chr8-127998344-C-A

Position:

• chr8-127998344-C-A

Variant summary

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

The NR_186119.1(PVT1):​n.1569C>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 0.125 in 152,182 control chromosomes in the GnomAD database, including 1,538 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 0.13 (1538 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PVT1 NR_186119.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

PVT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) 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_186119.1	n.1569C>A		non_coding_transcript_exon_variant	8/15
PVT1	NR_186120.1	n.1947C>A		non_coding_transcript_exon_variant	9/15
PVT1	NR_186123.1	n.1735C>A		non_coding_transcript_exon_variant	9/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000513868.6	n.971+9053C>A		intron_variant		1
PVT1	ENST00000522875.5	n.214C>A		non_coding_transcript_exon_variant	3/8	5
PVT1	ENST00000656999.1	n.316C>A		non_coding_transcript_exon_variant	1/6

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19049 AN: 152064 Hom.: 1539 Cov.: 32

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.124

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.125 AC: 19041 AN: 152182 Hom.: 1538 Cov.: 32 AF XY: 0.123 AC XY: 9187 AN XY: 74390

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0691

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.122

Alfa AF: 0.160 Hom.: 606

Bravo AF: 0.121

Asia WGS AF: 0.0720 AC: 249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10283090; hg19: chr8-129010590;