Variant rs2524073 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000494673.1(USP8P1):n.887G>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 0.106 in 758,738 control chromosomes in the GnomAD database, including 4,946 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 0.11 ( 1036 hom., cov: 33)

Exomes 𝑓: 0.10 ( 3910 hom. )

Consequence

USP8P1
ENST00000494673.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.511

Variant links:

Genes affected

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

USP8P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP8P1	ENST00000494673.1 linkuse as main transcript	n.887G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17258

AN:

152106

Hom.:

1035

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0710

Gnomad FIN

AF:

0.0527

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.104

AC:

63290

AN:

606512

Hom.:

3910

Cov.:

AF XY:

0.101

AC XY:

32474

AN XY:

322596

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.124

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.0921

Gnomad4 SAS exome

AF:

0.0421

Gnomad4 FIN exome

AF:

0.0546

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.113

AC:

17258

AN:

152226

Hom.:

1036

Cov.:

AF XY:

0.108

AC XY:

8058

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.119

Gnomad4 ASJ

AF:

0.150

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.0706

Gnomad4 FIN

AF:

0.0527

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.126

Hom.:

Bravo

AF:

0.120

Asia WGS

AF:

0.0890

AC:

310

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

9.9

DANN

Benign

0.84

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over