rs9461680

Positions:

• chr6-31275570-C-T

Variant summary

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

The 6-31275570-C-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1			upstream_gene_variant

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;