Variant rs3130696 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.536G>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 0.279 in 1,046,220 control chromosomes in the GnomAD database, including 47,284 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 0.24 ( 4408 hom., cov: 32)

Exomes 𝑓: 0.29 ( 42876 hom. )

Consequence

USP8P1
ENST00000494673.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.466

Variant links:

Genes affected

USP8P1 (HGNC:):

USP8P1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP8P1	use as main transcript	n.31276107G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1 linkuse as main transcript	n.536G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

36025

AN:

152014

Hom.:

4396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.248

GnomAD4 exome

AF:

0.286

AC:

255325

AN:

894088

Hom.:

42876

Cov.:

AF XY:

0.279

AC XY:

130533

AN XY:

467372

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.161

Gnomad4 EAS exome

AF:

0.297

Gnomad4 SAS exome

AF:

0.197

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.315

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.237

AC:

36068

AN:

152132

Hom.:

4408

Cov.:

AF XY:

0.235

AC XY:

17460

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.150

Gnomad4 EAS

AF:

0.256

Gnomad4 SAS

AF:

0.197

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.245

Hom.:

442

Bravo

AF:

0.243

Asia WGS

AF:

0.206

AC:

716

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.31

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