rs3132486

Variant names:

• chr6-31275393-G-A
• rs3132486
• ENST00000494673.1:n.-179G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31275393-G-A
• chr6-31275393-G-C

Variant summary

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

The ENST00000494673.1(USP8P1):​n.-179G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,952 control chromosomes in the GnomAD database, including 18,637 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 0.49 (18637 hom., cov: 31)
• Consequence: USP8P1 ENST00000494673.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 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.-179G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74840 AN: 151834 Hom.: 18623 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.493 AC: 74891 AN: 151952 Hom.: 18637 Cov.: 31 AF XY: 0.491 AC XY: 36460 AN XY: 74264

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.470

Alfa AF: 0.503 Hom.: 1758

Bravo AF: 0.490

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132486; hg19: chr6-31243170;