rs13249999

Positions:

• chr8-128037201-C-T

Variant summary

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

The ENST00000513868.6(PVT1):​n.972-32959C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,296 control chromosomes in the GnomAD database, including 306 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 0.060 (306 hom., cov: 33)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.1222-32959C>T		intron_variant
PVT1	NR_186119.1	n.1840+26757C>T		intron_variant
PVT1	NR_186120.1	n.2218+26757C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.972-32959C>T		intron_variant		1
PVT1	ENST00000512617.7	n.332-11247C>T		intron_variant		3
PVT1	ENST00000521600.5	n.76-11247C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9067 AN: 152178 Hom.: 305 Cov.: 33

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0414

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0596 AC: 9079 AN: 152296 Hom.: 306 Cov.: 33 AF XY: 0.0601 AC XY: 4474 AN XY: 74472

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0413

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.0328

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0703 Hom.: 138

Bravo AF: 0.0552

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13249999; hg19: chr8-129049447;