Genetic Variant USP8P1:n.-179G>A (chr6-31275393-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.80

Variant links:

Genes affected

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

USP8P1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	n.-179G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74840

AN:

151834

Hom.:

18623

Cov.:

show subpopulations

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.:

AF XY:

0.491

AC XY:

36460

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.446

AC:

18457

AN:

41402

American (AMR)

AF:

0.483

AC:

7370

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

1259

AN:

3472

East Asian (EAS)

AF:

0.659

AC:

3408

AN:

5170

South Asian (SAS)

AF:

0.442

AC:

2127

AN:

4816

European-Finnish (FIN)

AF:

0.508

AC:

5353

AN:

10542

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35440

AN:

67968

Other (OTH)

AF:

0.470

AC:

988

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1945

3890

5836

7781

9726

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.502

Hom.:

29037

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

(source)

DANN

Benign

0.25

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.

chr6-31275393-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over