rs16902486

Variant names:

• chr8-127942819-C-G
• rs16902486
• ENST00000513868.6:n.540+3143C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-127942819-C-G
• chr8-127942819-C-T

Variant summary

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

The ENST00000513868.6(PVT1):​n.540+3143C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,270 control chromosomes in the GnomAD database, including 677 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 0.063 (677 hom., cov: 32)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PVT1	NR_003367.4	n.790+3143C>G		intron_variant	Intron 3 of 8
PVT1	NR_186119.1	n.955+3143C>G		intron_variant	Intron 4 of 14
PVT1	NR_186120.1	n.905+3143C>G		intron_variant	Intron 4 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.540+3143C>G		intron_variant	Intron 2 of 7	1
PVT1	ENST00000665856.1	n.1342C>G		non_coding_transcript_exon_variant	Exon 5 of 5
PVT1	ENST00000667149.1	n.1285C>G		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9522 AN: 152152 Hom.: 675 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0627 AC: 9541 AN: 152270 Hom.: 677 Cov.: 32 AF XY: 0.0603 AC XY: 4493 AN XY: 74456

African (AFR) AF: 0.173 AC: 7168 AN: 41538

American (AMR) AF: 0.0312 AC: 477 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5180

South Asian (SAS) AF: 0.0384 AC: 185 AN: 4822

European-Finnish (FIN) AF: 0.0106 AC: 113 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0143 AC: 970 AN: 68022

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0444 Hom.: 50

Bravo AF: 0.0685

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.55
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs16902486; hg19: chr8-128955065;