ENST00000494673.1:n.-2C>T

Variant names:

• chr6-31275570-C-T
• rs9461680
• ENST00000494673.1:n.-2C>T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.-2C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 339,942 control chromosomes in the GnomAD database, including 6,849 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 0.19 (2970 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3879 hom.)
• Consequence: USP8P1 ENST00000494673.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

Genes affected

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1	n.-2C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29611 AN: 151882 Hom.: 2967 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.187 AC: 35089 AN: 187942 Hom.: 3879 Cov.: 0 AF XY: 0.183 AC XY: 18723 AN XY: 102222

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.0915

Gnomad4 EAS exome AF: 0.231

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.180

GnomAD4 genome AF: 0.195 AC: 29621 AN: 152000 Hom.: 2970 Cov.: 33 AF XY: 0.199 AC XY: 14761 AN XY: 74282

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.164

Alfa AF: 0.181 Hom.: 214

Bravo AF: 0.189

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461680; hg19: chr6-31243347;