Genetic Variant USP8P1:n.2186A>G (chr6-31277757-A-G) – 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.2186A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.128 in 1,601,346 control chromosomes in the GnomAD database, including 14,836 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 0.13 ( 1309 hom., cov: 33)

Exomes 𝑓: 0.13 ( 13527 hom. )

Consequence

USP8P1
ENST00000494673.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.11

Publications

15 publications found

Variant links:

Genes affected

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

USP8P1 links:

ENSG00000298396 (HGNC:):

ENSG00000298396 links:

Genome browser will be placed here

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=-0.62).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP8P1		n.31277757A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP8P1	ENST00000494673.1 link	n.2186A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298396	ENST00000755297.1 link	n.32+6651A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19054

AN:

152104

Hom.:

1309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.0536

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.0999

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.140

GnomAD4 exome

AF:

0.128

AC:

186004

AN:

1449124

Hom.:

13527

Cov.:

AF XY:

0.132

AC XY:

95126

AN XY:

721676

show subpopulations

African (AFR)

AF:

0.0952

AC:

3162

AN:

33214

American (AMR)

AF:

0.0848

AC:

3790

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

7879

AN:

26050

East Asian (EAS)

AF:

0.0292

AC:

1156

AN:

39638

South Asian (SAS)

AF:

0.181

AC:

15590

AN:

85978

European-Finnish (FIN)

AF:

0.0931

AC:

4968

AN:

53356

Middle Eastern (MID)

AF:

0.230

AC:

1319

AN:

5742

European-Non Finnish (NFE)

AF:

0.127

AC:

139686

AN:

1100486

Other (OTH)

AF:

0.141

AC:

8454

AN:

59962

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

8973

17946

26918

35891

44864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4850

9700

14550

19400

24250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.125

AC:

19058

AN:

152222

Hom.:

1309

Cov.:

AF XY:

0.125

AC XY:

9338

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.106

AC:

4415

AN:

41534

American (AMR)

AF:

0.110

AC:

1683

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1075

AN:

3470

East Asian (EAS)

AF:

0.0539

AC:

279

AN:

5176

South Asian (SAS)

AF:

0.165

AC:

796

AN:

4830

European-Finnish (FIN)

AF:

0.0999

AC:

1059

AN:

10602

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.135

AC:

9192

AN:

67996

Other (OTH)

AF:

0.138

AC:

291

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

834

1669

2503

3338

4172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.127

Hom.:

1982

Bravo

AF:

0.125

Asia WGS

AF:

0.0930

AC:

326

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

4.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over