rs2720709

Variant names:

• chr8-128046110-G-A
• rs2720709
• ENST00000513868.6:n.972-24050G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-128046110-G-A
• chr8-128046110-G-C

Variant summary

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

The ENST00000513868.6(PVT1):​n.972-24050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,962 control chromosomes in the GnomAD database, including 9,332 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 0.34 (9332 hom., cov: 32)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 17 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PVT1	NR_003367.4	n.1222-24050G>A		intron_variant	Intron 5 of 8
PVT1	NR_186119.1	n.1841-24050G>A		intron_variant	Intron 10 of 14
PVT1	NR_186120.1	n.2219-24050G>A		intron_variant	Intron 11 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.972-24050G>A		intron_variant	Intron 4 of 7	1
PVT1	ENST00000512617.7	n.332-2338G>A		intron_variant	Intron 2 of 5	3
PVT1	ENST00000521600.5	n.76-2338G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52354 AN: 151844 Hom.: 9319 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.345 AC: 52411 AN: 151962 Hom.: 9332 Cov.: 32 AF XY: 0.353 AC XY: 26200 AN XY: 74256

African (AFR) AF: 0.377 AC: 15638 AN: 41434

American (AMR) AF: 0.390 AC: 5961 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2614 AN: 5158

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4814

European-Finnish (FIN) AF: 0.399 AC: 4203 AN: 10546

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19926 AN: 67950

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.310 Hom.: 24179

Bravo AF: 0.346

Asia WGS AF: 0.452 AC: 1569 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	0.14
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2720709; hg19: chr8-129058356;