chr8-128140986-T-C

Variant summary

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

The ENST00000650846.1(PVT1):​n.277-6876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,224 control chromosomes in the GnomAD database, including 1,682 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 0.13 ( 1682 hom., cov: 32)

Consequence

PVT1
ENST00000650846.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.235
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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PVT1ENST00000650846.1 linkn.277-6876T>C intron_variant
PVT1ENST00000651587.1 linkn.1252-6876T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.134
AC:
20361
AN:
152106
Hom.:
1686
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.191
Gnomad AMR
AF:
0.182
Gnomad ASJ
AF:
0.0819
Gnomad EAS
AF:
0.422
Gnomad SAS
AF:
0.205
Gnomad FIN
AF:
0.133
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.118
Gnomad OTH
AF:
0.149
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.134
AC:
20363
AN:
152224
Hom.:
1682
Cov.:
32
AF XY:
0.138
AC XY:
10273
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.182
Gnomad4 ASJ
AF:
0.0819
Gnomad4 EAS
AF:
0.421
Gnomad4 SAS
AF:
0.204
Gnomad4 FIN
AF:
0.133
Gnomad4 NFE
AF:
0.118
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.126
Hom.:
333
Bravo
AF:
0.139
Asia WGS
AF:
0.319
AC:
1105
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.4
DANN
Benign
0.55

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: rs2608038; hg19: chr8-129153232; API