ENST00000650846.1:n.545-6531T>C

Variant names:

• chr8-128180025-T-C
• rs2019960
• ENST00000650846.1:n.545-6531T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650846.1(PVT1):​n.545-6531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,058 control chromosomes in the GnomAD database, including 6,192 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 0.27 (6192 hom., cov: 32)
• Consequence: PVT1 ENST00000650846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 66 publications found

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]

LOC124902020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650846.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVT1	ENST00000650846.1		n.545-6531T>C		intron	N/A
	PVT1	ENST00000651587.1		n.1899-6531T>C		intron	N/A
	PVT1	ENST00000844540.1		n.1010-6531T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40329 AN: 151940 Hom.: 6185 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0665

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.252

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.266 AC: 40376 AN: 152058 Hom.: 6192 Cov.: 32 AF XY: 0.261 AC XY: 19410 AN XY: 74340

African (AFR) AF: 0.420 AC: 17387 AN: 41434

American (AMR) AF: 0.293 AC: 4475 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3466

East Asian (EAS) AF: 0.0667 AC: 345 AN: 5174

South Asian (SAS) AF: 0.127 AC: 612 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1990 AN: 10592

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14150 AN: 67990

Other (OTH) AF: 0.251 AC: 530 AN: 2108

Alfa AF: 0.225 Hom.: 19431

Bravo AF: 0.281

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.49
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs2019960; hg19: chr8-129192271;