rs2648862

Positions:

• chr8-128049539-C-A

Variant summary

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

The ENST00000522414.2(PVT1):​n.152C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0312 in 152,228 control chromosomes in the GnomAD database, including 171 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 0.031 (171 hom., cov: 32)
• Consequence: PVT1 ENST00000522414.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.1222-20621C>A		intron_variant
PVT1	NR_186119.1	n.1841-20621C>A		intron_variant
PVT1	NR_186120.1	n.2219-20621C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.972-20621C>A		intron_variant		1
PVT1	ENST00000522414.2	n.152C>A		non_coding_transcript_exon_variant	1/4	2
PVT1	ENST00000652728.1	n.189C>A		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.0312 AC: 4748 AN: 152110 Hom.: 169 Cov.: 32

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0312 AC: 4751 AN: 152228 Hom.: 171 Cov.: 32 AF XY: 0.0352 AC XY: 2617 AN XY: 74410

Gnomad4 AFR AF: 0.0199

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0208 Hom.: 105

Bravo AF: 0.0326

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.3
DANN	Benign	0.82
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: rs2648862; hg19: chr8-129061785;