rs11780156

Positions:

• chr8-128182395-C-T

Variant summary

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

The ENST00000650846.1(PVT1):​n.545-4161C>T variant causes a intron 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 ENST00000650846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

PVT1 (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	Protein	UniProt
LOC124902020	XR_007061107.1	n.1905-4161C>T		intron_variant

Ensembl

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