8-128105690-A-G

Variant summary

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

The ENST00000651587.1(PVT1):​n.1251+9036A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,200 control chromosomes in the GnomAD database, including 29,017 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 ( 29017 hom., cov: 34)

Consequence

PVT1
ENST00000651587.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PVT1ENST00000651587.1 linkn.1251+9036A>G intron_variant Intron 6 of 10

Frequencies

GnomAD3 genomes
AF:
0.596
AC:
90667
AN:
152082
Hom.:
28957
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.811
Gnomad AMI
AF:
0.325
Gnomad AMR
AF:
0.657
Gnomad ASJ
AF:
0.571
Gnomad EAS
AF:
0.733
Gnomad SAS
AF:
0.654
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.609
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.596
AC:
90786
AN:
152200
Hom.:
29017
Cov.:
34
AF XY:
0.596
AC XY:
44391
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.812
Gnomad4 AMR
AF:
0.657
Gnomad4 ASJ
AF:
0.571
Gnomad4 EAS
AF:
0.733
Gnomad4 SAS
AF:
0.654
Gnomad4 FIN
AF:
0.404
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.614
Alfa
AF:
0.500
Hom.:
10928
Bravo
AF:
0.626
Asia WGS
AF:
0.710
AC:
2470
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
0.063
DANN
Benign
0.77

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: rs2720672; hg19: chr8-129117936; API