Variant 16-23068087-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_020718.4(USP31):c.4018A>G(p.Ser1340Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0031 in 1,614,210 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 8 hom. )

Consequence

USP31
NM_020718.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.83

Variant links:

Genes affected

USP31 (HGNC:20060): (ubiquitin specific peptidase 31) Enables thiol-dependent deubiquitinase. Involved in protein deubiquitination. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

USP31 links:

USP31 (HGNC:):

USP31 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007519901).

BP6

Variant 16-23068087-T-C is Benign according to our data. Variant chr16-23068087-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2646315.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP31	NM_020718.4 linkuse as main transcript	c.4018A>G	p.Ser1340Gly	missense_variant	16/16	ENST00000219689.12	NP_065769.3	Q70CQ4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP31	ENST00000219689.12 linkuse as main transcript	c.4018A>G	p.Ser1340Gly	missense_variant	16/16	1	NM_020718.4	ENSP00000219689.7		Q70CQ4-1
USP31	ENST00000567975.1 linkuse as main transcript	c.1897A>G	p.Ser633Gly	missense_variant	2/2	2		ENSP00000461621.1		I3L4X5

Frequencies

GnomAD3 genomes

AF:

0.00208

AC:

317

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000675

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00362

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00177

AC:

446

AN:

251324

Hom.:

AF XY:

0.00182

AC XY:

247

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00104

Gnomad ASJ exome

AF:

0.00198

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000294

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.00312

Gnomad OTH exome

AF:

0.00228

GnomAD4 exome

AF:

0.00320

AC:

4680

AN:

1461866

Hom.:

Cov.:

AF XY:

0.00315

AC XY:

2294

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.000448

Gnomad4 AMR exome

AF:

0.00121

Gnomad4 ASJ exome

AF:

0.00187

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000313

Gnomad4 FIN exome

AF:

0.000412

Gnomad4 NFE exome

AF:

0.00390

Gnomad4 OTH exome

AF:

0.00275

GnomAD4 genome

AF:

0.00208

AC:

317

AN:

152344

Hom.:

Cov.:

AF XY:

0.00184

AC XY:

137

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.000673

Gnomad4 AMR

AF:

0.00189

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00362

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00327

Hom.:

Bravo

AF:

0.00220

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.00415

AC:

ESP6500AA

AF:

0.000455

AC:

ESP6500EA

AF:

0.00349

AC:

ExAC

AF:

0.00175

AC:

212

EpiCase

AF:

0.00420

EpiControl

AF:

0.00314

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

Apr 01, 2023

USP31: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0073

T;.

Eigen

Benign

-0.028

Eigen_PC

Benign

0.11

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.81

T;T

M_CAP

Benign

0.0037

MetaRNN

Benign

0.0075

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

M;.

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.64

N;.

REVEL

Benign

0.052

Sift

Uncertain

0.011

D;.

Sift4G

Uncertain

0.015

D;T

Polyphen

0.012

B;.

Vest4

0.10

MVP

0.71

MPC

0.21

ClinPred

0.024

GERP RS

4.6

Varity_R

0.080

gMVP

0.26

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