chr8-127960475-A-G

Position:

• chr8-127960475-A-G

Variant summary

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

The ENST00000513868.6(PVT1):​n.540+20799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,974 control chromosomes in the GnomAD database, including 6,841 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 0.29 (6841 hom., cov: 31)
• Consequence: PVT1 ENST00000513868.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PVT1	NR_003367.4	n.790+20799A>G		intron_variant
PVT1	NR_186119.1	n.955+20799A>G		intron_variant
PVT1	NR_186120.1	n.905+20799A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.540+20799A>G		intron_variant		1
PVT1	ENST00000517525.2	n.954+20799A>G		intron_variant		3
PVT1	ENST00000517790.2	n.1274-28687A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43802 AN: 151856 Hom.: 6831 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.289 AC: 43852 AN: 151974 Hom.: 6841 Cov.: 31 AF XY: 0.291 AC XY: 21615 AN XY: 74290

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.316

Alfa AF: 0.308 Hom.: 1485

Bravo AF: 0.272

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	18
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9649959; hg19: chr8-128972721; COSMIC: COSV68680571;