8-127796593-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000521951.1(PVT1):​n.178+1859T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,992 control chromosomes in the GnomAD database, including 27,553 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 0.60 ( 27553 hom., cov: 31)

Consequence

PVT1
ENST00000521951.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PVT1NR_003367.4 linkn.211+1859T>C intron_variant Intron 1 of 8
PVT1NR_186119.1 linkn.211+1859T>C intron_variant Intron 1 of 14
PVT1NR_186120.1 linkn.326+585T>C intron_variant Intron 2 of 14

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PVT1ENST00000521951.1 linkn.178+1859T>C intron_variant Intron 1 of 2 1
PVT1ENST00000523328.6 linkn.170+1859T>C intron_variant Intron 1 of 4 1
PVT1ENST00000504719.7 linkn.200+1859T>C intron_variant Intron 1 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.599
AC:
91019
AN:
151874
Hom.:
27526
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.627
Gnomad AMI
AF:
0.609
Gnomad AMR
AF:
0.521
Gnomad ASJ
AF:
0.570
Gnomad EAS
AF:
0.510
Gnomad SAS
AF:
0.687
Gnomad FIN
AF:
0.587
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.605
Gnomad OTH
AF:
0.560
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.599
AC:
91097
AN:
151992
Hom.:
27553
Cov.:
31
AF XY:
0.597
AC XY:
44335
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.627
Gnomad4 AMR
AF:
0.522
Gnomad4 ASJ
AF:
0.570
Gnomad4 EAS
AF:
0.510
Gnomad4 SAS
AF:
0.687
Gnomad4 FIN
AF:
0.587
Gnomad4 NFE
AF:
0.605
Gnomad4 OTH
AF:
0.563
Alfa
AF:
0.604
Hom.:
17223
Bravo
AF:
0.592
Asia WGS
AF:
0.635
AC:
2211
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.1
DANN
Benign
0.43

Splicing

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: rs10956390; hg19: chr8-128808839; COSMIC: COSV68600068; API