chr8-128033045-C-G

Position:

• chr8-128033045-C-G

Variant summary

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

The ENST00000513868.6(PVT1):​n.972-37115C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,102 control chromosomes in the GnomAD database, including 8,438 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 0.32 (8438 hom., cov: 32)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.1222-37115C>G		intron_variant
PVT1	NR_186119.1	n.1840+22601C>G		intron_variant
PVT1	NR_186120.1	n.2218+22601C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.972-37115C>G		intron_variant		1
PVT1	ENST00000512617.7	n.332-15403C>G		intron_variant		3
PVT1	ENST00000521600.5	n.76-15403C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48395 AN: 151984 Hom.: 8423 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.318 AC: 48435 AN: 152102 Hom.: 8438 Cov.: 32 AF XY: 0.328 AC XY: 24415 AN XY: 74350

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.339

Alfa AF: 0.185 Hom.: 406

Bravo AF: 0.324

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505506; hg19: chr8-129045291;