rs13255292

Variant names:

• chr8-128064327-C-T
• rs13255292
• ENST00000667305.2:n.1177-5833C>T

Variant summary

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

The ENST00000667305.2(PVT1):​n.1177-5833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,202 control chromosomes in the GnomAD database, including 5,452 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 0.24 (5452 hom., cov: 33)
• Consequence: PVT1 ENST00000667305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 41 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667305.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVT1	NR_190187.1	MANE Select	n.1177-5833C>T		intron	N/A
	PVT1	NR_003367.4		n.1222-5833C>T		intron	N/A
	PVT1	NR_186119.1		n.1841-5833C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVT1	ENST00000667305.2	MANE Select	n.1177-5833C>T		intron	N/A
	PVT1	ENST00000513868.6	TSL:1	n.972-5833C>T		intron	N/A
	PVT1	ENST00000512617.7	TSL:3	n.494-5833C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37173 AN: 152084 Hom.: 5444 Cov.: 33

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.244 AC: 37175 AN: 152202 Hom.: 5452 Cov.: 33 AF XY: 0.245 AC XY: 18246 AN XY: 74412

African (AFR) AF: 0.0871 AC: 3616 AN: 41522

American (AMR) AF: 0.242 AC: 3703 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1016 AN: 4830

European-Finnish (FIN) AF: 0.339 AC: 3582 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22086 AN: 67998

Other (OTH) AF: 0.279 AC: 590 AN: 2114

Alfa AF: 0.306 Hom.: 24511

Bravo AF: 0.231

Asia WGS AF: 0.206 AC: 716 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs13255292; hg19: chr8-129076573;