rs16893188

chr8-128157862-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651587.1(PVT1):n.1772+2443C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,026 control chromosomes in the GnomAD database, including 1,741 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 0.15 (1741 hom., cov: 32)
• Consequence: PVT1 ENST00000651587.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902020	XR_007061107.1	n.1904+2443C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PVT1	ENST00000651587.1	n.1772+2443C>T		intron_variant, non_coding_transcript_variant
PVT1	ENST00000650846.1	n.544+5045C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22264 AN: 151908 Hom.: 1741 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22279 AN: 152026 Hom.: 1741 Cov.: 32 AF XY: 0.144 AC XY: 10734 AN XY: 74298

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.147

Alfa AF: 0.148 Hom.: 2271

Bravo AF: 0.152

Asia WGS AF: 0.0920 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.70
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16893188; hg19: chr8-129170108;