)
Consequence
PVT1
ENST00000513868.6 intron
ENST00000513868.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.23
Publications
5 publications found
Genes affected
PVT1 (HGNC:9709): (Pvt1 oncogene) This gene represents a long non-coding RNA locus that has been identified as a candidate oncogene. Increased copy number and overexpression of this gene are associated with many types of cancers including breast and ovarian cancers, acute myeloid leukemia and Hodgkin lymphoma. Allelic variants of this gene are also associated with end-stage renal disease attributed to type 1 diabetes. Consistent with its association with various types of cancer, transcription of this gene is regulated by the tumor suppressor p53 through a canonical p53-binding site, and it has been implicated in regulating levels of the proto-oncogene MYC to promote tumorigenesis. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.474 AC: 71968AN: 151810Hom.: 18338 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
71968
AN:
151810
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.474 AC: 71995AN: 151928Hom.: 18346 Cov.: 31 AF XY: 0.487 AC XY: 36158AN XY: 74260 show subpopulations
GnomAD4 genome
AF:
AC:
71995
AN:
151928
Hom.:
Cov.:
31
AF XY:
AC XY:
36158
AN XY:
74260
show subpopulations
African (AFR)
AF:
AC:
12107
AN:
41430
American (AMR)
AF:
AC:
9440
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
1908
AN:
3470
East Asian (EAS)
AF:
AC:
3299
AN:
5172
South Asian (SAS)
AF:
AC:
3363
AN:
4802
European-Finnish (FIN)
AF:
AC:
6038
AN:
10530
Middle Eastern (MID)
AF:
AC:
191
AN:
294
European-Non Finnish (NFE)
AF:
AC:
34012
AN:
67946
Other (OTH)
AF:
AC:
1089
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1852
3704
5557
7409
9261
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
664
1328
1992
2656
3320
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2118
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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