8-128140986-T-C

Position:

• chr8-128140986-T-C

Variant summary

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

The variant allele was found at a frequency of 0.134 in 152,224 control chromosomes in the GnomAD database, including 1,682 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 (1682 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.128140986T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PVT1	ENST00000650846.1	n.277-6876T>C		intron_variant
PVT1	ENST00000651587.1	n.1252-6876T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20361 AN: 152106 Hom.: 1686 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.134 AC: 20363 AN: 152224 Hom.: 1682 Cov.: 32 AF XY: 0.138 AC XY: 10273 AN XY: 74430

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.0819

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.148

Alfa AF: 0.126 Hom.: 333

Bravo AF: 0.139

Asia WGS AF: 0.319 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2608038; hg19: chr8-129153232;