chr8-127936977-A-G

Position:

• chr8-127936977-A-G

Variant summary

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

The ENST00000513868.6(PVT1):​n.372-2531A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,078 control chromosomes in the GnomAD database, including 33,793 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 0.66 (33793 hom., cov: 33)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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 (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.622-2531A>G		intron_variant
PVT1	NR_186119.1	n.787-2531A>G		intron_variant
PVT1	NR_186120.1	n.737-2531A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.372-2531A>G		intron_variant		1
PVT1	ENST00000521951.1	n.589-2531A>G		intron_variant		1
PVT1	ENST00000517525.2	n.786-2531A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100663 AN: 151960 Hom.: 33767 Cov.: 33

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.662 AC: 100733 AN: 152078 Hom.: 33793 Cov.: 33 AF XY: 0.661 AC XY: 49112 AN XY: 74336

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.697

Alfa AF: 0.662 Hom.: 4968

Bravo AF: 0.643

Asia WGS AF: 0.653 AC: 2270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365371; hg19: chr8-128949223;