8-127907951-G-A

Position:

• chr8-127907951-G-A

Variant summary

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

The ENST00000513868.6(PVT1):​n.371+16953G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00779 in 152,214 control chromosomes in the GnomAD database, including 31 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 0.0078 (31 hom., cov: 31)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

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 (EAS) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.621+16953G>A		intron_variant
PVT1	NR_186119.1	n.786+16953G>A		intron_variant
PVT1	NR_186120.1	n.736+16953G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.371+16953G>A		intron_variant		1
PVT1	ENST00000521951.1	n.588+16953G>A		intron_variant		1
PVT1	ENST00000523328.6	n.802+16953G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.00780 AC: 1186 AN: 152096 Hom.: 31 Cov.: 31

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00275

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000867

Gnomad OTH AF: 0.00908

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

GnomAD4 genome AF: 0.00779 AC: 1185 AN: 152214 Hom.: 31 Cov.: 31 AF XY: 0.00832 AC XY: 619 AN XY: 74422

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.00275

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.0218

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.000868

Gnomad4 OTH AF: 0.00804

Alfa AF: 0.00106 Hom.: 0

Bravo AF: 0.00812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16902460; hg19: chr8-128920197;