Variant 8-7333568-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001256873.1(USP17L1):c.1182C>T(p.Leu394Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000385 in 1,468,248 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 23)

Exomes 𝑓: 0.00040 ( 18 hom. )

Consequence

USP17L1
NM_001256873.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.57

Variant links:

Genes affected

USP17L1 (HGNC:37182): (ubiquitin specific peptidase 17 like family member 1) Predicted to enable cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein deubiquitination and regulation of apoptotic process. Predicted to be located in endoplasmic reticulum. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

USP17L1 links:

FAM66B (HGNC:):

FAM66B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 8-7333568-C-T is Benign according to our data. Variant chr8-7333568-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658357.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.57 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP17L1	NM_001256873.1 linkuse as main transcript	c.1182C>T	p.Leu394Leu	synonymous_variant	1/1	ENST00000529559.1	NP_001243802.1	Q7RTZ2
FAM66B	NR_027423.2 linkuse as main transcript	n.618-8370G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP17L1	ENST00000529559.1 linkuse as main transcript	c.1182C>T	p.Leu394Leu	synonymous_variant	1/1	6	NM_001256873.1	ENSP00000485364.1		Q7RTZ2

Frequencies

GnomAD3 genomes

AF:

0.000240

AC:

AN:

129312

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000287

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000717

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000426

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000196

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000290

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000685

AC:

134

AN:

195520

Hom.:

AF XY:

0.000645

AC XY:

AN XY:

106900

show subpopulations

Gnomad AFR exome

AF:

0.00573

Gnomad AMR exome

AF:

0.000921

Gnomad ASJ exome

AF:

0.000110

Gnomad EAS exome

AF:

0.000765

Gnomad SAS exome

AF:

0.000373

Gnomad FIN exome

AF:

0.000154

Gnomad NFE exome

AF:

0.000474

Gnomad OTH exome

AF:

0.000577

GnomAD4 exome

AF:

0.000399

AC:

534

AN:

1338886

Hom.:

Cov.:

AF XY:

0.000412

AC XY:

277

AN XY:

672178

show subpopulations

Gnomad4 AFR exome

AF:

0.000666

Gnomad4 AMR exome

AF:

0.000431

Gnomad4 ASJ exome

AF:

0.0000398

Gnomad4 EAS exome

AF:

0.000490

Gnomad4 SAS exome

AF:

0.000386

Gnomad4 FIN exome

AF:

0.000378

Gnomad4 NFE exome

AF:

0.000398

Gnomad4 OTH exome

AF:

0.000397

GnomAD4 genome

AF:

0.000240

AC:

AN:

129362

Hom.:

Cov.:

AF XY:

0.000206

AC XY:

AN XY:

63046

show subpopulations

Gnomad4 AFR

AF:

0.000286

Gnomad4 AMR

AF:

0.0000716

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000427

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000196

Gnomad4 NFE

AF:

0.000290

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000633

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

USP17L1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.1

DANN

Benign

0.56

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