ENST00000513868.6:n.541-17824A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000513868.6(PVT1):​n.541-17824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,044 control chromosomes in the GnomAD database, including 11,979 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 0.39 ( 11979 hom., cov: 32)

Consequence

PVT1
ENST00000513868.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PVT1NR_003367.4 linkn.791-17824A>G intron_variant Intron 3 of 8
PVT1NR_186119.1 linkn.956-17824A>G intron_variant Intron 4 of 14
PVT1NR_186120.1 linkn.906-16280A>G intron_variant Intron 4 of 14

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PVT1ENST00000513868.6 linkn.541-17824A>G intron_variant Intron 2 of 7 1
PVT1ENST00000517525.2 linkn.955-23082A>G intron_variant Intron 4 of 5 3
PVT1ENST00000517790.2 linkn.1274-23082A>G intron_variant Intron 2 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.389
AC:
59160
AN:
151926
Hom.:
11987
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.306
Gnomad AMI
AF:
0.484
Gnomad AMR
AF:
0.470
Gnomad ASJ
AF:
0.412
Gnomad EAS
AF:
0.598
Gnomad SAS
AF:
0.472
Gnomad FIN
AF:
0.441
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.389
Gnomad OTH
AF:
0.390
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59167
AN:
152044
Hom.:
11979
Cov.:
32
AF XY:
0.397
AC XY:
29495
AN XY:
74310
show subpopulations
African (AFR)
AF:
0.306
AC:
12683
AN:
41454
American (AMR)
AF:
0.470
AC:
7188
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.412
AC:
1428
AN:
3466
East Asian (EAS)
AF:
0.597
AC:
3089
AN:
5174
South Asian (SAS)
AF:
0.471
AC:
2267
AN:
4810
European-Finnish (FIN)
AF:
0.441
AC:
4657
AN:
10568
Middle Eastern (MID)
AF:
0.476
AC:
140
AN:
294
European-Non Finnish (NFE)
AF:
0.389
AC:
26457
AN:
67974
Other (OTH)
AF:
0.388
AC:
818
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1823
3645
5468
7290
9113
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
576
1152
1728
2304
2880
<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:
0.394
Hom.:
41593
Bravo
AF:
0.390
Asia WGS
AF:
0.481
AC:
1674
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.0
DANN
Benign
0.47
PhyloP100
0.25

Splicing

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

Publications

Other links and lift over

dbSNP: rs755520; hg19: chr8-128978326; API