Variant 16-8894529-CGG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003470.3(USP7):c.3202+19_3202+20del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,488,068 control chromosomes in the GnomAD database, including 120 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 9 hom., cov: 0)

Exomes 𝑓: 0.0033 ( 111 hom. )

Consequence

USP7
NM_003470.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.00

Variant links:

Genes affected

USP7 (HGNC:12630): (ubiquitin specific peptidase 7) The protein encoded by this gene belongs to the peptidase C19 family, which includes ubiquitinyl hydrolases. This protein deubiquitinates target proteins such as p53 (a tumor suppressor protein) and WASH (essential for endosomal protein recycling), and regulates their activities by counteracting the opposing ubiquitin ligase activity of proteins such as HDM2 and TRIM27, involved in the respective process. Mutations in this gene have been implicated in a neurodevelopmental disorder. [provided by RefSeq, Mar 2016]

USP7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 16-8894529-CGG-C is Benign according to our data. Variant chr16-8894529-CGG-C is described in ClinVar as [Benign]. Clinvar id is 1666910.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-8894529-CGG-C is described in Lovd as [Likely_benign].

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP7	NM_003470.3 linkuse as main transcript	c.3202+19_3202+20del		intron_variant		ENST00000344836.9	NP_003461.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP7	ENST00000344836.9 linkuse as main transcript	c.3202+19_3202+20del		intron_variant		1	NM_003470.3	ENSP00000343535	P1	Q93009-1

Frequencies

GnomAD3 genomes

AF:

0.00418

AC:

631

AN:

150996

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00119

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.0439

Gnomad SAS

AF:

0.00251

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000280

Gnomad OTH

AF:

0.00531

GnomAD3 exomes

AF:

0.0107

AC:

2254

AN:

211410

Hom.:

AF XY:

0.00874

AC XY:

1004

AN XY:

114926

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.0431

Gnomad ASJ exome

AF:

0.00253

Gnomad EAS exome

AF:

0.0541

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.0000605

Gnomad NFE exome

AF:

0.000278

Gnomad OTH exome

AF:

0.00822

GnomAD4 exome

AF:

0.00334

AC:

4465

AN:

1336964

Hom.:

111

AF XY:

0.00315

AC XY:

2093

AN XY:

665360

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.0402

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.0584

Gnomad4 SAS exome

AF:

0.00313

Gnomad4 FIN exome

AF:

0.000109

Gnomad4 NFE exome

AF:

0.000228

Gnomad4 OTH exome

AF:

0.00334

GnomAD4 genome

AF:

0.00416

AC:

629

AN:

151104

Hom.:

Cov.:

AF XY:

0.00507

AC XY:

374

AN XY:

73764

show subpopulations

Gnomad4 AFR

AF:

0.00119

Gnomad4 AMR

AF:

0.0201

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.0439

Gnomad4 SAS

AF:

0.00251

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000280

Gnomad4 OTH

AF:

0.00525

Alfa

AF:

0.00182

Hom.:

1411

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over