rs11780156

chr8-128182395-C-T

Variant summary

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

The ENST00000651587.1(PVT1):n.1899-4161C>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 0.139 in 152,166 control chromosomes in the GnomAD database, including 1,814 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 0.14 (1814 hom., cov: 32)
• Consequence: PVT1 ENST00000651587.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902020	XR_007061107.1	n.1905-4161C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PVT1	ENST00000651587.1	n.1899-4161C>T		intron_variant, non_coding_transcript_variant
PVT1	ENST00000650846.1	n.545-4161C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21144 AN: 152048 Hom.: 1812 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.139 AC: 21147 AN: 152166 Hom.: 1814 Cov.: 32 AF XY: 0.141 AC XY: 10493 AN XY: 74394

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.163

Alfa AF: 0.175 Hom.: 1481

Bravo AF: 0.136

Asia WGS AF: 0.191 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11780156; hg19: chr8-129194641;