GeneBe

8-128082343-C-T

Position:

Variant summary

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

The ENST00000513868.6(PVT1):​n.1084+12071C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0837 in 152,254 control chromosomes in the GnomAD database, including 832 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 0.084 ( 832 hom., cov: 32)

Consequence

PVT1
ENST00000513868.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29
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 (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PVT1NR_003367.4 linkn.1334+12071C>T intron_variant
PVT1NR_186119.1 linkn.2132-410C>T intron_variant
PVT1NR_186120.1 linkn.2509+8852C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PVT1ENST00000513868.6 linkn.1084+12071C>T intron_variant 1
PVT1ENST00000512617.7 linkn.695+11982C>T intron_variant 3
PVT1ENST00000521600.5 linkn.350+12071C>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0837
AC:
12734
AN:
152136
Hom.:
826
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0392
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.215
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.173
Gnomad SAS
AF:
0.163
Gnomad FIN
AF:
0.0455
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.0717
Gnomad OTH
AF:
0.0967
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0837
AC:
12746
AN:
152254
Hom.:
832
Cov.:
32
AF XY:
0.0881
AC XY:
6558
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.0391
Gnomad4 AMR
AF:
0.215
Gnomad4 ASJ
AF:
0.115
Gnomad4 EAS
AF:
0.173
Gnomad4 SAS
AF:
0.163
Gnomad4 FIN
AF:
0.0455
Gnomad4 NFE
AF:
0.0717
Gnomad4 OTH
AF:
0.0990
Alfa
AF:
0.0827
Hom.:
862
Bravo
AF:
0.0975
Asia WGS
AF:
0.163
AC:
569
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
0.26
DANN
Benign
0.76

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: rs1499368; hg19: chr8-129094589; API