rs5029317

Variant names:

• chr8-128114607-T-C
• rs5029317
• ENST00000651587.1:n.1251+17953T>C

Variant summary

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

The ENST00000651587.1(PVT1):​n.1251+17953T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 152,324 control chromosomes in the GnomAD database, including 855 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 0.091 (855 hom., cov: 33)
• Consequence: PVT1 ENST00000651587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 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]

ENSG00000309986 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651587.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PVT1	ENST00000651587.1		n.1251+17953T>C		intron	N/A
	PVT1	ENST00000844540.1		n.868+17953T>C		intron	N/A
	PVT1	ENST00000844541.1		n.851+17953T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13881 AN: 152208 Hom.: 852 Cov.: 33

Gnomad AFR AF: 0.0365

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0912 AC: 13893 AN: 152324 Hom.: 855 Cov.: 33 AF XY: 0.0936 AC XY: 6971 AN XY: 74490

African (AFR) AF: 0.0364 AC: 1515 AN: 41580

American (AMR) AF: 0.198 AC: 3027 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.0978 AC: 508 AN: 5194

South Asian (SAS) AF: 0.107 AC: 515 AN: 4828

European-Finnish (FIN) AF: 0.0895 AC: 951 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6783 AN: 68026

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.0994 Hom.: 1014

Bravo AF: 0.0937

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.26
DANN	Benign	0.31
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5029317; hg19: chr8-129126853;